97 def get_steps ( a ):
- 98 """Get forward difference of 2D array `a`, with repeated last elements.
- 99 100 The repeated last elements ensure that output and input arrays have equal shape.
-101 102 Examples:
-103 104 >>> get_steps(np.array([1, 2, 3, 4, 5]))
-105 array([[1, 1, 1, 1, 1]])
-106 107 >>> get_steps(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10]]))
-108 array([[1, 1, 1, 1, 1],
-109 [2, 3, 3, 1, 1]])
-110 111 >>> get_steps(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10], [1, 0, 0, 0, np.inf]]))
-112 array([[ 1., 1., 1., 1., 1.],
-113 [ 2., 3., 3., 1., 1.],
-114 [-1., 0., 0., inf, nan]])
-115 116 """
-117 a2 = np . atleast_2d ( a )
-118 return np . diff (
-119 a2 , append = np . reshape ( a2 [:, - 1 ] + ( a2 [:, - 1 ] - a2 [:, - 2 ]), ( a2 . shape [ 0 ], 1 ))
-120 )
+
+ 97 def diff_like ( a ):
+ 98 """Get forward difference of 2D array `a`, with repeated last elements.
+ 99 100 The repeated last elements ensure that output and input arrays have equal shape.
+101 102 Examples:
+103 104 >>> diff_like(np.array([1, 2, 3, 4, 5]))
+105 array([[1, 1, 1, 1, 1]])
+106 107 >>> diff_like(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10]]))
+108 array([[1, 1, 1, 1, 1],
+109 [2, 3, 3, 1, 1]])
+110 111 >>> diff_like(np.array([[1, 2, 3, 4, 5], [1, 3, 6, 9, 10], [1, 0, 0, 0, np.inf]]))
+112 array([[ 1., 1., 1., 1., 1.],
+113 [ 2., 3., 3., 1., 1.],
+114 [-1., 0., 0., inf, nan]])
+115 116 """
+117 a2 = np . atleast_2d ( a )
+118 return np . diff (
+119 a2 , append = np . reshape ( a2 [:, - 1 ] + ( a2 [:, - 1 ] - a2 [:, - 2 ]), ( a2 . shape [ 0 ], 1 ))
+120 )
Examples:
-
>>> get_steps ( np . array ([ 1 , 2 , 3 , 4 , 5 ]))
+>>> diff_like ( np . array ([ 1 , 2 , 3 , 4 , 5 ]))
array([[1, 1, 1, 1, 1]])
-
>>> get_steps ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ]]))
+>>> diff_like ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ]]))
array([[1, 1, 1, 1, 1],
[2, 3, 3, 1, 1]])
-
>>> get_steps ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ], [ 1 , 0 , 0 , 0 , np . inf ]]))
+>>> diff_like ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ], [ 1 , 0 , 0 , 0 , np . inf ]]))
array([[ 1., 1., 1., 1., 1.],
[ 2., 3., 3., 1., 1.],
[-1., 0., 0., inf, nan]])
diff --git a/pydrex/velocity.html b/pydrex/velocity.html
index bf4117d3..e81b1aa5 100644
--- a/pydrex/velocity.html
+++ b/pydrex/velocity.html
@@ -212,8 +212,8 @@
122 Args:
123 - `direction` (one of {"X", "Y", "Z"}) — velocity vector direction
124 - `deformation_plane` (one of {"X", "Y", "Z"}) — direction of velocity gradient
-125 - `strain_rate` (float) — 1/2 × strength of velocity gradient (i.e. magnitude of the
-126 velocity at a unit distance from the shear plane)
+125 - `strain_rate` (float) — 1/2 × magnitude of the largest eigenvalue of the velocity
+126 gradient
127 128 .. note::
129 Input arrays to the returned callables must have homogeneous element types.
@@ -457,8 +457,8 @@
123 Args:
124 - `direction` (one of {"X", "Y", "Z"}) — velocity vector direction
125 - `deformation_plane` (one of {"X", "Y", "Z"}) — direction of velocity gradient
-126 - `strain_rate` (float) — 1/2 × strength of velocity gradient (i.e. magnitude of the
-127 velocity at a unit distance from the shear plane)
+126 - `strain_rate` (float) — 1/2 × magnitude of the largest eigenvalue of the velocity
+127 gradient
128 129 .. note::
130 Input arrays to the returned callables must have homogeneous element types.
@@ -518,8 +518,8 @@
direction (one of {"X", "Y", "Z"}) — velocity vector directiondeformation_plane (one of {"X", "Y", "Z"}) — direction of velocity gradientstrain_rate (float) — 1/2 × strength of velocity gradient (i.e. magnitude of the
-velocity at a unit distance from the shear plane)strain_rate (float) — 1/2 × magnitude of the largest eigenvalue of the velocity
+gradient
diff --git a/search.js b/search.js
index da3fded2..c7d7a300 100644
--- a/search.js
+++ b/search.js
@@ -1,6 +1,6 @@
window.pdocSearch = (function(){
/** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. 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This software is currently in early development (pre-alpha)\nand therefore subject to breaking changes without notice.
\n\n
About \n\nViscoplastic deformation of minerals, e.g. in Earth's mantle, leads to distinct\nsignatures in the mineral texture. Many minerals naturally occur in\npolycrystalline form, which means that they are composed of many grains with\ndifferent volumes and lattice orientations. Preferential alignment of the\naverage lattice orientation is called crystallographic preferred orientation\n(CPO). PyDRex simulates the development and evolution of CPO in deforming\npolycrystals, as well as tracking macroscopic finite strain measures.\nCurrently, the code supports olivine and enstatite mineral phases. The\nfollowing features are provided:
\n\n\nJIT-compiled CPO solver, based on the D-Rex model, which updates the\npolycrystal orientation distribution depending on the macroscopic velocity\ngradients \nMineral class which stores attributes of a distinct mineral phase in the\npolycrystal and its texture snapshotsVoigt averaging to calculate the average elastic tensor of a textured,\nmultiphase polycrystal \nDecomposition of average elastic tensors into components attributed to\nminerals with distinct lattice symmetries \nCrystallographic pole figure visualisation (contouring is a work in progress) \n[work in progress] Texture diagnostics: M-index, bingham average,\nPoint-Girdle-Random symmetry, coaxial a.k.a \"BA\" index, etc. \n[work in progress] Seismic anisotropy diagnostics: % tensorial anisotropy,\nhexagonal symmetry a.k.a transverse isotropy direction, etc. \n \n\nThe core CPO solver is based on the original Fortran 90 implementation by \u00c9douard Kaminski,\nwhich can be downloaded from this link (~90KB) .\nThe reference papers are Kaminski & Ribe (2001) \nand Kaminski & Ribe (2004) ,\nand an open-access paper which discusses the model is Fraters & Billen (2021) .
\n\nInstallation \n\nThe minimum required Python version is set using requires-python in the\npyproject.tomlthe README file.
\n\nDocumentation \n\nThe website menu can be used to discover the public API of this package.\nSome of the tests are also documented and can serve as usage examples.\nTheir docstrings can be viewed in this section .\nDocumentation is also available from the Python REPL via the help() method.
\n\nThe D-Rex kinematic CPO model \n\nThe D-Rex model is used to compute crystallographic preferred orientation (CPO)\nfor polycrystals deforming by plastic deformation and dynamic recrystallization.\nPolycrystals are discretized into \"grains\" which represent fractional volumes\nof the total crystal that are characterised by a particular crystal lattice\norientation. For numerical efficiency, the number of grains in the model does\nnot change, and should only be interpreted as an approximation of the number\nof (unrecrystallised) physical grains. Dynamic recrystallization is modelled using\nstatistical expressions which approximate the interaction of each grain with an\neffective medium based on the averaged dislocation energy of all other grains. Note that\nthe model is not suited to situations where static recrystallization processes are\nsignificant.
\n\nThe primary microphysical mechanism for plastic deformation of the polycrystal\nis dislocation creep, which involves dislocation glide (\"slip\") along symmetry\nplanes of the mineral and dislocation climb, which allows for dislocations to\nannihilate each other so that the number of dislocations reaches a steady-state.\nThe D-Rex model does not simulate dislocation climb, but implicitly assumes that\nthe dislocations are in steady-state so that the dislocation density of the\ncrystal can be described by
\n\n$$\n\u03c1 \u221d b^{-2} \\left(\\frac{\u03c3}{\u03bc}\\right)^{p}\n$$
\n\nwhere $b$ is the length of the Burgers' vector, $\u03c3$ is the stress\nand $\u03bc$ is the shear modulus. The value of the exponent $p$ is given by the\nstress_exponent input parameter. For an overview of available parameters,\nsee [the pydrex.mock source code, for now...]
\n\nThe effects of dynamic recrystallization are twofold. Grains with a higher than\naverage dislocation density may be affected by either grain nucleation, which is\nthe formation of initially small, strain-free sub-grains, or grain boundary\nmigration, by which process other grains of lower strain energy annex a portion\nof its volume. Nucleation occurs mostly in grains oriented favourably for\ndislocation glide, and the new grains also grow by grain boundary migration.\nIf nucleation is too inefficient, the dislocation density in deformation-aligned\ngrains will remain high and these grains will therefore shrink in volume. On the\nother hand, if grain boundaries are too immobile, then nucleated grains will take\nlonger to grow, reducing the speed of CPO development and re-orientation.\nBecause nucleated grains are assumed to inherit the orientation of the parent,\nthey do not affect the model except by reducing the average dislocation density.\nA grain boundary mobility parameter of $M^{\u2217} = 0$ will therefore disable any\nrecrystallization effects. Finally, the process of grain boundary sliding can\nalso be included, which simply disallows rotation of grains with very small volume.\nThis only affects CPO evolution by introducing a latency for the onset of grain\nboundary migration in nucleated grains. It also manifests as an upper bound on\ntexture strength.
\n\nParameter reference \n\nModel parameters will eventually be provided in a .toml file.\nFor now just pass a dictionary to config in the Mineral.update_orientations method.\nA draft of the input file spec is shown below:
\n\n\n
# PyDRex TOML configuration specification. \n# Exactly one valid combination of fields from the [input] section are required, \n# the rest is optional. \n\n# Simulation name is optional but recommended. \nname = "pydrex-spec" \n\n# Input files/options are given in this section: \n[input] \n\n# Input data can be provided in one of three ways: \n# 1. An input mesh with the steady-state numerical velocity gradient field \n# and a plain text SCSV file specifying the FINAL locations of the polycrystals. \n# In this case, polycrystals will first be back-propagated along flow pathlines, \n# and then forward-propagated while the CPO is calculated. \n# The SCSV file should have column names 'X', 'Y', 'Z' for 3D or any two of those for 2D. \n# 2. A built-in (analytical) velocity gradient function from `pydrex.velocity_gradients`, \n# its arguments, and INITIAL locations of the polycrystals. In this case, \n# polycrystals will immediately be forward-advected in the specified field. \n# 3. Pre-computed pathline files with velocity gradients at each point. \n# These can be either plain text SCSV files or binary NPZ files. \n# They should have columns/fields called: 'X_id', 'Y_id', 'Z_id', 'L11_id', 'L12_id', 'L13_id', etc. \n# where 'id' is replaced by an unique identifier of the particle/pathline. \n# If a field called 't' is also present, it will be used for the timestamps. \n# Alternatively, a fixed timestep for all paths can be specified using `timestep`. \n# 4. Names of fields to be read from a geodynamics framework during runtime (not implemented yet). \n\n# Example for method 1, not only .vtu but any format supported by meshio should work: \n# mesh = "filename.vtu" \n# locations_final = "filename.scsv" \n# timestep = 1e9 \n\n# Example for method 2: \nvelocity_gradient = [ "simple_shear_2d" , "Y" , "X" , 5e-6 ] \nlocations_initial = "start.scsv" \ntimestep = 1e9 \n\n# Example for method 3: \n# timestep = 1e9 \n# paths = ["path001.npz", "path002.scsv"] \n\n# In cases where the pathlines do not exit the domain, \n# a maximum strain threshold can bee provided, after which advection is halted. \n# max_strain = 10 \n\n# Output files/options are given in this section: \n[output] \n\n# Optional output directory, will be created if missing. \n# This is also relative to the parent directory of the TOML file, \n# unless an absolute path is given. \ndirectory = "out" \n\n# Optional choice of mineral phases to include in raw output. \n# Raw output means rotation matrices and grain volumes, so 10 floats per grain per mineral. \n# By default, raw output for all supported minerals is saved. \nraw_output = [ "olivine" ] \n\n# Optional choice of mineral phases to include in diagnostic output. \n# Diagnostic output includes texture symmetry, strength and mean angle results. \n# By default, diagnostic output for all supported minerals is saved. \ndiagnostics = [ "olivine" ] \n\n# Should anisotropy postprocessing results be calculated? \n# This uses voigt averaging so the effective values for the multiphase polycrystal are calculated. \nanisotropy = true \n\n# Optional pathline output files (velocity gradients, positions, timestamps, particle ids). \n# Pathline output files use the same format as pathline inputs (by default, they are not produced). \n# They are stored inside the output directory unless absolute paths are given. \n# paths = ["pathline001.scsv"] \n\n# Optional logging level for log files. \n# This sets the log level for all log files, overriding the default value of "WARNING". \n# Supported levels are controlled by Python's logging module. \n# Usually they are "CRITICAL", "ERROR", "WARNING", "INFO" and "DEBUG". \nlog_level = "DEBUG" \n\n# DREX and simulation parameters are given in this section: \n[parameters] \n\n# Optional olivine volume fraction to use for multiphase simulations. \n# If enstatite_fraction is provided, they must sum to 1. \n# Otherwise, the remainder is assumed to be enstatite. \n# olivine_fraction = 1. \n\n# Optional enstatite volume fraction to use for multiphase simulations. \n# If olivine_fraction is provided, they must sum to 1. \n# Otherwise, the remainder is assumed to be olivine. \n# enstatite_fraction = 0. \n\n# Optional initial olivine fabric. A-type by default. \ninitial_olivine_fabric = "A" \n\n# Optional DREX stress_exponent, see documentation for details. \nstress_exponent = 1.5 \n\n# Optional DREX deformation_exponent, see documentation for details. \ndeformation_exponent = 3.5 \n\n# Optional DREX grain boudary mobility, see documentation for details. \ngbm_mobility = 125 \n\n# Optional DREX grain boundary sliding threshold, see documentation for details. \ngbs_threshold = 0.3 \n\n# Optional DREX nucleation efficiency, see documentation for details. \nnucleation_efficiency = 5.0 \n\n# Optional number of (initial) grains per mineral phase per polycrystal. \nnumber_of_grains = 2000 \n\n
\n PyDRex: Custom Matplotlib Axes subclasses.
\n \n"}, "pydrex.axes.PoleFigureAxes": {"fullname": "pydrex.axes.PoleFigureAxes", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes", "kind": "class", "doc": "Axes class designed for crystallographic pole figures.
\n\nThin matplotlib Axes wrapper for crystallographic pole figures.
\n\n\n\n
Projections are not performed automatically using default methods like\nscatter or plot. To actually plot the pole figures, use polefigure.
\n\n
\n", "default_value": "'pydrex.polefigure'"}, "pydrex.axes.PoleFigureAxes.polefigure": {"fullname": "pydrex.axes.PoleFigureAxes.polefigure", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.polefigure", "kind": "function", "doc": "Plot pole figure of crystallographic texture.
\n\nArgs:
\n\n\ndata (array) \u2014 Nx3x3 array of orientation matricesdensity (bool, optional) \u2014 plot contoured pole figures, False by defaultref_axes (string, optional) \u2014 letters specifying the horizontal and vertical\naxes of the pole figure, and respective labelshkl (array, optional) \u2014 crystallographic axis (one of the slip\ndirections of olivine, i.e. [1, 0, 0], [0, 1, 0] or [0, 0, 1])density_kwargs (dict, optional) \u2014 keyword arguments to pass to\npydrex.stats.point_density if density=True \n\nAny additional keyword arguments are passed to either tripcolor if\ndensity=True or scatter if density=False
\n", "signature": "(\tself , \tdata , \tdensity = False , \tref_axes = 'xz' , \thkl = [ 1 , 0 , 0 ] , \tdensity_kwargs = None , \t** kwargs ): ", "funcdef": "def"}, "pydrex.axes.PoleFigureAxes.set": {"fullname": "pydrex.axes.PoleFigureAxes.set", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.set", "kind": "function", "doc": "Set multiple properties at once.
\n\nSupported properties are
\n\nProperties:\n adjustable: {'box', 'datalim'}\n agg_filter: a filter function, which takes a (m, n, 3) float array and a dpi value, and returns a (m, n, 3) array and two offsets from the bottom left corner of the image\n alpha: scalar or None\n anchor: (float, float) or {'C', 'SW', 'S', 'SE', 'E', 'NE', ...}\n animated: bool\n aspect: {'auto', 'equal'} or float\n autoscale_on: bool\n autoscalex_on: unknown\n autoscaley_on: unknown\n axes_locator: Callable[[Axes, Renderer], Bbox]\n axisbelow: bool or 'line'\n box_aspect: float or None\n clip_box: ~matplotlib.transforms.BboxBase or None\n clip_on: bool\n clip_path: Patch or (Path, Transform) or None\n facecolor or fc: color\n figure: ~matplotlib.figure.Figure\n frame_on: bool\n gid: str\n in_layout: bool\n label: object\n mouseover: bool\n navigate: bool\n navigate_mode: unknown\n path_effects: list of .AbstractPathEffect\n picker: None or bool or float or callable\n position: [left, bottom, width, height] or ~matplotlib.transforms.Bbox\n prop_cycle: ~cycler.Cycler\n rasterization_zorder: float or None\n rasterized: bool\n sketch_params: (scale: float, length: float, randomness: float)\n snap: bool or None\n subplotspec: unknown\n title: str\n transform: ~matplotlib.transforms.Transform\n url: str\n visible: bool\n xbound: (lower: float, upper: float)\n xlabel: str\n xlim: (left: float, right: float)\n xmargin: float greater than -0.5\n xscale: unknown\n xticklabels: unknown\n xticks: unknown\n ybound: (lower: float, upper: float)\n ylabel: str\n ylim: (bottom: float, top: float)\n ymargin: float greater than -0.5\n yscale: unknown\n yticklabels: unknown\n yticks: unknown\n zorder: float
\n", "signature": "(\tself , \t* , \tadjustable =< UNSET > , \tagg_filter =< UNSET > , \talpha =< UNSET > , \tanchor =< UNSET > , \tanimated =< UNSET > , \taspect =< UNSET > , \tautoscale_on =< UNSET > , \tautoscalex_on =< UNSET > , \tautoscaley_on =< UNSET > , \taxes_locator =< UNSET > , \taxisbelow =< UNSET > , \tbox_aspect =< UNSET > , \tclip_box =< UNSET > , \tclip_on =< UNSET > , \tclip_path =< UNSET > , \tfacecolor =< UNSET > , \tframe_on =< UNSET > , \tgid =< UNSET > , \tin_layout =< UNSET > , \tlabel =< UNSET > , \tmouseover =< UNSET > , \tnavigate =< UNSET > , \tpath_effects =< UNSET > , \tpicker =< UNSET > , \tposition =< UNSET > , \tprop_cycle =< UNSET > , \trasterization_zorder =< UNSET > , \trasterized =< UNSET > , \tsketch_params =< UNSET > , \tsnap =< UNSET > , \tsubplotspec =< UNSET > , \ttitle =< UNSET > , \ttransform =< UNSET > , \turl =< UNSET > , \tvisible =< UNSET > , \txbound =< UNSET > , \txlabel =< UNSET > , \txlim =< UNSET > , \txmargin =< UNSET > , \txscale =< UNSET > , \txticklabels =< UNSET > , \txticks =< UNSET > , \tybound =< UNSET > , \tylabel =< UNSET > , \tylim =< UNSET > , \tymargin =< UNSET > , \tyscale =< UNSET > , \tyticklabels =< UNSET > , \tyticks =< UNSET > , \tzorder =< UNSET > ): ", "funcdef": "def"}, "pydrex.cli": {"fullname": "pydrex.cli", "modulename": "pydrex.cli", "kind": "module", "doc": "\n PyDRex: Entry points and argument handling for command line tools.
\n \n\nAll CLI handlers should be registered in the CLI_HANDLERS namedtuple,\nwhich ensures that they will be installed as executable scripts alongside the package.
\n"}, "pydrex.cli.NPZFileInspector": {"fullname": "pydrex.cli.NPZFileInspector", "modulename": "pydrex.cli", "qualname": "NPZFileInspector", "kind": "class", "doc": "PyDRex script to show information about serialized CPO data.
\n\nLists the keys that should be used for the postfix in pydrex.Mineral.load and\npydrex.Mineral.from_file.
\n"}, "pydrex.cli.PoleFigureVisualiser": {"fullname": "pydrex.cli.PoleFigureVisualiser", "modulename": "pydrex.cli", "qualname": "PoleFigureVisualiser", "kind": "class", "doc": "PyDRex script to plot pole figures of serialized CPO data.
\n\nProduces [100], [010] and [001] pole figures for serialized pydrex.Minerals.\nIf the range of indices is not specified,\na maximum of 25 of each pole figure will be produced by default.
\n"}, "pydrex.cli.CLI_HANDLERS": {"fullname": "pydrex.cli.CLI_HANDLERS", "modulename": "pydrex.cli", "qualname": "CLI_HANDLERS", "kind": "variable", "doc": "
\n", "default_value": "CLI_HANDLERS(pole_figure_visualiser=PoleFigureVisualiser(), npz_file_inspector=NPZFileInspector())"}, "pydrex.core": {"fullname": "pydrex.core", "modulename": "pydrex.core", "kind": "module", "doc": "\n PyDRex: Core D-Rex functions and enums.
\n \n\nThe function derivatives implements the core D-Rex solver, which computes the\ncrystallographic rotation rate and changes in fractional grain volumes.
\n\nAcronyms:
\n\n\nCRSS = Critical Resolved Shear Stress,\ni.e. threshold stress required to initiate slip on a slip system,\nnormalised to the stress required to initiate slip on the softest slip system \n \n"}, "pydrex.core.PERMUTATION_SYMBOL": {"fullname": "pydrex.core.PERMUTATION_SYMBOL", "modulename": "pydrex.core", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "
\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.core.MineralPhase": {"fullname": "pydrex.core.MineralPhase", "modulename": "pydrex.core", "qualname": "MineralPhase", "kind": "class", "doc": "Supported mineral phases.
\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralPhase.olivine": {"fullname": "pydrex.core.MineralPhase.olivine", "modulename": "pydrex.core", "qualname": "MineralPhase.olivine", "kind": "variable", "doc": "
\n", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.core.MineralPhase.enstatite": {"fullname": "pydrex.core.MineralPhase.enstatite", "modulename": "pydrex.core", "qualname": "MineralPhase.enstatite", "kind": "variable", "doc": "
\n", "default_value": "<MineralPhase.enstatite: 1>"}, "pydrex.core.DeformationRegime": {"fullname": "pydrex.core.DeformationRegime", "modulename": "pydrex.core", "qualname": "DeformationRegime", "kind": "class", "doc": "Deformation mechanism regimes.
\n", "bases": "enum.IntEnum"}, "pydrex.core.DeformationRegime.diffusion": {"fullname": "pydrex.core.DeformationRegime.diffusion", "modulename": "pydrex.core", "qualname": "DeformationRegime.diffusion", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.diffusion: 0>"}, "pydrex.core.DeformationRegime.dislocation": {"fullname": "pydrex.core.DeformationRegime.dislocation", "modulename": "pydrex.core", "qualname": "DeformationRegime.dislocation", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.core.DeformationRegime.byerlee": {"fullname": "pydrex.core.DeformationRegime.byerlee", "modulename": "pydrex.core", "qualname": "DeformationRegime.byerlee", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.byerlee: 2>"}, "pydrex.core.DeformationRegime.max_viscosity": {"fullname": "pydrex.core.DeformationRegime.max_viscosity", "modulename": "pydrex.core", "qualname": "DeformationRegime.max_viscosity", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.max_viscosity: 3>"}, "pydrex.core.MineralFabric": {"fullname": "pydrex.core.MineralFabric", "modulename": "pydrex.core", "qualname": "MineralFabric", "kind": "class", "doc": "Supported mineral fabrics.
\n\nThe following fabric types are supported:
\n\n\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralFabric.olivine_A": {"fullname": "pydrex.core.MineralFabric.olivine_A", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_A", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.core.MineralFabric.olivine_B": {"fullname": "pydrex.core.MineralFabric.olivine_B", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_B", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_B: 1>"}, "pydrex.core.MineralFabric.olivine_C": {"fullname": "pydrex.core.MineralFabric.olivine_C", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_C", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_C: 2>"}, "pydrex.core.MineralFabric.olivine_D": {"fullname": "pydrex.core.MineralFabric.olivine_D", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_D", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_D: 3>"}, "pydrex.core.MineralFabric.olivine_E": {"fullname": "pydrex.core.MineralFabric.olivine_E", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_E", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_E: 4>"}, "pydrex.core.MineralFabric.enstatite_AB": {"fullname": "pydrex.core.MineralFabric.enstatite_AB", "modulename": "pydrex.core", "qualname": "MineralFabric.enstatite_AB", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.enstatite_AB: 5>"}, "pydrex.core.get_crss": {"fullname": "pydrex.core.get_crss", "modulename": "pydrex.core", "qualname": "get_crss", "kind": "function", "doc": "Get Critical Resolved Shear Stress for the mineral phase and fabric.
\n\nReturns an array of the normalised threshold stresses required to activate slip on\neach slip system. Olivine slip systems are ordered according to the convention used\nfor pydrex.minerals.OLIVINE_SLIP_SYSTEMS.
\n", "signature": "(phase , fabric ): ", "funcdef": "def"}, "pydrex.core.derivatives": {"fullname": "pydrex.core.derivatives", "modulename": "pydrex.core", "qualname": "derivatives", "kind": "function", "doc": "Get derivatives of orientation and volume distribution.
\n\nArgs:
\n\n\nphase (MineralPhase) \u2014 ordinal number of the mineral phasefabric (MineralFabric) \u2014 ordinal number of the fabric typen_grains (int) \u2014 number of \"grains\" i.e. discrete volume segmentsorientations (array) \u2014 n_grainsx3x3 orientations (direction cosines)fractions (array) \u2014 volume fractions of the grains relative to aggregate volumestrain_rate (array) \u2014 3x3 dimensionless macroscopic strain-rate tensorvelocity_gradient (array) \u2014 3x3 dimensionless macroscopic velocity gradientstress_exponent (float) \u2014 p in dislocation_density \u221d shear_stress^pdeformation_exponent (float) \u2014 n in shear_stress \u221d |deformation_rate|^(1/n)nucleation_efficiency (float) \u2014 parameter controlling grain nucleationgmb_mobility (float) \u2014 grain boundary mobility parametervolume_fraction (float) \u2014 volume fraction of the mineral phase relative to\nother phases (multiphase simulations) \n\nReturns a tuple with the rotation rates and grain volume fraction changes.
\n", "signature": "(\tphase , \tfabric , \tn_grains , \torientations , \tfractions , \tstrain_rate , \tvelocity_gradient , \tstress_exponent , \tdeformation_exponent , \tnucleation_efficiency , \tgbm_mobility , \tvolume_fraction ): ", "funcdef": "def"}, "pydrex.diagnostics": {"fullname": "pydrex.diagnostics", "modulename": "pydrex.diagnostics", "kind": "module", "doc": "\n PyDRex: Methods to calculate texture and strain diagnostics.
\n \n\n\n\n
Calculations expect orientation matrices $a$ to represent passive\n(i.e. alias) rotations, which are defined in terms of the extrinsic ZXZ\neuler angles $\u03d5, \u03b8, \u03c6$ as\n$$\na = \\begin{bmatrix}\n \\cos\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\sin\u03c6 & \\cos\u03b8\\cos\u03d5\\sin\u03c6 + \\cos\u03c6\\sin\u03d5 & \\sin\u03c6\\sin\u03b8 \\cr\n -\\sin\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\cos\u03c6 & \\cos\u03b8\\cos\u03d5\\cos\u03c6 - \\sin\u03c6\\sin\u03d5 & \\cos\u03c6\\sin\u03b8 \\cr\n \\sin\u03b8\\sin\u03d5 & -\\sin\u03b8\\cos\u03d5 & \\cos\u03b8\n \\end{bmatrix}\n$$\nsuch that a[i, j] gives the direction cosine of the angle between the i-th\ngrain axis and the j-th external axis (in the global Eulerian frame).
\n\n
Calculate elasticity decompositions for the given elasticity tensors.
\n\nArgs:
\n\n\nvoigt_matrices (array) \u2014 the Nx6x6 Voigt matrix representations of the averaged\nelasticity tensors for a series of polycrystal textures \n\nReturns a dictionary with the following data series:
\n\n\n'bulk_modulus' \u2014 the computed bulk modulus for each Voigt matrix C'shear_modulus' \u2014 the computed shear modulus for each Voigt matrix C'percent_anisotropy' \u2014 for each Voigt matrix C, the total percentage of the\nnorm of the elastic tensor ||C|| that deviates from the norm of the \"closest\"\nisotropic elasticity tensor'percent_hexagonal' \u2014 for each C, the percentage of ||C|| attributed to\nhexagonally symmetric minerals'percent_tetragonal' \u2014 for each C, the percentage of ||C|| attributed to\ntetragonally symmetric minerals'percent_orthorhombic' \u2014 for each C, the percentage of ||C|| attributed to\northorhombically symmetric minerals'percent_monoclinic' \u2014 for each C, the percentage of ||C|| attributed to\nmonoclinically symmetric minerals'percent_triclinic' \u2014 for each C, the percentage of ||C|| attributed to\ntriclinically \"symmetric\" minerals (no mirror planes)'hexagonal_axis' \u2014 for each C, the axis of hexagonal symmetry for the \"closest\"\nhexagonally symmetric approximation to C, a.k.a. the \"transverse isotropy\" axis \n\n\n\n
Only 5 symmetry classes are relevant for elasticity decomposition,\ncompared to the usual 6 used to describe crystal families.\nCrystals with cubic symmetry contribute to the isotropic elasticity tensor,\nbecause the lattice spacing is identical in all orthogonal directions.\nNote also that the trigonal crystal system is not a crystal family\n(it belongs to the hexagonal family).
\n\n
(voigt_matrices ): ", "funcdef": "def"}, "pydrex.diagnostics.bingham_average": {"fullname": "pydrex.diagnostics.bingham_average", "modulename": "pydrex.diagnostics", "qualname": "bingham_average", "kind": "function", "doc": "Compute Bingham average of orientation matrices.
\n\nReturns the antipodally symmetric average orientation\nof the given crystallographic axis, or the a-axis by default.\nValid axis specifiers are \"a\" for [100], \"b\" for [010] and \"c\" for [001].
\n\nSee also: Watson (1966) ,\nMardia & Jupp, \u201cDirectional Statistics\u201d .
\n", "signature": "(orientations , axis = 'a' ): ", "funcdef": "def"}, "pydrex.diagnostics.finite_strain": {"fullname": "pydrex.diagnostics.finite_strain", "modulename": "pydrex.diagnostics", "qualname": "finite_strain", "kind": "function", "doc": "Extract measures of finite strain from the deformation gradient.
\n\nExtracts the largest principal strain value and the vector defining the axis of\nmaximum extension (longest semiaxis of the finite strain ellipsoid) from the 3x3\ndeformation gradient tensor.
\n", "signature": "(deformation_gradient , driver = 'ev' ): ", "funcdef": "def"}, "pydrex.diagnostics.symmetry_pgr": {"fullname": "pydrex.diagnostics.symmetry_pgr", "modulename": "pydrex.diagnostics", "qualname": "symmetry_pgr", "kind": "function", "doc": "Compute texture symmetry eigenvalue diagnostics from grain orientation matrices.
\n\nCompute Point, Girdle and Random symmetry diagnostics\nfor ternary texture classification.\nReturns the tuple (P, G, R) where\n$$\n\\begin{align*}\nP &= (\u03bb_{1} - \u03bb_{2}) / N \\cr\nG &= 2 (\u03bb_{2} - \u03bb_{3}) / N \\cr\nR &= 3 \u03bb_{3} / N\n\\end{align*}\n$$\nwith $N$ the sum of the eigenvalues $\u03bb_{1} \u2265 \u03bb_{2} \u2265 \u03bb_{3}$\nof the scatter (inertia) matrix.
\n\nSee e.g. Vollmer (1990) .
\n", "signature": "(orientations , axis = 'a' ): ", "funcdef": "def"}, "pydrex.diagnostics.misorientation_indices": {"fullname": "pydrex.diagnostics.misorientation_indices", "modulename": "pydrex.diagnostics", "qualname": "misorientation_indices", "kind": "function", "doc": "Calculate M-indices for a series of polycrystal textures.
\n\nCalculate M-index using misorientation_index for a series of texture snapshots.\nThe orientation_stack is a NxMx3x3 array of orientations where N is the number of\ntexture snapshots and M is the number of grains.
\n\nUses the multiprocessing library to calculate texture indices for multiple snapshots\nsimultaneously. If ncpus is None the number of CPU cores to use is chosen\nautomatically based on the maximum number available to the Python interpreter,\notherwise the specified number of cores is requested. Alternatively, an existing\ninstance of multiprocessing.Pool can be provided.
\n\nSee misorientation_index for documentation of the remaining arguments.
\n", "signature": "(\torientation_stack , \tsystem : pydrex . geometry . LatticeSystem , \tbins = None , \tncpus = None , \tpool = None ): ", "funcdef": "def"}, "pydrex.diagnostics.misorientation_index": {"fullname": "pydrex.diagnostics.misorientation_index", "modulename": "pydrex.diagnostics", "qualname": "misorientation_index", "kind": "function", "doc": "Calculate M-index for polycrystal orientations.
\n\nThe bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.
\n\n\n\n
This method must be able to allocate an array of shape\n$ \\frac{N!}{2(N-2)!}\u00d7 M^{2} $\nfor N the length of orientations and M the number of symmetry operations for\nthe given system.
\n\n
See Skemer et al. (2005) .
\n", "signature": "(orientations , system : pydrex . geometry . LatticeSystem , bins = None ): ", "funcdef": "def"}, "pydrex.diagnostics.coaxial_index": {"fullname": "pydrex.diagnostics.coaxial_index", "modulename": "pydrex.diagnostics", "qualname": "coaxial_index", "kind": "function", "doc": "Calculate coaxial \u201cBA\u201d index for a combination of two crystal axes.
\n\nThe BA index of Mainprice et al. (2015) \nis derived from the eigenvalue symmetry diagnostics and measures point vs girdle\nsymmetry in the aggregate. $BA \u2208 [0, 1]$ where $BA = 0$ corresponds to a perfect\naxial girdle texture and $BA = 1$ represents a point symmetry texture assuming that\nthe random component $R$ is negligible. May be less susceptible to random\nfluctuations compared to the raw eigenvalue diagnostics.
\n", "signature": "(orientations , axis1 = 'b' , axis2 = 'a' ): ", "funcdef": "def"}, "pydrex.diagnostics.smallest_angle": {"fullname": "pydrex.diagnostics.smallest_angle", "modulename": "pydrex.diagnostics", "qualname": "smallest_angle", "kind": "function", "doc": "Get smallest angle between a unit vector and a bidirectional axis.
\n\nThe axis is specified using either of its two parallel unit vectors.\nOptionally project the vector onto the plane (given by its unit normal)\nbefore calculating the angle.
\n", "signature": "(vector , axis , plane = None ): ", "funcdef": "def"}, "pydrex.exceptions": {"fullname": "pydrex.exceptions", "modulename": "pydrex.exceptions", "kind": "module", "doc": "\n PyDRex: Custom exceptions (subclasses of pydrex.Error).
\n \n"}, "pydrex.exceptions.Error": {"fullname": "pydrex.exceptions.Error", "modulename": "pydrex.exceptions", "qualname": "Error", "kind": "class", "doc": "Base class for exceptions in PyDRex.
\n", "bases": "builtins.Exception"}, "pydrex.exceptions.ConfigError": {"fullname": "pydrex.exceptions.ConfigError", "modulename": "pydrex.exceptions", "qualname": "ConfigError", "kind": "class", "doc": "Exception raised for errors in the input configuration.
\n\nAttributes:\n message \u2014 explanation of the error
\n", "bases": "Error"}, "pydrex.exceptions.ConfigError.__init__": {"fullname": "pydrex.exceptions.ConfigError.__init__", "modulename": "pydrex.exceptions", "qualname": "ConfigError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.ConfigError.message": {"fullname": "pydrex.exceptions.ConfigError.message", "modulename": "pydrex.exceptions", "qualname": "ConfigError.message", "kind": "variable", "doc": "
\n"}, "pydrex.exceptions.MeshError": {"fullname": "pydrex.exceptions.MeshError", "modulename": "pydrex.exceptions", "qualname": "MeshError", "kind": "class", "doc": "Exception raised for errors in the input mesh.
\n\nAttributes:\n message \u2014 explanation of the error
\n", "bases": "Error"}, "pydrex.exceptions.MeshError.__init__": {"fullname": "pydrex.exceptions.MeshError.__init__", "modulename": "pydrex.exceptions", "qualname": "MeshError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.MeshError.message": {"fullname": "pydrex.exceptions.MeshError.message", "modulename": "pydrex.exceptions", "qualname": "MeshError.message", "kind": "variable", "doc": "
\n"}, "pydrex.exceptions.IterationError": {"fullname": "pydrex.exceptions.IterationError", "modulename": "pydrex.exceptions", "qualname": "IterationError", "kind": "class", "doc": "Exception raised for errors in numerical iteration schemes.
\n\nAttributes:\n message \u2014 explanation of the error
\n", "bases": "Error"}, "pydrex.exceptions.IterationError.__init__": {"fullname": "pydrex.exceptions.IterationError.__init__", "modulename": "pydrex.exceptions", "qualname": "IterationError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.IterationError.message": {"fullname": "pydrex.exceptions.IterationError.message", "modulename": "pydrex.exceptions", "qualname": "IterationError.message", "kind": "variable", "doc": "
\n"}, "pydrex.exceptions.SCSVError": {"fullname": "pydrex.exceptions.SCSVError", "modulename": "pydrex.exceptions", "qualname": "SCSVError", "kind": "class", "doc": "Exception raised for errors in SCSV file I/O.
\n\nAttributes:
\n\n\nmessage \u2014 explanation of the error \n \n", "bases": "Error"}, "pydrex.exceptions.SCSVError.__init__": {"fullname": "pydrex.exceptions.SCSVError.__init__", "modulename": "pydrex.exceptions", "qualname": "SCSVError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.SCSVError.message": {"fullname": "pydrex.exceptions.SCSVError.message", "modulename": "pydrex.exceptions", "qualname": "SCSVError.message", "kind": "variable", "doc": "
\n"}, "pydrex.geometry": {"fullname": "pydrex.geometry", "modulename": "pydrex.geometry", "kind": "module", "doc": "\n PyDRex: Functions for geometric coordinate conversions and projections.
\n \n"}, "pydrex.geometry.LatticeSystem": {"fullname": "pydrex.geometry.LatticeSystem", "modulename": "pydrex.geometry", "qualname": "LatticeSystem", "kind": "class", "doc": "Crystallographic lattice systems supported by postprocessing methods.
\n\nThe value of a member is (a, b) with a and b as given in the table below.\nThe additional row lists the maximum misorientation angle between two crystallites\nfor the given lattice system.
\n\n triclinic monoclinic orthorhombic rhombohedral tetragonal hexagonal\n------------------------------------------------------------------------------\na 1 2 2 3 4 6\nb 1 2 4 6 8 12\n\u03b8max 180\u00b0 180\u00b0 120\u00b0 120\u00b0 90\u00b0 90\u00b0\nThis is identically Table 1 in Grimmer (1979) .
\n", "bases": "enum.Enum"}, "pydrex.geometry.LatticeSystem.triclinic": {"fullname": "pydrex.geometry.LatticeSystem.triclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.triclinic", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.triclinic: (1, 1)>"}, "pydrex.geometry.LatticeSystem.monoclinic": {"fullname": "pydrex.geometry.LatticeSystem.monoclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.monoclinic", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.monoclinic: (2, 2)>"}, "pydrex.geometry.LatticeSystem.orthorhombic": {"fullname": "pydrex.geometry.LatticeSystem.orthorhombic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.orthorhombic", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.orthorhombic: (2, 4)>"}, "pydrex.geometry.LatticeSystem.rhombohedral": {"fullname": "pydrex.geometry.LatticeSystem.rhombohedral", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.rhombohedral", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.rhombohedral: (3, 6)>"}, "pydrex.geometry.LatticeSystem.tetragonal": {"fullname": "pydrex.geometry.LatticeSystem.tetragonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.tetragonal", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.tetragonal: (4, 8)>"}, "pydrex.geometry.LatticeSystem.hexagonal": {"fullname": "pydrex.geometry.LatticeSystem.hexagonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.hexagonal", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.hexagonal: (6, 12)>"}, "pydrex.geometry.to_cartesian": {"fullname": "pydrex.geometry.to_cartesian", "modulename": "pydrex.geometry", "qualname": "to_cartesian", "kind": "function", "doc": "Convert spherical to cartesian coordinates in \u211d\u00b3.
\n\nSpherical coordinate convention:
\n\n\n\u03d5 is the longitude (\u201cazimuth\u201d) \u2208 [0, 2\u03c0) \n\u03b8 is the colatitude (\u201cinclination\u201d) \u2208 [0, \u03c0) \n \n\nBy default, a radius of r = 1 is used for the sphere.\nReturns a tuple containing arrays of x, y, and z values.
\n", "signature": "(\u03c6 , \u03b8 , r = 1 ): ", "funcdef": "def"}, "pydrex.geometry.to_spherical": {"fullname": "pydrex.geometry.to_spherical", "modulename": "pydrex.geometry", "qualname": "to_spherical", "kind": "function", "doc": "Convert cartesian coordinates in \u211d\u00b3 to spherical coordinates.
\n\nSpherical coordinate convention:
\n\n\n\u03d5 is the longitude (\u201cazimuth\u201d) \u2208 [0, 2\u03c0) \n\u03b8 is the colatitude (\u201cinclination\u201d) \u2208 [0, \u03c0) \n \n\nReturns a tuple containing arrays of r, \u03d5 and \u03b8 values.
\n", "signature": "(x , y , z ): ", "funcdef": "def"}, "pydrex.geometry.misorientation_angles": {"fullname": "pydrex.geometry.misorientation_angles", "modulename": "pydrex.geometry", "qualname": "misorientation_angles", "kind": "function", "doc": "Calculate minimum misorientation angles for collections of rotation quaternions.
\n\nCalculate the smallest angular distance between any quaternions q1_array[:, i] and\nq2_array[:, j], where i == j and the first dimensions of q1_array and q2_array\nare of equal length (the output will also be this long):
\n\nq1_array.shape q2_array.shape len(output)\n---------------------------------------------------\nNxAx4 NxBx4 N\n\n\n
This method must be able to allocate a floating point array of shape Nx(A*B)
\n\n
Uses ~25% less memory than the same operation with rotation matrices.
\n\nSee also:
\n\n\n", "signature": "(q1_array , q2_array ): ", "funcdef": "def"}, "pydrex.geometry.symmetry_operations": {"fullname": "pydrex.geometry.symmetry_operations", "modulename": "pydrex.geometry", "qualname": "symmetry_operations", "kind": "function", "doc": "Get sequence of symmetry operations for the given LatticeSystem.
\n\nReturned transforms are either quaternions (for rotations of the lattice) or 4x4\nmatrices which pre-multiply a quaternion to give a reflected variant (reflections\nare improper rotations and cannot be represented as quaternions or SciPy rotation\nmatrices).
\n", "signature": "(system : pydrex . geometry . LatticeSystem ): ", "funcdef": "def"}, "pydrex.geometry.poles": {"fullname": "pydrex.geometry.poles", "modulename": "pydrex.geometry", "qualname": "poles", "kind": "function", "doc": "Extract 3D vectors of crystallographic directions from orientation matrices.
\n\nExpects orientations to be an array with shape (N, 3, 3).\nThe optional arguments ref_axes and hkl can be used to change\nthe global reference axes and the crystallographic direction respectively.\nThe reference axes should be given as a string of two letters,\ne.g. \"xz\" (default), which specify the second and third axes\nof the global right-handed reference frame. The third letter in the set \"xyz\"\ndetermines the first axis. The ref_axes will therefore become the\nhorizontal and vertical axes of pole figures used to plot the directions.
\n", "signature": "(orientations , ref_axes = 'xz' , hkl = [ 1 , 0 , 0 ] ): ", "funcdef": "def"}, "pydrex.geometry.lambert_equal_area": {"fullname": "pydrex.geometry.lambert_equal_area", "modulename": "pydrex.geometry", "qualname": "lambert_equal_area", "kind": "function", "doc": "Project axial data from a 3D sphere onto a 2D disk.
\n\nProject points from a 3D sphere of radius 1, given in Cartesian coordinates,\nto points on a 2D disk using a Lambert equal area azimuthal projection.\nReturns arrays of the X and Y coordinates in the unit disk.
\n\nThis implementation first maps all points onto the same hemisphere,\nand then projects that hemisphere onto the disk.
\n", "signature": "(xvals , yvals , zvals ): ", "funcdef": "def"}, "pydrex.geometry.shirley_concentric_squaredisk": {"fullname": "pydrex.geometry.shirley_concentric_squaredisk", "modulename": "pydrex.geometry", "qualname": "shirley_concentric_squaredisk", "kind": "function", "doc": "Project points from a square onto a disk using the concentric Shirley method.
\n\nThe concentric method of Shirley & Chiu (1997) \nis optimised to preserve area. See also: http://marc-b-reynolds.github.io/math/2017/01/08/SquareDisc.html .
\n\nThis can be used to set up uniform grids on a disk, e.g.
\n\n\n
>>> a = [ x / 5.0 for x in range ( - 5 , 6 )] \n>>> x = [[ x ] * len ( a ) for x in a ] \n>>> y = [ a for _ in a ] \n>>> x_flat = [ j for i in x for j in i ] \n>>> y_flat = [ j for i in y for j in i ] \n>>> x_disk , y_disk = shirley_concentric_squaredisk ( x_flat , y_flat ) \n>>> r = x_disk ** 2 + y_disk ** 2 \n>>> r . reshape (( len ( a ), len ( a ))) \narray([[1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ], \n [1. , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.04, 0. , 0.04, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1. ], \n [1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ]]) \n>>> from math import atan2 \n>>> \u03b8 = [ atan2 ( y , x ) for y , x in zip ( y_disk , x_disk )] \n>>> max ( \u03b8 ) \n3.141592653589793 \n>>> min ( \u03b8 ) \n-2.9845130209101467 \n\n
(xvals , yvals ): ", "funcdef": "def"}, "pydrex.io": {"fullname": "pydrex.io", "modulename": "pydrex.io", "kind": "module", "doc": "\n PyDRex: Mesh, configuration and supporting data Input/Output functions.
\n \n\nPyDRex can read/write three kinds of plain text files:
\n\n\nPyDRex configuration files, which specify simulation parameters and initial conditions \n'SCSV' files, CSV files with YAML frontmatter for (small) scientific datasets \nMesh files via meshio, to set up final mineral positions in steady flows. \n \n\nSCSV files are our custom CSV files with a YAML header. The header is used for data\nattribution and metadata, as well as a column type spec. There is no official spec for\nSCSV files at the moment but they should follow the format of existing SCSV files in\nthe data/ folder of the source repository. For supported cell types, see\nSCSV_TYPEMAP.
\n"}, "pydrex.io.DEFAULT_PARAMS": {"fullname": "pydrex.io.DEFAULT_PARAMS", "modulename": "pydrex.io", "qualname": "DEFAULT_PARAMS", "kind": "variable", "doc": "Default simulation parameters.
\n", "default_value": "{'olivine_fraction': 1.0, 'enstatite_fraction': 0.0, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5.0, 'number_of_grains': 3500, 'initial_olivine_fabric': 'A'}"}, "pydrex.io.SCSV_TYPEMAP": {"fullname": "pydrex.io.SCSV_TYPEMAP", "modulename": "pydrex.io", "qualname": "SCSV_TYPEMAP", "kind": "variable", "doc": "Mapping of supported SCSV field types to corresponding Python types.
\n", "default_value": "{'string': <class 'str'>, 'integer': <class 'int'>, 'float': <class 'float'>, 'boolean': <class 'bool'>, 'complex': <class 'complex'>}"}, "pydrex.io.read_scsv": {"fullname": "pydrex.io.read_scsv", "modulename": "pydrex.io", "qualname": "read_scsv", "kind": "function", "doc": "Read data from an SCSV file.
\n\nPrints the YAML header section to output and returns a NamedTuple with columns of\nthe csv data. See also save_scsv.
\n", "signature": "(file ): ", "funcdef": "def"}, "pydrex.io.write_scsv_header": {"fullname": "pydrex.io.write_scsv_header", "modulename": "pydrex.io", "qualname": "write_scsv_header", "kind": "function", "doc": "Write YAML header to an SCSV stream.
\n\nArgs:
\n\n\nstream \u2014 open output stream (e.g. file handle) where data should be writtenschema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keyscomments (optional) \u2014 array of comments to be written above the schema, each on\na new line with an '#' prefix \n\nSee also read_scsv, save_scsv.
\n", "signature": "(stream , schema , comments = None ): ", "funcdef": "def"}, "pydrex.io.save_scsv": {"fullname": "pydrex.io.save_scsv", "modulename": "pydrex.io", "qualname": "save_scsv", "kind": "function", "doc": "Save data to SCSV file.
\n\nArgs:
\n\n\nfile \u2014 path to the file where the data should be writtenschema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keysdata \u2014 data arrays (columns) of equal length \n\nOptional keyword arguments are passed to write_scsv_header. See also read_scsv.
\n", "signature": "(file , schema , data , ** kwargs ): ", "funcdef": "def"}, "pydrex.io.parse_config": {"fullname": "pydrex.io.parse_config", "modulename": "pydrex.io", "qualname": "parse_config", "kind": "function", "doc": "Parse a TOML file containing PyDRex configuration.
\n", "signature": "(path ): ", "funcdef": "def"}, "pydrex.io.resolve_path": {"fullname": "pydrex.io.resolve_path", "modulename": "pydrex.io", "qualname": "resolve_path", "kind": "function", "doc": "Resolve relative paths and create parent directories if necessary.
\n\nRelative paths are interpreted with respect to the current working directory,\ni.e. the directory from whith the current Python process was executed,\nunless a specific reference directory is provided with refdir.
\n", "signature": "(path , refdir = None ): ", "funcdef": "def"}, "pydrex.io.stringify": {"fullname": "pydrex.io.stringify", "modulename": "pydrex.io", "qualname": "stringify", "kind": "function", "doc": "Return a cleaned version of a string for use in filenames, etc.
\n", "signature": "(s ): ", "funcdef": "def"}, "pydrex.io.data": {"fullname": "pydrex.io.data", "modulename": "pydrex.io", "qualname": "data", "kind": "function", "doc": "Get resolved path to a pydrex data directory.
\n", "signature": "(directory ): ", "funcdef": "def"}, "pydrex.logger": {"fullname": "pydrex.logger", "modulename": "pydrex.logger", "kind": "module", "doc": "\n PyDRex: logger settings and boilerplate.
\n \n\nPython's logging module is weird and its methods don't allow us to specify\nwhich logger to use, so just using logging.debug for example always uses\nthe \"root\" logger, which spams a bunch of messages from other imports/modules.\nInstead, the methods in this module are thin wrappers that use custom\nlogging objects (pydrex.logger.LOGGER and pydrex.logger.CONSOLE_LOGGER).\nThe method quiet_aliens can be invoked to suppress most messages\nfrom third-party modules, except critical errors and warnings from Numba.
\n\nBy default, PyDRex emits INFO level messages to the console.\nThis can be changed globally by setting the new level with CONSOLE_LOGGER.setLevel:
\n\n\n
from pydrex import logger as _log \n_log . info ( "this message will be printed to the console" ) \n\n_log . CONSOLE_LOGGER . setLevel ( "ERROR" ) \n_log . info ( "this message will NOT be printed to the console" ) \n_log . error ( "this message will be printed to the console" ) \n\n
To change the console logging level for a particular local context,\nuse the handler_level context manager:
\n\n\n
_log . CONSOLE_LOGGER . setLevel ( "INFO" ) \n_log . info ( "this message will be printed to the console" ) \n\nwith handler_level ( "ERROR" ): \n _log . info ( "this message will NOT be printed to the console" ) \n\n_log . info ( "this message will be printed to the console" ) \n\n
To save debug logs to a file, the logfile_enable context manager is recommended.\nAlways use the old printf style formatting for log messages, not fstrings,\notherwise compute time will be wasted on string conversions when logging is disabled:
\n\n\n
_log . quiet_aliens () # Suppress third-party log messages except CRITICAL from Numba. \nwith _log . logfile_enable ( "my_log_file.log" ): # Overwrite existing file unless mode="a". \n value = 42 \n _log . critical ( "critical error with value: %s " , value ) \n _log . error ( "runtime error with value: %s " , value ) \n _log . warning ( "warning with value: %s " , value ) \n _log . info ( "information message with value: %s " , value ) \n _log . debug ( "verbose debugging message with value: %s " , value ) \n ... # Construct Minerals, update orientations, etc. \n\n
Log formatter that uses terminal color codes.
\n", "bases": "logging.Formatter"}, "pydrex.logger.ConsoleFormatter.colorfmt": {"fullname": "pydrex.logger.ConsoleFormatter.colorfmt", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.colorfmt", "kind": "function", "doc": "
\n", "signature": "(self , code ): ", "funcdef": "def"}, "pydrex.logger.ConsoleFormatter.format": {"fullname": "pydrex.logger.ConsoleFormatter.format", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.format", "kind": "function", "doc": "Format the specified record as text.
\n\nThe record's attribute dictionary is used as the operand to a\nstring formatting operation which yields the returned string.\nBefore formatting the dictionary, a couple of preparatory steps\nare carried out. The message attribute of the record is computed\nusing LogRecord.getMessage(). If the formatting string uses the\ntime (as determined by a call to usesTime(), formatTime() is\ncalled to format the event time. If there is exception information,\nit is formatted using formatException() and appended to the message.
\n", "signature": "(self , record ): ", "funcdef": "def"}, "pydrex.logger.LOGGER": {"fullname": "pydrex.logger.LOGGER", "modulename": "pydrex.logger", "qualname": "LOGGER", "kind": "variable", "doc": "
\n", "default_value": "<Logger pydrex (DEBUG)>"}, "pydrex.logger.CONSOLE_LOGGER": {"fullname": "pydrex.logger.CONSOLE_LOGGER", "modulename": "pydrex.logger", "qualname": "CONSOLE_LOGGER", "kind": "variable", "doc": "
\n", "default_value": "<StreamHandler (INFO)>"}, "pydrex.logger.handle_exception": {"fullname": "pydrex.logger.handle_exception", "modulename": "pydrex.logger", "qualname": "handle_exception", "kind": "function", "doc": "
\n", "signature": "(exec_type , exec_value , exec_traceback ): ", "funcdef": "def"}, "pydrex.logger.handler_level": {"fullname": "pydrex.logger.handler_level", "modulename": "pydrex.logger", "qualname": "handler_level", "kind": "function", "doc": "Set logging handler level for current context.
\n\nArgs:
\n\n\nlevel (string) \u2014 logging level name e.g. \"DEBUG\", \"ERROR\", etc.\nSee Python's logging module for details.handler (optional, logging.Handler) \u2014 alternative handler to control instead\nof the default, CONSOLE_LOGGER. \n", "signature": "(level , handler =< StreamHandler ( INFO ) > ): ", "funcdef": "def"}, "pydrex.logger.logfile_enable": {"fullname": "pydrex.logger.logfile_enable", "modulename": "pydrex.logger", "qualname": "logfile_enable", "kind": "function", "doc": "Enable logging to a file at path with given level.
\n", "signature": "(path , level = 10 , mode = 'w' ): ", "funcdef": "def"}, "pydrex.logger.critical": {"fullname": "pydrex.logger.critical", "modulename": "pydrex.logger", "qualname": "critical", "kind": "function", "doc": "Log a CRITICAL message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.error": {"fullname": "pydrex.logger.error", "modulename": "pydrex.logger", "qualname": "error", "kind": "function", "doc": "Log an ERROR message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.warning": {"fullname": "pydrex.logger.warning", "modulename": "pydrex.logger", "qualname": "warning", "kind": "function", "doc": "Log a WARNING message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.info": {"fullname": "pydrex.logger.info", "modulename": "pydrex.logger", "qualname": "info", "kind": "function", "doc": "Log an INFO message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.debug": {"fullname": "pydrex.logger.debug", "modulename": "pydrex.logger", "qualname": "debug", "kind": "function", "doc": "Log a DEBUG message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.exception": {"fullname": "pydrex.logger.exception", "modulename": "pydrex.logger", "qualname": "exception", "kind": "function", "doc": "Log a message with level ERROR but retain exception information.
\n\nThis function should only be called from an exception handler.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.quiet_aliens": {"fullname": "pydrex.logger.quiet_aliens", "modulename": "pydrex.logger", "qualname": "quiet_aliens", "kind": "function", "doc": "Restrict alien loggers \ud83d\udc7d because I'm trying to find MY bugs, thanks.
\n", "signature": "(): ", "funcdef": "def"}, "pydrex.minerals": {"fullname": "pydrex.minerals", "modulename": "pydrex.minerals", "kind": "module", "doc": "\n PyDRex: Computations of mineral texture and elasticity.
\n \n\nAcronyms:
\n\n\nCPO = Crystallographic preferred orientation,\ni.e. preferential clustering of polycrystal grain orientations in SO(3),\nleading to an overall anisotropic orientation distribution \n \n"}, "pydrex.minerals.OLIVINE_STIFFNESS": {"fullname": "pydrex.minerals.OLIVINE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_STIFFNESS", "kind": "variable", "doc": "Stiffness tensor for olivine (Voigt representation), with units of GPa.
\n\nThe source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz \n[88K download]
\n", "default_value": "array([[320.71, 69.84, 71.22, 0. , 0. , 0. ],\n [ 69.84, 197.25, 74.8 , 0. , 0. , 0. ],\n [ 71.22, 74.8 , 234.32, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 63.77, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 77.67, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 78.36]])"}, "pydrex.minerals.ENSTATITE_STIFFNESS": {"fullname": "pydrex.minerals.ENSTATITE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "ENSTATITE_STIFFNESS", "kind": "variable", "doc": "Stiffness tensor for enstatite (Voigt representation), with units of GPa.
\n\nThe source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz \n[88K download]
\n", "default_value": "array([[236.9, 79.6, 63.2, 0. , 0. , 0. ],\n [ 79.6, 180.5, 56.8, 0. , 0. , 0. ],\n [ 63.2, 56.8, 230.4, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 84.3, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 79.4, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 80.1]])"}, "pydrex.minerals.OLIVINE_PRIMARY_AXIS": {"fullname": "pydrex.minerals.OLIVINE_PRIMARY_AXIS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_PRIMARY_AXIS", "kind": "variable", "doc": "Primary slip axis name for for the given olivine fabric.
\n", "default_value": "{<MineralFabric.olivine_A: 0>: 'a', <MineralFabric.olivine_B: 1>: 'c', <MineralFabric.olivine_C: 2>: 'c', <MineralFabric.olivine_D: 3>: 'a', <MineralFabric.olivine_E: 4>: 'a'}"}, "pydrex.minerals.OLIVINE_SLIP_SYSTEMS": {"fullname": "pydrex.minerals.OLIVINE_SLIP_SYSTEMS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_SLIP_SYSTEMS", "kind": "variable", "doc": "Slip systems for olivine in conventional order.
\n\nTuples contain the slip plane normal and slip direction vectors.\nThe order of slip systems returned matches the order of critical shear stresses\nreturned by pydrex.core.get_crss.
\n", "default_value": "(([0, 1, 0], [1, 0, 0]), ([0, 0, 1], [1, 0, 0]), ([0, 1, 0], [0, 0, 1]), ([1, 0, 0], [0, 0, 1]))"}, "pydrex.minerals.voigt_averages": {"fullname": "pydrex.minerals.voigt_averages", "modulename": "pydrex.minerals", "qualname": "voigt_averages", "kind": "function", "doc": "Calculate elastic tensors as the Voigt averages of a collection of minerals.
\n\nArgs:
\n\n\nminerals \u2014 list of pydrex.minerals.Mineral instances storing orientations and\nfractional volumes of the grains within each distinct mineral phaseweights (dict) \u2014 dictionary containing weights of each mineral\nphase, as a fraction of 1, in keys named \"_fraction\",\ne.g. \"olivine_fraction\" \n\nRaises a ValueError if the minerals contain an unequal number of grains or stored\ntexture results.
\n", "signature": "(minerals , weights ): ", "funcdef": "def"}, "pydrex.minerals.Mineral": {"fullname": "pydrex.minerals.Mineral", "modulename": "pydrex.minerals", "qualname": "Mineral", "kind": "class", "doc": "Class for storing polycrystal texture for a single mineral phase.
\n\nA Mineral stores texture data for an aggregate of grains*.\nAdditionally, mineral fabric type and deformation regime are also tracked.\nTo provide an initial texture for the mineral, use the constructor arguments\nfractions_init and orientations_init. By default,\na uniform volume distribution of random orientations is generated.
\n\nThe update_orientations method computes new orientations and grain volumes\nfor a given velocity gradient. These results are stored in the .orientations and\n.fractions attributes of the Mineral instance. The method also returns the\nupdated macroscopic deformation gradient based on the provided initial deformation\ngradient.
\n\n*Note that the \"number of grains\" is a static integer value that\ndoes not track the actual number of physical grains in the deforming polycrystal.\nInstead, this number acts as a \"number of bins\" for the statistical resolution of\nthe crystallographic orientation distribution. The value is roughly equivalent to\n(a multiple of) the number of initial, un-recrystallised grains in the polycrystal.\nIt is assumed that recrystallised grains do not grow large enough to require\nrotation tracking.
\n\nExamples:
\n\nMineral with isotropic initial texture:
\n\n\n
>>> import pydrex \n>>> olA = pydrex . Mineral ( \n... phase = pydrex . MineralPhase . olivine , \n... fabric = pydrex . MineralFabric . olivine_A , \n... regime = pydrex . DeformationRegime . dislocation , \n... n_grains = 2000 \n... ) \n>>> olA . phase \n<MineralPhase.olivine: 0> \n>>> olA . fabric \n<MineralFabric.olivine_A: 0> \n>>> olA . regime \n<DeformationRegime.dislocation: 1> \n>>> olA . n_grains \n2000 \n\n
Mineral with specified initial texture and default phase, fabric and regime settings\nwhich are for an olivine A-type mineral in the dislocation creep regime.\nThe initial grain volume fractions should be normalised.
\n\n\n
>>> import numpy as np \n>>> from scipy.spatial.transform import Rotation \n>>> import pydrex \n>>> rng = np . random . default_rng () \n>>> n_grains = 2000 \n>>> olA = pydrex . Mineral ( \n... n_grains = n_grains , \n... fractions_init = np . full ( n_grains , 1 / n_grains ), \n... orientations_init = Rotation . from_euler ( \n... "zxz" , [ \n... [ x * np . pi / 2 , np . pi / 2 , np . pi / 2 ] for x in rng . random ( n_grains ) \n... ] \n... ) . inv () . as_matrix (), \n... ) \n>>> len ( olA . orientations ) \n1 \n>>> type ( olA . orientations ) \n<class 'list'> \n>>> olA . orientations [ 0 ] . shape \n(2000, 3, 3) \n>>> olA . fractions [ 0 ] . shape \n(2000,) \n\n
Note that minerals can also be constructed from serialized data,\nsee Mineral.load and Mineral.from_file.
\n\nAttributes:
\n\n\nphase (pydrex.core.MineralPhase) \u2014 ordinal number of the mineral phasefabric (pydrex.core.MineralFabric) \u2014 ordinal number of the fabric typeregime (pydrex.core.DeformationRegime) \u2014 ordinal number of the deformation\nregimen_grains (int) \u2014 number of grains in the aggregatefractions (list of arrays) \u2014 grain volume fractions for each texture snapshotorientations (list of arrays) \u2014 grain orientation matrices for each texture\nsnapshotseed (int) \u2014 seed used by the random number generator to set up the isotropic\ninitial condition when fractions_init or orientations_init are not providedlband (int) \u2014 passed to the scipy.integrate.LSODA solveruband (int) \u2014 passed to the scipy.integrate.LSODA solver \n"}, "pydrex.minerals.Mineral.__init__": {"fullname": "pydrex.minerals.Mineral.__init__", "modulename": "pydrex.minerals", "qualname": "Mineral.__init__", "kind": "function", "doc": "
\n", "signature": "(\tphase : int = < MineralPhase . olivine : 0 > , \tfabric : int = < MineralFabric . olivine_A : 0 > , \tregime : int = < DeformationRegime . dislocation : 1 > , \tn_grains : int = 3500 , \tfractions_init : numpy . ndarray = None , \torientations_init : numpy . ndarray = None , \tfractions : list = < factory > , \torientations : list = < factory > , \tseed : int = None , \tlband : int = None , \tuband : int = None ) "}, "pydrex.minerals.Mineral.phase": {"fullname": "pydrex.minerals.Mineral.phase", "modulename": "pydrex.minerals", "qualname": "Mineral.phase", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.minerals.Mineral.fabric": {"fullname": "pydrex.minerals.Mineral.fabric", "modulename": "pydrex.minerals", "qualname": "Mineral.fabric", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.minerals.Mineral.regime": {"fullname": "pydrex.minerals.Mineral.regime", "modulename": "pydrex.minerals", "qualname": "Mineral.regime", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.minerals.Mineral.n_grains": {"fullname": "pydrex.minerals.Mineral.n_grains", "modulename": "pydrex.minerals", "qualname": "Mineral.n_grains", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "3500"}, "pydrex.minerals.Mineral.fractions_init": {"fullname": "pydrex.minerals.Mineral.fractions_init", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions_init", "kind": "variable", "doc": "
\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.orientations_init": {"fullname": "pydrex.minerals.Mineral.orientations_init", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations_init", "kind": "variable", "doc": "
\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.fractions": {"fullname": "pydrex.minerals.Mineral.fractions", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions", "kind": "variable", "doc": "
\n", "annotation": ": list"}, "pydrex.minerals.Mineral.orientations": {"fullname": "pydrex.minerals.Mineral.orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations", "kind": "variable", "doc": "
\n", "annotation": ": list"}, "pydrex.minerals.Mineral.seed": {"fullname": "pydrex.minerals.Mineral.seed", "modulename": "pydrex.minerals", "qualname": "Mineral.seed", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.lband": {"fullname": "pydrex.minerals.Mineral.lband", "modulename": "pydrex.minerals", "qualname": "Mineral.lband", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.uband": {"fullname": "pydrex.minerals.Mineral.uband", "modulename": "pydrex.minerals", "qualname": "Mineral.uband", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.update_orientations": {"fullname": "pydrex.minerals.Mineral.update_orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.update_orientations", "kind": "function", "doc": "Update orientations and volume distribution for the Mineral.
\n\nUpdate crystalline orientations and grain volume distribution\nfor minerals undergoing plastic deformation. Return the updated deformation\ngradient measuring the corresponding macroscopic deformation.
\n\nArgs:
\n\n\nconfig (dict) \u2014 PyDRex configuration dictionarydeformation_gradient (array) \u2014 3x3 initial deformation gradient tensorget_velocity_gradient (function) \u2014 callable with signature f(x) that returns\na 3x3 velocity gradient matrix at position x (vector)pathline (tuple) \u2014 tuple consisting of:\n\nthe time at which to start the CPO integration (t_start) \nthe time at which to stop the CPO integration (t_end) \ncallable with signature f(t) that returns the position of the mineral at\ntime t \u2208 [t_start, t_end] \n \n\nAny additional (optional) keyword arguments are passed to\nscipy.integrate.LSODA.
\n\nArray values must provide a NumPy-compatible interface:\nhttps://numpy.org/doc/stable/user/whatisnumpy.html
\n", "signature": "(\tself , \tconfig , \tdeformation_gradient , \tget_velocity_gradient , \tpathline , \t** kwargs ): ", "funcdef": "def"}, "pydrex.minerals.Mineral.save": {"fullname": "pydrex.minerals.Mineral.save", "modulename": "pydrex.minerals", "qualname": "Mineral.save", "kind": "function", "doc": "Save CPO data for all stored timesteps to a numpy NPZ file.
\n\nIf postfix is not None, the data is appended to the NPZ file\nin fields ending with \"_postfix\".
\n\nRaises a ValueError if the data shapes are not compatible.
\n\nSee also: numpy.savez, Mineral.load, Mineral.from_file.
\n", "signature": "(self , filename , postfix = None ): ", "funcdef": "def"}, "pydrex.minerals.Mineral.load": {"fullname": "pydrex.minerals.Mineral.load", "modulename": "pydrex.minerals", "qualname": "Mineral.load", "kind": "function", "doc": "Load CPO data from a numpy NPZ file.
\n\nIf postfix is not None, data is read from fields ending with \"_postfix\".
\n\nSee also: Mineral.save, Mineral.from_file.
\n", "signature": "(self , filename , postfix = None ): ", "funcdef": "def"}, "pydrex.minerals.Mineral.from_file": {"fullname": "pydrex.minerals.Mineral.from_file", "modulename": "pydrex.minerals", "qualname": "Mineral.from_file", "kind": "function", "doc": "Construct a Mineral instance using data from a numpy NPZ file.
\n\nIf postfix is not None, data is read from fields ending with \u201c_postfix\u201d.
\n\nSee also: Mineral.save, Mineral.load.
\n", "signature": "(cls , filename , postfix = None ): ", "funcdef": "def"}, "pydrex.mock": {"fullname": "pydrex.mock", "modulename": "pydrex.mock", "kind": "module", "doc": "\n PyDRex: Mock objects for testing and reproducibility.
\n \n"}, "pydrex.mock.PARAMS_FRATERS2021": {"fullname": "pydrex.mock.PARAMS_FRATERS2021", "modulename": "pydrex.mock", "qualname": "PARAMS_FRATERS2021", "kind": "variable", "doc": "Values used for tests 1, 2 and 4 in https://doi.org/10.1029/2021gc009846 .
\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5, 'number_of_grains': 5000}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SOLID", "kind": "variable", "doc": "Values used for the M*=0 test in https://doi.org/10.1016/s0012-821x(01)00356-9 .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 0, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "kind": "variable", "doc": "Values used for the M*=50 test in https://doi.org/10.1016/s0012-821x(01)00356-9 .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 50, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_LONGDASH", "kind": "variable", "doc": "Values used for the M*=200 test in https://doi.org/10.1016/s0012-821x(01)00356-9 .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 200, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "kind": "variable", "doc": "Values used for the \u03c7=0.4 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.4, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_SQUARES", "kind": "variable", "doc": "Values used for the \u03c7=0.2 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_CIRCLES", "kind": "variable", "doc": "Values used for the \u03c7=0 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_HEDJAZIAN2017": {"fullname": "pydrex.mock.PARAMS_HEDJAZIAN2017", "modulename": "pydrex.mock", "qualname": "PARAMS_HEDJAZIAN2017", "kind": "variable", "doc": "Values used for the MOR model in https://doi.org/10.1016/j.epsl.2016.12.004 .
\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 10, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 2197}"}, "pydrex.pathlines": {"fullname": "pydrex.pathlines", "modulename": "pydrex.pathlines", "kind": "module", "doc": "\n PyDRex: Functions for pathline construction.
\n \n"}, "pydrex.pathlines.get_pathline": {"fullname": "pydrex.pathlines.get_pathline", "modulename": "pydrex.pathlines", "qualname": "get_pathline", "kind": "function", "doc": "Determine the pathline for a particle in a steady state flow.
\n\nThe pathline will terminate at the given final_location and follow a curve\ndetermined by the velocity gradient. It works for both 2D (rectangular) and 3D\n(orthopiped\u00b9) domains, so long as the provided callables expect/return arrays of the\nappropriate dimension.
\n\n\n\n
The pathline is calculated backwards in time (t < 0) from the given endpoint.\nTherefore, the returned position callable should be evaluated at negative times.
\n\n
Args:
\n\n\nfinal_location (array) \u2014 coordinates of the final locationget_velocity (callable) \u2014 returns velocity vector at a pointget_velocity_gradient (callable) \u2014 returns velocity gradient matrix at a pointmin_coords (array) \u2014 lower bound coordinates of the boxmax_coords (array) \u2014 upper bound coordinates of the boxmax_strain (float) \u2014 target strain (given as \u201ctensorial\u201d strain \u03b5) at the final\nlocation, useful if the pathline never inflows into the domain (the pathline will\nonly be traced backwards until a strain of 0 is reached, unless a domain boundary\nis reached first) \n\nOptional keyword arguments will be passed to scipy.integrate.solve_ivp. However,\nsome of the arguments to the solve_ivp call may not be modified, and a warning\nwill be raised if they are provided.
\n\nReturns a tuple containing the time points and an interpolant that can be used\nto evaluate the pathline position (see scipy.integrate.OdeSolution).
\n\n\u00b9An \u201corthopiped\u201d is a 3D rectangle (called a \u201cbox\u201d when we are in a hurry), see\nhttps://www.whatistoday.net/2020/04/cuboid-dilemma.html .
\n", "signature": "(\tfinal_location , \tget_velocity , \tget_velocity_gradient , \tmin_coords , \tmax_coords , \tmax_strain , \t** kwargs ): ", "funcdef": "def"}, "pydrex.stats": {"fullname": "pydrex.stats", "modulename": "pydrex.stats", "kind": "module", "doc": "\n PyDRex: Statistical methods for orientation and elasticity data.
\n \n"}, "pydrex.stats.resample_orientations": {"fullname": "pydrex.stats.resample_orientations", "modulename": "pydrex.stats", "qualname": "resample_orientations", "kind": "function", "doc": "Return new samples from orientations weighted by the volume distribution.
\n\nArgs:
\n\n\norientations (array) \u2014 NxMx3x3 array of orientationsfractions (array) \u2014 NxM array of grain volume fractionsn_samples (int) \u2014 optional number of samples to return, default is Mseed (int) \u2014 optional seed for the random number generator, which is used to\npick random grain volume samples from the discrete distribution \n\nReturns the Nxn_samplesx3x3 orientations and associated sorted (ascending) grain\nvolumes.
\n", "signature": "(orientations , fractions , n_samples = None , seed = None ): ", "funcdef": "def"}, "pydrex.stats.misorientation_hist": {"fullname": "pydrex.stats.misorientation_hist", "modulename": "pydrex.stats", "qualname": "misorientation_hist", "kind": "function", "doc": "Calculate misorientation histogram for polycrystal orientations.
\n\nThe bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.
\n\n\n\n
This method must be able to allocate an array of shape\n$ \\frac{N!}{2(N-2)!}\u00d7 M^{2} $\nfor N the length of orientations and M the number of symmetry operations for\nthe given system.
\n\n
See Skemer et al. (2005) .
\n", "signature": "(orientations , system : pydrex . geometry . LatticeSystem , bins = None ): ", "funcdef": "def"}, "pydrex.stats.misorientations_random": {"fullname": "pydrex.stats.misorientations_random", "modulename": "pydrex.stats", "qualname": "misorientations_random", "kind": "function", "doc": "Get expected count of misorientation angles for an isotropic aggregate.
\n\nEstimate the expected number of misorientation angles between grains\nthat would fall within $($low, high$)$ in degrees for an aggregate\nwith randomly oriented grains, where low $\u2208 [0, $high$)$,\nand high is bounded by the maximum theoretical misorientation angle\nfor the given lattice symmetry system.\nSee _geo.LatticeSystem for supported systems.
\n", "signature": "(low , high , system : pydrex . geometry . LatticeSystem ): ", "funcdef": "def"}, "pydrex.stats.point_density": {"fullname": "pydrex.stats.point_density", "modulename": "pydrex.stats", "qualname": "point_density", "kind": "function", "doc": "Estimate point density of orientation data on the unit sphere.
\n\nEstimates the density of orientations on the unit sphere by counting the input data\nthat falls within small areas around a uniform grid of spherical counting locations.\nThe input data is expected in cartesian coordinates, and the contouring is performed\nusing kernel functions defined in Vollmer 1995 .\nThe following optional parameters control the contouring method:
\n\n\ngridsteps (int) \u2014 the number of steps, i.e. number of points along a diameter of\nthe spherical counting gridweights (array) \u2014 auxiliary weights for each data pointkernel (string) \u2014 the name of the kernel function to use, see\nSPHERICAL_COUNTING_KERNELSaxial (bool) \u2014 toggle axial versions of the kernel functions\n(for crystallographic data this should normally be kept as True) \n\nAny other keyword arguments are passed to the kernel function calls.\nMost kernels accept a parameter \u03c3 to control the degree of smoothing.
\n", "signature": "(\tx_data , \ty_data , \tz_data , \tgridsteps = 101 , \tweights = 1 , \tkernel = 'linear_inverse_kamb' , \taxial = True , \t** kwargs ): ", "funcdef": "def"}, "pydrex.stats.exponential_kamb": {"fullname": "pydrex.stats.exponential_kamb", "modulename": "pydrex.stats", "qualname": "exponential_kamb", "kind": "function", "doc": "Kernel function from Vollmer 1995 for exponential smoothing.
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.linear_inverse_kamb": {"fullname": "pydrex.stats.linear_inverse_kamb", "modulename": "pydrex.stats", "qualname": "linear_inverse_kamb", "kind": "function", "doc": "Kernel function from Vollmer 1995 for linear smoothing.
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.square_inverse_kamb": {"fullname": "pydrex.stats.square_inverse_kamb", "modulename": "pydrex.stats", "qualname": "square_inverse_kamb", "kind": "function", "doc": "Kernel function from Vollmer 1995 for inverse square smoothing.
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.kamb_count": {"fullname": "pydrex.stats.kamb_count", "modulename": "pydrex.stats", "qualname": "kamb_count", "kind": "function", "doc": "Original Kamb 1959 kernel function (raw count within radius).
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.schmidt_count": {"fullname": "pydrex.stats.schmidt_count", "modulename": "pydrex.stats", "qualname": "schmidt_count", "kind": "function", "doc": "Schmidt (a.k.a. 1%) counting kernel function.
\n", "signature": "(cos_dist , axial = None ): ", "funcdef": "def"}, "pydrex.stats.SPHERICAL_COUNTING_KERNELS": {"fullname": "pydrex.stats.SPHERICAL_COUNTING_KERNELS", "modulename": "pydrex.stats", "qualname": "SPHERICAL_COUNTING_KERNELS", "kind": "variable", "doc": "Kernel functions that return an un-summed distribution and a normalization factor.
\n\nSupported kernel functions are based on the discussion in\nVollmer 1995 .\nKamb methods accept the parameter \u03c3 (default: 10) to control the degree of smoothing.\nValues lower than 3 and higher than 20 are not recommended.
\n", "default_value": "{'kamb_count': <function kamb_count>, 'schmidt_count': <function schmidt_count>, 'exponential_kamb': <function exponential_kamb>, 'linear_inverse_kamb': <function linear_inverse_kamb>, 'square_inverse_kamb': <function square_inverse_kamb>}"}, "pydrex.tensors": {"fullname": "pydrex.tensors", "modulename": "pydrex.tensors", "kind": "module", "doc": "\n PyDRex: Tensor operation functions and helpers.
\n \n\nFor Voigt notation, the symmetric 6x6 matrix representation is used,\nwhich assumes that the fourth order tensor being represented as such is also symmetric.\nThe vectorial notation uses 21 components which are the independent components of the\nsymmetric 6x6 matrix.
\n"}, "pydrex.tensors.PERMUTATION_SYMBOL": {"fullname": "pydrex.tensors.PERMUTATION_SYMBOL", "modulename": "pydrex.tensors", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "
\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.tensors.voigt_decompose": {"fullname": "pydrex.tensors.voigt_decompose", "modulename": "pydrex.tensors", "qualname": "voigt_decompose", "kind": "function", "doc": "Decompose elastic tensor (as 6x6 Voigt matrix) into distinct contractions.
\n\nReturn the only two independent contractions of the elastic tensor given as a 6x6\nVoigt matrix. With reference to the full 4-th order elastic tensor, the\ncontractions are defined as:
\n\n\n$d_{ij} = C_{ijkk}$ (dilatational stiffness tensor) \n$v_{ij} = C_{ijkj}$ (deviatoric stiffness tensor) \n \n\nAny vector which is an eigenvector of both $d_{ij}$ and $v_{ij}$ is always normal to\na symmetry plane of the elastic medium.
\n\nSee Equations 3.4 & 3.5 in Browaeys & Chevrot (2004) .
\n", "signature": "(matrix ): ", "funcdef": "def"}, "pydrex.tensors.mono_project": {"fullname": "pydrex.tensors.mono_project", "modulename": "pydrex.tensors", "qualname": "mono_project", "kind": "function", "doc": "Project 21-component voigt_vector onto monoclinic symmetry subspace.
\n\nMonoclinic symmetry is characterised by 13 independent elasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.ortho_project": {"fullname": "pydrex.tensors.ortho_project", "modulename": "pydrex.tensors", "qualname": "ortho_project", "kind": "function", "doc": "Project 21-component voigt_vector onto orthorhombic symmetry subspace.
\n\nOrthorhombic symmetry is characterised by 9 independent elasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.tetr_project": {"fullname": "pydrex.tensors.tetr_project", "modulename": "pydrex.tensors", "qualname": "tetr_project", "kind": "function", "doc": "Project 21-component voigt_vector onto tetragonal symmetry subspace.
\n\nTetragonal symmetry is characterised by 6 independent elasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.hex_project": {"fullname": "pydrex.tensors.hex_project", "modulename": "pydrex.tensors", "qualname": "hex_project", "kind": "function", "doc": "Project 21-component voigt_vector onto hexagonal symmetry subspace.
\n\nHexagonal symmetry (a.k.a. transverse isotropy) is characterised by 5 independent\nelasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.upper_tri_to_symmetric": {"fullname": "pydrex.tensors.upper_tri_to_symmetric", "modulename": "pydrex.tensors", "qualname": "upper_tri_to_symmetric", "kind": "function", "doc": "Create symmetric array using upper triangle of input array.
\n\n\n
>>> import numpy as np \n>>> upper_tri_to_symmetric ( np . array ([ \n... [ 1. , 2. , 3. , 4. ], \n... [ 0. , 5. , 6. , 7. ], \n... [ 0. , 0. , 8. , 9. ], \n... [ 9. , 0. , 0. , 10. ] \n... ])) \narray([[ 1., 2., 3., 4.], \n [ 2., 5., 6., 7.], \n [ 3., 6., 8., 9.], \n [ 4., 7., 9., 10.]]) \n\n
(arr ): ", "funcdef": "def"}, "pydrex.tensors.voigt_to_elastic_tensor": {"fullname": "pydrex.tensors.voigt_to_elastic_tensor", "modulename": "pydrex.tensors", "qualname": "voigt_to_elastic_tensor", "kind": "function", "doc": "Create 4-th order elastic tensor from an equivalent Voigt matrix.
\n\nSee also: elastic_tensor_to_voigt.
\n", "signature": "(matrix ): ", "funcdef": "def"}, "pydrex.tensors.elastic_tensor_to_voigt": {"fullname": "pydrex.tensors.elastic_tensor_to_voigt", "modulename": "pydrex.tensors", "qualname": "elastic_tensor_to_voigt", "kind": "function", "doc": "Create a 6x6 Voigt matrix from an equivalent 4-th order elastic tensor.
\n", "signature": "(tensor ): ", "funcdef": "def"}, "pydrex.tensors.voigt_matrix_to_vector": {"fullname": "pydrex.tensors.voigt_matrix_to_vector", "modulename": "pydrex.tensors", "qualname": "voigt_matrix_to_vector", "kind": "function", "doc": "Create the 21-component Voigt vector equivalent to the 6x6 Voigt matrix.
\n", "signature": "(matrix ): ", "funcdef": "def"}, "pydrex.tensors.voigt_vector_to_matrix": {"fullname": "pydrex.tensors.voigt_vector_to_matrix", "modulename": "pydrex.tensors", "qualname": "voigt_vector_to_matrix", "kind": "function", "doc": "Create the 6x6 matrix representation of the 21-component Voigt vector.
\n\nSee also: voigt_matrix_to_vector.
\n", "signature": "(vector ): ", "funcdef": "def"}, "pydrex.tensors.rotate": {"fullname": "pydrex.tensors.rotate", "modulename": "pydrex.tensors", "qualname": "rotate", "kind": "function", "doc": "Rotate 4-th order tensor using a 3x3 rotation matrix.
\n", "signature": "(tensor , rotation ): ", "funcdef": "def"}, "pydrex.utils": {"fullname": "pydrex.utils", "modulename": "pydrex.utils", "kind": "module", "doc": "\n PyDRex: Miscellaneous utility methods.
\n \n"}, "pydrex.utils.strain_increment": {"fullname": "pydrex.utils.strain_increment", "modulename": "pydrex.utils", "qualname": "strain_increment", "kind": "function", "doc": "Calculate strain increment for a given time increment and velocity gradient.
\n\nReturns \u201ctensorial\u201d strain increment \u03b5, which is equal to \u03b3/2 where \u03b3 is the\n\u201c(engineering) shear strain\u201d increment.
\n", "signature": "(dt , velocity_gradient ): ", "funcdef": "def"}, "pydrex.utils.apply_gbs": {"fullname": "pydrex.utils.apply_gbs", "modulename": "pydrex.utils", "qualname": "apply_gbs", "kind": "function", "doc": "Apply grain boundary sliding for small grains.
\n", "signature": "(orientations , fractions , gbs_threshold , orientations_prev , n_grains ): ", "funcdef": "def"}, "pydrex.utils.extract_vars": {"fullname": "pydrex.utils.extract_vars", "modulename": "pydrex.utils", "qualname": "extract_vars", "kind": "function", "doc": "Extract deformation gradient, orientation matrices and grain sizes from y.
\n", "signature": "(y , n_grains ): ", "funcdef": "def"}, "pydrex.utils.remove_nans": {"fullname": "pydrex.utils.remove_nans", "modulename": "pydrex.utils", "qualname": "remove_nans", "kind": "function", "doc": "Remove NaN values from array.
\n", "signature": "(a ): ", "funcdef": "def"}, "pydrex.utils.default_ncpus": {"fullname": "pydrex.utils.default_ncpus", "modulename": "pydrex.utils", "qualname": "default_ncpus", "kind": "function", "doc": "Get a safe default number of CPUs available for multiprocessing.
\n\nOn Linux platforms that support it, the method os.sched_getaffinity() is used.\nOn Mac OS, the command sysctl -n hw.ncpu is used.\nOn Windows, the environment variable NUMBER_OF_PROCESSORS is queried.\nIf any of these fail, a fallback of 1 is used and a warning is logged.
\n", "signature": "(): ", "funcdef": "def"}, "pydrex.utils.get_steps": {"fullname": "pydrex.utils.get_steps", "modulename": "pydrex.utils", "qualname": "get_steps", "kind": "function", "doc": "Get forward difference of 2D array a, with repeated last elements.
\n\nThe repeated last elements ensure that output and input arrays have equal shape.
\n\nExamples:
\n\n\n
>>> get_steps ( np . array ([ 1 , 2 , 3 , 4 , 5 ])) \narray([[1, 1, 1, 1, 1]]) \n\n
\n
>>> get_steps ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ]])) \narray([[1, 1, 1, 1, 1], \n [2, 3, 3, 1, 1]]) \n\n
\n
>>> get_steps ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ], [ 1 , 0 , 0 , 0 , np . inf ]])) \narray([[ 1., 1., 1., 1., 1.], \n [ 2., 3., 3., 1., 1.], \n [-1., 0., 0., inf, nan]]) \n\n
(a ): ", "funcdef": "def"}, "pydrex.utils.angle_fse_simpleshear": {"fullname": "pydrex.utils.angle_fse_simpleshear", "modulename": "pydrex.utils", "qualname": "angle_fse_simpleshear", "kind": "function", "doc": "Get angle of FSE long axis anticlockwise from the X axis in simple shear.
\n", "signature": "(strain ): ", "funcdef": "def"}, "pydrex.utils.lag_2d_corner_flow": {"fullname": "pydrex.utils.lag_2d_corner_flow", "modulename": "pydrex.utils", "qualname": "lag_2d_corner_flow", "kind": "function", "doc": "Get predicted grain orientation lag for 2D corner flow.
\n\nSee eq. 11 in Kaminski & Ribe (2002) .
\n", "signature": "(\u03b8 ): ", "funcdef": "def"}, "pydrex.utils.quat_product": {"fullname": "pydrex.utils.quat_product", "modulename": "pydrex.utils", "qualname": "quat_product", "kind": "function", "doc": "Quaternion product, q1, q2 and output are in scalar-last (x,y,z,w) format.
\n", "signature": "(q1 , q2 ): ", "funcdef": "def"}, "pydrex.utils.redraw_legend": {"fullname": "pydrex.utils.redraw_legend", "modulename": "pydrex.utils", "qualname": "redraw_legend", "kind": "function", "doc": "Redraw legend on matplotlib axis or figure.
\n\nTransparency is removed from legend symbols.\nIf fig is not None and remove_all is True,\nall legends are first removed from the parent figure.\nOptional keyword arguments are passed to matplotlib.axes.Axes.legend by default,\nor matplotlib.figure.Figure.legend if fig is not None.
\n\nIf legendax is not None, the axis legend will be redrawn using the legendax axes\ninstead of taking up space in the original axes. This option requires fig=None.
\n\n\n\n
Note that if fig is not None, the legend may be cropped from the saved\nfigure due to a Matplotlib bug. In this case, it is required to add the\narguments bbox_extra_artists=(legend,) and bbox_inches=\"tight\" to savefig,\nwhere legend is the object returned by this function. To prevent the legend\nfrom consuming axes/subplot space, it is further required to add the lines:\nlegend.set_in_layout(False), fig.canvas.draw(), legend.set_layout(True)\nand fig.set_layout_engine(\"none\") before saving the figure.
\n\n
(ax , fig = None , legendax = None , remove_all = True , ** kwargs ): ", "funcdef": "def"}, "pydrex.utils.add_subplot_labels": {"fullname": "pydrex.utils.add_subplot_labels", "modulename": "pydrex.utils", "qualname": "add_subplot_labels", "kind": "function", "doc": "Add subplot labels to axes mosaic.
\n\nUse labelmap to specify a dictionary that maps keys in mosaic to subplot labels.\nIf labelmap is None, the keys in axs will be used as the labels by default.
\n\nIf internal is False (default), the axes titles will be used.\nOtherwise, internal labels will be drawn with ax.text,\nin which case loc must be a tuple of floats.
\n\nAny axes in axs corresponding to the special key legend are skipped.
\n", "signature": "(\tmosaic , \tlabelmap = None , \tloc = 'left' , \tfontsize = 'medium' , \tinternal = False , \t** kwargs ): ", "funcdef": "def"}, "pydrex.velocity": {"fullname": "pydrex.velocity", "modulename": "pydrex.velocity", "kind": "module", "doc": "\n PyDRex: Steady-state solutions of velocity (gradients) for various flows.
\n \n\nFor the sake of consistency, all callables returned from methods in this module expect a\n3D position vector as input. They also return 3D tensors in all cases. This means they\ncan be directly used as arguments to e.g. pydrex.minerals.Mineral.update_orientations.
\n"}, "pydrex.velocity.simple_shear_2d": {"fullname": "pydrex.velocity.simple_shear_2d", "modulename": "pydrex.velocity", "qualname": "simple_shear_2d", "kind": "function", "doc": "Return simple shear velocity and velocity gradient callables.
\n\nThe returned callables have signature f(x) where x is a 3D position vector.
\n\nArgs:
\n\n\ndirection (one of {\"X\", \"Y\", \"Z\"}) \u2014 velocity vector directiondeformation_plane (one of {\"X\", \"Y\", \"Z\"}) \u2014 direction of velocity gradientstrain_rate (float) \u2014 1/2 \u00d7 strength of velocity gradient (i.e. magnitude of the\nvelocity at a unit distance from the shear plane) \n\n\n\n
Input arrays to the returned callables must have homogeneous element types.\nArrays with e.g. both floating point and integer values are not supported.
\n\n
Examples:
\n\n\n
>>> import numpy as np \n>>> u , L = simple_shear_2d ( "X" , "Z" , 1e-4 ) \n>>> u ( np . array ([ 0 , 0 , 0 ])) \narray([0., 0., 0.]) \n>>> u ( np . array ([ 0 , 0 , 1 ])) \narray([0.0001, 0. , 0. ]) \n>>> u ( np . array ([ 0.0 , 0.0 , 2.0 ])) \narray([0.0002, 0. , 0. ]) \n>>> L ( np . array ([ 0 , 0 , 0 ])) \narray([[0. , 0. , 0.0002], \n [0. , 0. , 0. ], \n [0. , 0. , 0. ]]) \n>>> L ( np . array ([ 0.0 , 0.0 , 1.0 ])) \narray([[0. , 0. , 0.0002], \n [0. , 0. , 0. ], \n [0. , 0. , 0. ]]) \n\n
(direction , deformation_plane , strain_rate ): ", "funcdef": "def"}, "pydrex.velocity.cell_2d": {"fullname": "pydrex.velocity.cell_2d", "modulename": "pydrex.velocity", "qualname": "cell_2d", "kind": "function", "doc": "Get velocity and velocity gradient callables for a steady-state 2D Stokes cell.
\n\nThe cell is centered at (0,0) and the velocity field is defined by:\n$$\n\\bm{u} = U\\cos(\u03c0 x/d)\\sin(\u03c0 z/d) \\bm{\\hat{h}} - U\\sin(\u03c0 x/d)\\cos(\u03c0 z/d) \\bm{\\hat{v}}\n$$\nwhere $\\bm{\\hat{h}}$ and $\\bm{\\hat{v}}$ are unit vectors in the chosen horizontal\nand vertical directions, respectively. The velocity at the cell edge has a magnitude\nof $U$ and $d$ is the length of a cell edge.
\n\nThe returned callables have signature f(x) where x is a 3D position vector.
\n\nArgs:
\n\n\nhorizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal directionvertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical directionvelocity_edge (float) \u2014 velocity magnitude at the center of the cell edgeedge_length (float, optional) \u2014 the edge length of the cell (= 2 by default) \n\nExamples:
\n\n\n
>>> import numpy as np \n>>> u , L = cell_2d ( "X" , "Z" , 1 ) \n>>> u ( np . array ([ 0 , 0 , 0 ])) \narray([ 0., 0., -0.]) \n>>> u ( np . array ([ 0 , 0 , 1 ])) \narray([ 1., 0., -0.]) \n>>> u ( np . array ([ 0 , 1 , 0 ])) # Y-value is not used. \narray([ 0., 0., -0.]) \n>>> u ( np . array ([ 0 , 0 , - 1 ])) \narray([-1., 0., -0.]) \n>>> u ( np . array ([ 1 , 0 , 0 ])) \narray([ 0., 0., -1.]) \n>>> u ( np . array ([ - 0.5 , 0.0 , 0.0 ])) \narray([0. , 0. , 0.70710678]) \n>>> L ( np . array ([ 0 , 0 , 0 ])) \narray([[-0. , 0. , 1.57079633], \n [ 0. , 0. , 0. ], \n [ 0. , 0. , -1.57079633]]) \n>>> L ( np . array ([ 0.5 , 0.0 , 0.0 ])) \narray([[-0. , 0. , 1.11072073], \n [ 0. , 0. , 0. ], \n [ 0. , 0. , -1.11072073]]) \n>>> L ( np . array ([ 0 , 0 , 0 ])) == L ( np . array ([ 0 , 1 , 0 ])) # Y-value is not used. \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 1 , 0 , 0 ])) == L ( np . array ([ 0 , 0 , 1 ])) \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 1 , 0 , 0 ])) == L ( np . array ([ - 1 , 0 , 0 ])) \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 1 , 0 , 0 ])) == L ( np . array ([ 0 , 0 , - 1 ])) \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 0.5 , 0.0 , 0.5 ])) \narray([[-0.78539816, 0. , 0.78539816], \n [ 0. , 0. , 0. ], \n [ 0.78539816, 0. , -0.78539816]]) \n\n
\n
>>> u , L = cell_2d ( "X" , "Z" , 6.3e-10 , 1e5 ) \n>>> u ( np . array ([ 0 , 0 , 0 ])) \narray([ 0., 0., -0.]) \n>>> u ( np . array ([ 0.0 , 0.0 , - 5e4 ])) \narray([-6.3e-10, 0.0e+00, -0.0e+00]) \n>>> u ( np . array ([ 2e2 , 0e0 , 0e0 ])) \narray([ 0.0000000e+00, 0.0000000e+00, -3.9583807e-12]) \n\n
(horizontal , vertical , velocity_edge , edge_length = 2 ): ", "funcdef": "def"}, "pydrex.velocity.corner_2d": {"fullname": "pydrex.velocity.corner_2d", "modulename": "pydrex.velocity", "qualname": "corner_2d", "kind": "function", "doc": "Get velocity and velocity gradient callables for a steady-state 2D corner flow.
\n\nThe velocity field is defined by:\n$$\n\\bm{u} = \\frac{dr}{dt} \\bm{\\hat{r}} + r \\frac{d\u03b8}{dt} \\bm{\\hat{\u03b8}}\n= \\frac{2 U}{\u03c0}(\u03b8\\sin\u03b8 - \\cos\u03b8) \u22c5 \\bm{\\hat{r}} + \\frac{2 U}{\u03c0}\u03b8\\cos\u03b8 \u22c5 \\bm{\\hat{\u03b8}}\n$$\nwhere $\u03b8 = 0$ points vertically downwards along the ridge axis\nand $\u03b8 = \u03c0/2$ points along the surface. $U$ is the half spreading velocity.\nStreamlines for the flow obey:\n$$\n\u03c8 = \\frac{2 U r}{\u03c0}\u03b8\\cos\u03b8\n$$\nand are related to the velocity through:\n$$\n\\bm{u} = -\\frac{1}{r} \u22c5 \\frac{d\u03c8}{d\u03b8} \u22c5 \\bm{\\hat{r}} + \\frac{d\u03c8}{dr}\\bm{\\hat{\u03b8}}\n$$\nConversion to Cartesian ($x,y,z$) coordinates yields:\n$$\n\\bm{u} = \\frac{2U}{\u03c0} \\left[\n\\tan^{-1}\\left(\\frac{x}{-z}\\right) + \\frac{xz}{x^{2} + z^{2}} \\right] \\bm{\\hat{x}} +\n\\frac{2U}{\u03c0} \\frac{z^{2}}{x^{2} + z^{2}} \\bm{\\hat{z}}\n$$\nwhere\n\\begin{align*}\nx &= r \\sin\u03b8 \\cr\nz &= -r \\cos\u03b8\n\\end{align*}\nand the velocity gradient is:\n$$\nL = \\frac{4 U}{\u03c0{(x^{2}+z^{2})}^{2}} \u22c5\n\\begin{bmatrix}\n -x^{2}z & 0 & x^{3} \\cr\n 0 & 0 & 0 \\cr\n -xz^{2} & 0 & x^{2}z\n\\end{bmatrix}\n$$\nSee also Fig. 5 in Kaminski & Ribe, 2002 .
\n\nThe returned callables have signature f(x) where x is a 3D position vector.
\n\nArgs:
\n\n\nhorizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal directionvertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical directionplate_speed (float) \u2014 speed of the \u201cplate\u201d i.e. upper boundary \n", "signature": "(horizontal , vertical , plate_speed ): ", "funcdef": "def"}, "pydrex.visualisation": {"fullname": "pydrex.visualisation", "modulename": "pydrex.visualisation", "kind": "module", "doc": "\n PyDRex: Visualisation functions for test outputs and examples.
\n \n"}, "pydrex.visualisation.polefigures": {"fullname": "pydrex.visualisation.polefigures", "modulename": "pydrex.visualisation", "qualname": "polefigures", "kind": "function", "doc": "Plot pole figures of a series of (Nx3x3) orientation matrix stacks.
\n\nProduces [100], [010] and [001] pole figures for (resampled) orientations.\nFor the argument specification, check the output of pydrex-polefigures --help\non the command line.
\n", "signature": "(\torientations , \tref_axes , \ti_range , \tdensity = False , \tsavefile = 'polefigures.png' , \tstrains = None , \t** kwargs ): ", "funcdef": "def"}, "pydrex.visualisation.pathline_box2d": {"fullname": "pydrex.visualisation.pathline_box2d", "modulename": "pydrex.visualisation", "qualname": "pathline_box2d", "kind": "function", "doc": "Plot pathlines and velocity arrows for a 2D box domain.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nArgs:
\n\n\nget_velocity (callable) \u2014 object with call signature f(x) that returns\nthe 3D velocity vector at a given 3D position vectorref_axes (two letters from {\"x\", \"y\", \"z\"}) \u2014 labels for the horizontal and\nvertical axes (these also define the projection for the 3D velocity/position)colors (array) \u2014 monotonic values along a representative pathline in the flowpositions (Nx3 array) \u2014 3D position vectors along the same pathlinemin_coords (array) \u2014 2D coordinates of the lower left corner of the domainmax_coords (array) \u2014 2D coordinates of the upper right corner of the domainresolution (array) \u2014 2D resolution of the velocity arrow grid (i.e. number of\ngrid points in the horizontal and vertical directions) which can be set to None to\nprevent drawing velocity vectorsaspect (str|float, optional) \u2014 see matplotlib.axes.Axes.set_aspectcmap (Matplotlib color map, optional) \u2014 color map for colorscpo_vectors (array, optional) \u2014 vectors to plot as bars at pathline locationscpo_strengths (array, optional) \u2014 strengths used to scale the cpo barstick_formatter (callable, optional) \u2014 function used to format tick labels \n\nAdditional keyword arguments are passed to the matplotlib.axes.Axes.quiver call\nused to plot the velocity vectors.
\n\nReturns the figure handle, the axes handle, the quiver collection (velocities) and\nthe scatter collection (pathline).
\n", "signature": "(\tax , \tget_velocity , \tref_axes , \tcolors , \tpositions , \tmarker , \tmin_coords , \tmax_coords , \tresolution , \taspect = 'equal' , \tcmap =< matplotlib . colors . ListedColormap object > , \tcpo_vectors = None , \tcpo_strengths = None , \ttick_formatter =< function < lambda >> , \t** kwargs ): ", "funcdef": "def"}, "pydrex.visualisation.alignment": {"fullname": "pydrex.visualisation.alignment", "modulename": "pydrex.visualisation", "qualname": "alignment", "kind": "function", "doc": "Plot angles (in degrees) versus strains on the given axis.
\n\nAlignment angles could be either bingham averages or the a-axis in the hexagonal\nsymmetry projection, measured from e.g. the shear direction. In the first case,\nthey should be calculated from resampled grain orientations. Expects as many\nmarkers and labels as there are data series in angles.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nArgs:
\n\n\nstrains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain seriesangles (array) \u2014 Y-values, may be a 2D array of multiple angle seriesmarkers (sequence) \u2014 MatPlotLib markers to use for the data serieslabels (sequence) \u2014 labels to use for the data serieserr (array, optional) \u2014 standard errors for the angles, shapes must match\u03b8_max (int) \u2014 maximum angle (\u00b0) to show on the plot, should be less than 90\u03b8_fse (array, optional) \u2014 an array of angles from the long axis of the finite\nstrain ellipsoid to the reference direction (e.g. shear direction)colors (array, optional) \u2014 color coordinates for series of anglescmaps (Matplotlib color maps, optional) \u2014 color maps for colors \n\nIf colors and cmaps are used, then angle values are colored individually within\neach angle series.
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tstrains , \tangles , \tmarkers , \tlabels , \terr = None , \t\u03b8_max = 90 , \t\u03b8_fse = None , \tcolors = None , \tcmaps = None ): ", "funcdef": "def"}, "pydrex.visualisation.strengths": {"fullname": "pydrex.visualisation.strengths", "modulename": "pydrex.visualisation", "qualname": "strengths", "kind": "function", "doc": "Plot CPO strengths (e.g. M-indices) versus strains on the given axis.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nArgs:
\n\n\nstrains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain seriesstrengths (array) \u2014 Y-values, may be a 2D array of multiple strength seriesmarkers (sequence) \u2014 MatPlotLib markers to use for the data serieslabels (sequence) \u2014 labels to use for the data serieserr (array, optional) \u2014 standard errors for the strengths, shapes must matchcolors (array, optional) \u2014 color coordinates for series of strengthscpo_threshold (float, optional) \u2014 plot a dashed line at this thresholdcmaps (Matplotlib color maps, optional) \u2014 color maps for colors \n\nIf colors and cmaps are used, then strength values are colored individually\nwithin each strength series.
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tstrains , \tstrengths , \tylabel , \tmarkers , \tlabels , \terr = None , \tcpo_threshold = None , \tcolors = None , \tcmaps = None ): ", "funcdef": "def"}, "pydrex.visualisation.grainsizes": {"fullname": "pydrex.visualisation.grainsizes", "modulename": "pydrex.visualisation", "qualname": "grainsizes", "kind": "function", "doc": "Plot grain volume fractions versus strains on the given axis.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n", "signature": "(ax , strains , fractions ): ", "funcdef": "def"}, "pydrex.visualisation.show_Skemer2016_ShearStrainAngles": {"fullname": "pydrex.visualisation.show_Skemer2016_ShearStrainAngles", "modulename": "pydrex.visualisation", "qualname": "show_Skemer2016_ShearStrainAngles", "kind": "function", "doc": "Show data from src/pydrex/data/thirdparty/Skemer2016_ShearStrainAngles.scsv.
\n\nPlot data from the Skemer 2016 datafile on the axis given by ax. Select the\nstudies from which to plot the data, which must be a list of strings with exact\nmatches in the study column in the datafile.\nAlso filter the data to select only the given fabric\n(see pydrex.core.MineralFabric).
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nReturns a tuple containing:
\n\n\nthe figure handle \nthe axes handle \nthe set of colors used for the data series plots \nthe Skemer 2016 dataset \nthe indices used to select data according to the \"studies\" and \"fabric\" filters \n \n", "signature": "(ax , studies , markers , colors , fillstyles , labels , fabric ): ", "funcdef": "def"}, "pydrex.visualisation.spin": {"fullname": "pydrex.visualisation.spin", "modulename": "pydrex.visualisation", "qualname": "spin", "kind": "function", "doc": "Plot rotation rates of grains with known, unique initial [100] angles from X.
\n\nIf ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tinitial_angles , \trotation_rates , \ttarget_initial_angles = None , \ttarget_rotation_rates = None , \tlabels = ( 'target' , 'computed' ) , \tshear_axis = None ): ", "funcdef": "def"}, "pydrex.visualisation.growth": {"fullname": "pydrex.visualisation.growth", "modulename": "pydrex.visualisation", "qualname": "growth", "kind": "function", "doc": "Plot grain growth of grains with known, unique initial [100] angles from X.
\n\nIf ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tinitial_angles , \tfractions_diff , \ttarget_initial_angles = None , \ttarget_fractions_diff = None , \tlabels = ( 'target' , 'computed' ) , \tshear_axis = None ): ", "funcdef": "def"}, "pydrex.visualisation.figure_unless": {"fullname": "pydrex.visualisation.figure_unless", "modulename": "pydrex.visualisation", "qualname": "figure_unless", "kind": "function", "doc": "Create figure and axes if ax is None, or return existing figure for ax.
\n\nIf ax is None, a new figure is created for the axes with a few opinionated default\nsettings (grid, constrained layout, high DPI).
\n\nReturns a tuple containing the figure handle and the axes object.
\n", "signature": "(ax ): ", "funcdef": "def"}, "pydrex.visualisation.figure": {"fullname": "pydrex.visualisation.figure", "modulename": "pydrex.visualisation", "qualname": "figure", "kind": "function", "doc": "Create new figure with a few opinionated default settings.
\n\n(e.g. grid, constrained layout, high DPI).
\n\nThe keyword argument figscale can be used to scale the figure width and height\nrelative to the default values by passing a tuple. Any additional keyword arguments\nare passed to matplotlib.pyplot.figure().
\n", "signature": "(figscale = None , ** kwargs ): ", "funcdef": "def"}, "tests": {"fullname": "tests", "modulename": "tests", "kind": "module", "doc": "PyDRex tests \n\nRunning the tests requires pytest .\nFrom the root of the source tree, run pytest.\nTo print more verbose information (including INFO level logging),\nsuch as detailed test progress, use the flag pytest -v.\nThe custom optional flag --outdir=\"OUT\" is recommended\nto produce output figures, data dumps and logs and save them in the directory \"OUT\".\nThe value \".\" can be used to save these in the current directory.
\n\nIn total, the following custom pytest command line flags are defined by PyDRex:
\n\n\n--outdir (described above)--runbig (enable tests which require a large amount of RAM)--runslow (enable slow tests which require HPC resources, implies --runbig)--ncpus (number of CPU cores to use for shared memory multiprocessing, set to one less than the available maximum by default)--fontsize (Matplotlib rcParams[\"font.size\"])--markersize (Matplotlib rcParams[\"lines.markersize\"])--linewidth (Matplotlib rcParams[\"lines.linewidth\"]) \n\nTests which require a \u201csignificant\u201d amount of memory (> ~16GB RAM) are disabled by default.\nTo fully check the functionality of the code, it is recommended to run these locally\nby using the --runbig flag before moving to larger simulations.
\n\nLong tests/examples are also disabled by default and can be enabled with --runslow.\nIt is recommended to run these on a HPC cluster infrastructure (>100GB RAM, >32 cores).\nThe number of cores to use for shared memory multiprocessing can be specified with --ncpus.
\n\nWriting tests \n\nFor quick sanity checks and inline unit tests, use python doctests .\nThese will also appear as inline examples in the generated documentation.\nMore comprehensive unit tests and larger integration tests should be organised\ninto submodules of the test module.
\n\n\nTo mark a test as \u201cbig\u201d (i.e. requiring more than ~16GB RAM), apply the\n@pytest.mark.big decorator to the corresponding method definition.
To mark a test as \u201cslow\u201d (i.e. requiring more than ~32 cores), apply the\n@pytest.mark.slow decorator to the corresponding method definition.
\n\nTests should not produce persistent output by default.\nIf a test method can produce such output for debugging or visualisation,\nit should accept the outdir positional argument,\nand check if its value is not None.\nIf outdir is None then no persistent output should be produced.\nIf outdir is a directory path (string):
\n\n\nlogs can be saved by using the pydrex.logger.logfile_enable context manager,\nwhich accepts a path name and an optional logging level as per Python's logging module\n(the default is logging.DEBUG which implies the most verbose output), \nfigures can be saved by (implementing and) calling a helper from pydrex.visualisation, and \ndata dumps can be saved to outdir, e.g. in .npz format (see the pydrex.minerals.Mineral.save method)\nIn all cases, saving to outdir should handle creation of parent directories.\nTo handle this as well as relative paths, we provide pydrex.io.resolve_path,\nwhich is a thin wrapper around some pathlib methods. \n \n"}, "tests.conftest": {"fullname": "tests.conftest", "modulename": "tests.conftest", "kind": "module", "doc": "\n Configuration and fixtures for PyDRex tests.
\n \n"}, "tests.conftest.pytest_addoption": {"fullname": "tests.conftest.pytest_addoption", "modulename": "tests.conftest", "qualname": "pytest_addoption", "kind": "function", "doc": "
\n", "signature": "(parser ): ", "funcdef": "def"}, "tests.conftest.PytestConsoleLogger": {"fullname": "tests.conftest.PytestConsoleLogger", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger", "kind": "class", "doc": "Pytest plugin that allows linking up a custom console logger.
\n", "bases": "_pytest.logging.LoggingPlugin"}, "tests.conftest.PytestConsoleLogger.__init__": {"fullname": "tests.conftest.PytestConsoleLogger.__init__", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.__init__", "kind": "function", "doc": "Create a new plugin to capture log messages.
\n\nThe formatter can be safely shared across all handlers so\ncreate a single one for the entire test session here.
\n", "signature": "(config , * args , ** kwargs "}, "tests.conftest.PytestConsoleLogger.name": {"fullname": "tests.conftest.PytestConsoleLogger.name", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.name", "kind": "variable", "doc": "
\n", "default_value": "'pytest-console-logger'"}, "tests.conftest.PytestConsoleLogger.log_cli_handler": {"fullname": "tests.conftest.PytestConsoleLogger.log_cli_handler", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.log_cli_handler", "kind": "variable", "doc": "
\n"}, "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown": {"fullname": "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.pytest_runtest_teardown", "kind": "function", "doc": "
\n", "signature": "(self , item ): ", "funcdef": "def"}, "tests.conftest.pytest_configure": {"fullname": "tests.conftest.pytest_configure", "modulename": "tests.conftest", "qualname": "pytest_configure", "kind": "function", "doc": "
\n", "signature": "(config ): ", "funcdef": "def"}, "tests.conftest.pytest_collection_modifyitems": {"fullname": "tests.conftest.pytest_collection_modifyitems", "modulename": "tests.conftest", "qualname": "pytest_collection_modifyitems", "kind": "function", "doc": "
\n", "signature": "(config , items ): ", "funcdef": "def"}, "tests.conftest.outdir": {"fullname": "tests.conftest.outdir", "modulename": "tests.conftest", "qualname": "outdir", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.ncpus": {"fullname": "tests.conftest.ncpus", "modulename": "tests.conftest", "qualname": "ncpus", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.console_handler": {"fullname": "tests.conftest.console_handler", "modulename": "tests.conftest", "qualname": "console_handler", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.params_Fraters2021": {"fullname": "tests.conftest.params_Fraters2021", "modulename": "tests.conftest", "qualname": "params_Fraters2021", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_solid": {"fullname": "tests.conftest.params_Kaminski2001_fig5_solid", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_solid", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_shortdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_shortdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_shortdash", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_longdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_longdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_longdash", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_triangles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_triangles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_triangles", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_squares": {"fullname": "tests.conftest.params_Kaminski2004_fig4_squares", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_squares", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_circles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_circles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_circles", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Hedjazian2017": {"fullname": "tests.conftest.params_Hedjazian2017", "modulename": "tests.conftest", "qualname": "params_Hedjazian2017", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.n_grains": {"fullname": "tests.conftest.n_grains", "modulename": "tests.conftest", "qualname": "n_grains", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.hkl": {"fullname": "tests.conftest.hkl", "modulename": "tests.conftest", "qualname": "hkl", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.ref_axes": {"fullname": "tests.conftest.ref_axes", "modulename": "tests.conftest", "qualname": "ref_axes", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.seeds": {"fullname": "tests.conftest.seeds", "modulename": "tests.conftest", "qualname": "seeds", "kind": "function", "doc": "1000 unique seeds for ensemble runs that need an RNG seed.
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.seed": {"fullname": "tests.conftest.seed", "modulename": "tests.conftest", "qualname": "seed", "kind": "function", "doc": "Default seed for test RNG.
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.seeds_nearX45": {"fullname": "tests.conftest.seeds_nearX45", "modulename": "tests.conftest", "qualname": "seeds_nearX45", "kind": "function", "doc": "41 seeds which have the initial hexagonal symmetry axis near 45\u00b0 from X.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_config": {"fullname": "tests.test_config", "modulename": "tests.test_config", "kind": "module", "doc": "\n PyDRex: tests for configuration file format.
\n \n"}, "tests.test_config.test_specfile": {"fullname": "tests.test_config.test_specfile", "modulename": "tests.test_config", "qualname": "test_specfile", "kind": "function", "doc": "Test TOML spec file parsing.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_core": {"fullname": "tests.test_core", "modulename": "tests.test_core", "kind": "module", "doc": "\n PyDRex: Tests for core D-Rex routines.
\n \n"}, "tests.test_core.SUBDIR": {"fullname": "tests.test_core.SUBDIR", "modulename": "tests.test_core", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'core'"}, "tests.test_core.TestDislocationCreepOPX": {"fullname": "tests.test_core.TestDislocationCreepOPX", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX", "kind": "class", "doc": "Single-grain orthopyroxene crystallographic rotation rate tests.
\n"}, "tests.test_core.TestDislocationCreepOPX.class_id": {"fullname": "tests.test_core.TestDislocationCreepOPX.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.class_id", "kind": "variable", "doc": "
\n", "default_value": "'dislocation_creep_OPX'"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dudz": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dudz", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dudz", "kind": "function", "doc": "
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dvdx", "kind": "function", "doc": "
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA": {"fullname": "tests.test_core.TestDislocationCreepOlivineA", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA", "kind": "class", "doc": "Single-grain A-type olivine analytical rotation rate tests.
\n"}, "tests.test_core.TestDislocationCreepOlivineA.class_id": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'dislocation_creep_OlA'"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "kind": "function", "doc": "Single grain of A-type olivine, slip on (010)[100].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "kind": "function", "doc": "Single grain of A-type olivine, slip on (001)[100].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 2 \\cr 0 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "kind": "function", "doc": "Single grain of A-type olivine, slip on (001)[100].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 0 \\cr 2 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "kind": "function", "doc": "Single grain of A-type olivine, slip on (010)[001].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 2 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D": {"fullname": "tests.test_core.TestRecrystallisation2D", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D", "kind": "class", "doc": "Basic recrystallisation tests for 2D simple shear.
\n"}, "tests.test_core.TestRecrystallisation2D.class_id": {"fullname": "tests.test_core.TestRecrystallisation2D.class_id", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.class_id", "kind": "variable", "doc": "
\n", "default_value": "'recrystallisation_2D'"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "kind": "function", "doc": "360000 grains of A-type olivine with uniform spread of a-axes on a circle.
\n\nGrain growth rates are compared to analytical calculations.\nThe a-axes are distributed in the YX plane (i.e.\\ rotated around Z).
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "kind": "function", "doc": "360000 grains of A-type olivine with uniform spread of a-axes on a circle.
\n\nUnlike test_shear_dvdx_circle_inplane, two slip systems are active here,\nwith cyclical variety in which one is dominant depending on grain orientation.\nThe a-axes are distributed in the YZ plane\n(i.e.\\ extrinsic rotation around Z by 90\u00b0 and then around X).
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_corner_flow_2d": {"fullname": "tests.test_corner_flow_2d", "modulename": "tests.test_corner_flow_2d", "kind": "module", "doc": "\n PyDRex: 2D corner flow tests.
\n \n"}, "tests.test_corner_flow_2d.SUBDIR": {"fullname": "tests.test_corner_flow_2d.SUBDIR", "modulename": "tests.test_corner_flow_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'2d_cornerflow'"}, "tests.test_corner_flow_2d.TestCornerOlivineA": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA", "kind": "class", "doc": "Tests for pure A-type olivine polycrystals in 2D corner flows.
\n"}, "tests.test_corner_flow_2d.TestCornerOlivineA.class_id": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA.class_id", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'corner_olivineA'"}, "tests.test_corner_flow_2d.TestCornerOlivineA.run": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA.run", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA.run", "kind": "function", "doc": "Run 2D corner flow A-type olivine simulation.
\n", "signature": "(\tcls , \tparams , \tseed , \tget_velocity , \tget_velocity_gradient , \tmin_coords , \tmax_coords , \tmax_strain , \tn_timesteps , \tfinal_location ): ", "funcdef": "def"}, "tests.test_corner_flow_2d.TestCornerOlivineA.test_prescribed": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA.test_prescribed", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA.test_prescribed", "kind": "function", "doc": "Test CPO evolution in prescribed 2D corner flow.
\n\nInitial condition: random orientations and uniform volumes in all Minerals.
\n\nPlate velocity: 2 cm/yr
\n\n\n\n
This example takes about 11 CPU hours to run and uses around 60GB of RAM.\nIt is recommended to only use ncpus=4 which matches the number of\npathlines, because higher numbers can lead to redundant cross-core\ncommunication.
\n\n
(self , outdir , seed , ncpus ): ", "funcdef": "def"}, "tests.test_diagnostics": {"fullname": "tests.test_diagnostics", "modulename": "tests.test_diagnostics", "kind": "module", "doc": "\n PyDRex: tests for texture diagnostics.
\n \n"}, "tests.test_diagnostics.TestElasticityComponents": {"fullname": "tests.test_diagnostics.TestElasticityComponents", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents", "kind": "class", "doc": "Test symmetry decomposition of elastic tensors.
\n"}, "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_olivine_Browaeys2004", "kind": "function", "doc": "
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_enstatite_Browaeys2004", "kind": "function", "doc": "
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR": {"fullname": "tests.test_diagnostics.TestSymmetryPGR", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR", "kind": "class", "doc": "Test Point-Girdle-Random (eigenvalue) symmetry diagnostics.
\n"}, "tests.test_diagnostics.TestSymmetryPGR.test_pointX": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_pointX", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_pointX", "kind": "function", "doc": "Test diagnostics of point symmetry aligned to the X axis.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_random": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_random", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_random", "kind": "function", "doc": "Test diagnostics of random grain orientations.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_girdle": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_girdle", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_girdle", "kind": "function", "doc": "Test diagnostics of girdled orientations.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting": {"fullname": "tests.test_diagnostics.TestVolumeWeighting", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting", "kind": "class", "doc": "Tests for volumetric resampling of orientation data.
\n"}, "tests.test_diagnostics.TestVolumeWeighting.test_output_shape": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_output_shape", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_output_shape", "kind": "function", "doc": "Test that we get the correct output shape.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_upsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_upsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_upsample", "kind": "function", "doc": "Test upsampling of the raw orientation data.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_downsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_downsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_downsample", "kind": "function", "doc": "Test downsampling of orientation data.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_common_input_errors", "kind": "function", "doc": "Test that exceptions are raised for bad input data.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats": {"fullname": "tests.test_diagnostics.TestBinghamStats", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats", "kind": "class", "doc": "Tests for antipodally symmetric (bingham) statistics.
\n"}, "tests.test_diagnostics.TestBinghamStats.test_average_0": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_0", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_0", "kind": "function", "doc": "Test bingham average of vectors aligned to the reference frame.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_twopoles90Z", "kind": "function", "doc": "Test bingham average of vectors rotated by \u00b190\u00b0 around Z.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_spread10X": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_spread10X", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_spread10X", "kind": "function", "doc": "Test bingham average of vectors spread within 10\u00b0 of the \u00b1X-axis.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex": {"fullname": "tests.test_diagnostics.TestMIndex", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex", "kind": "class", "doc": "Tests for the M-index texture strength diagnostic.
\n"}, "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_uniform_ortho", "kind": "function", "doc": "Test with random (uniform distribution) orthorhombic grain orientations.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread10X_ortho", "kind": "function", "doc": "Test for orthorhombic grains spread within 10\u00b0 of the \u00b1X axis.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread45X_ortho", "kind": "function", "doc": "Test for orthorhombic grains spread within 45\u00b0 of the \u00b1X axis.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_textures_increasing_ortho", "kind": "function", "doc": "Test M-index for textures of increasing strength.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_girdle_ortho", "kind": "function", "doc": "Test M-index for girdled texture.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_doctests": {"fullname": "tests.test_doctests", "modulename": "tests.test_doctests", "kind": "module", "doc": "\n PyDRex: Run doctests for all submodules.
\n \n"}, "tests.test_doctests.test_doctests": {"fullname": "tests.test_doctests.test_doctests", "modulename": "tests.test_doctests", "qualname": "test_doctests", "kind": "function", "doc": "Run doctests for all submodules.
\n", "signature": "(module ): ", "funcdef": "def"}, "tests.test_geometry": {"fullname": "tests.test_geometry", "modulename": "tests.test_geometry", "kind": "module", "doc": "\n PyDRex: Tests for geometric conversions and projections.
\n \n"}, "tests.test_geometry.test_poles_example": {"fullname": "tests.test_geometry.test_poles_example", "modulename": "tests.test_geometry", "qualname": "test_poles_example", "kind": "function", "doc": "Test poles (directions of crystallographic axes) of example data.
\n", "signature": "(hkl , ref_axes ): ", "funcdef": "def"}, "tests.test_geometry.test_lambert_equal_area": {"fullname": "tests.test_geometry.test_lambert_equal_area", "modulename": "tests.test_geometry", "qualname": "test_lambert_equal_area", "kind": "function", "doc": "Test Lambert equal area projection.
\n", "signature": "(seed ): ", "funcdef": "def"}, "tests.test_scsv": {"fullname": "tests.test_scsv", "modulename": "tests.test_scsv", "kind": "module", "doc": "\n PyDRex: tests for the SCSV plain text file format.
\n \n"}, "tests.test_scsv.test_validate_schema": {"fullname": "tests.test_scsv.test_validate_schema", "modulename": "tests.test_scsv", "qualname": "test_validate_schema", "kind": "function", "doc": "Test SCSV schema validation.
\n", "signature": "(console_handler ): ", "funcdef": "def"}, "tests.test_scsv.test_read_specfile": {"fullname": "tests.test_scsv.test_read_specfile", "modulename": "tests.test_scsv", "qualname": "test_read_specfile", "kind": "function", "doc": "Test SCSV spec file parsing.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_save_specfile": {"fullname": "tests.test_scsv.test_save_specfile", "modulename": "tests.test_scsv", "qualname": "test_save_specfile", "kind": "function", "doc": "Test SCSV spec file reproduction.
\n", "signature": "(outdir ): ", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2002": {"fullname": "tests.test_scsv.test_read_Kaminski2002", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2002", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_save_scsv_errors": {"fullname": "tests.test_scsv.test_save_scsv_errors", "modulename": "tests.test_scsv", "qualname": "test_save_scsv_errors", "kind": "function", "doc": "Check that we raise errors when attempting to write bad SCSV data.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2004": {"fullname": "tests.test_scsv.test_read_Kaminski2004", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2004", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_read_Skemer2016": {"fullname": "tests.test_scsv.test_read_Skemer2016", "modulename": "tests.test_scsv", "qualname": "test_read_Skemer2016", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_simple_shear_2d": {"fullname": "tests.test_simple_shear_2d", "modulename": "tests.test_simple_shear_2d", "kind": "module", "doc": "\n PyDRex: 2D simple shear tests.
\n \n"}, "tests.test_simple_shear_2d.SUBDIR": {"fullname": "tests.test_simple_shear_2d.SUBDIR", "modulename": "tests.test_simple_shear_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'2d_simple_shear'"}, "tests.test_simple_shear_2d.TestOlivineA": {"fullname": "tests.test_simple_shear_2d.TestOlivineA", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA", "kind": "class", "doc": "Tests for stationary A-type olivine polycrystals in 2D simple shear.
\n"}, "tests.test_simple_shear_2d.TestOlivineA.class_id": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.class_id", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'olivineA'"}, "tests.test_simple_shear_2d.TestOlivineA.get_position": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.get_position", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.get_position", "kind": "function", "doc": "
\n", "signature": "(cls , t ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.run": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.run", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.run", "kind": "function", "doc": "Reusable logic for 2D olivine (A-type) simple shear tests.
\n\nReturns a tuple with the mineral and the FSE angle (or None if return_fse is\nNone).
\n", "signature": "(\tcls , \tparams , \ttimestamps , \tstrain_rate , \tget_velocity_gradient , \tshear_direction , \tseed = None , \treturn_fse = None ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_Kaminski2001", "kind": "function", "doc": "Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_FortranDRex", "kind": "function", "doc": "Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_FortranDRex", "kind": "function", "doc": "Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_long_FortranDRex", "kind": "function", "doc": "Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_Kaminski2004", "kind": "function", "doc": "Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_zero_recrystallisation", "kind": "function", "doc": "Check that M*=0 is a reliable switch to turn off recrystallisation.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_grainsize_median", "kind": "function", "doc": "Check that M={50,100,150}, \u03bb =5 causes decreasing grain size median.
\n", "signature": "(self , seed , gbm_mobility ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_ensemble", "kind": "function", "doc": "Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(\tself , \toutdir , \tseeds_nearX45 , \tncpus , \tgbs_threshold , \tnucleation_efficiency ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_GBM", "kind": "function", "doc": "Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).
\n\nVelocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$
\n\nResults are compared to the Fortran 90 output.
\n", "signature": "(self , outdir , seeds_nearX45 , ncpus ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_GBM_calibration", "kind": "function", "doc": "Compare results for various values of $$M^\u2217$$ to A-type olivine data.
\n\nVelocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$
\n\nUnlike test_dvdx_GBM,\ngrain boudary sliding is enabled here (see _io.DEFAULT_PARAMS).\nData are provided by Skemer & Hansen, 2016 .
\n", "signature": "(self , outdir , seeds , ncpus ): ", "funcdef": "def"}, "tests.test_simple_shear_3d": {"fullname": "tests.test_simple_shear_3d", "modulename": "tests.test_simple_shear_3d", "kind": "module", "doc": "\n PyDRex: Simple shear 3D tests.
\n \n"}, "tests.test_simple_shear_3d.SUBDIR": {"fullname": "tests.test_simple_shear_3d.SUBDIR", "modulename": "tests.test_simple_shear_3d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'3d_simple_shear'"}, "tests.test_simple_shear_3d.TestFraters2021": {"fullname": "tests.test_simple_shear_3d.TestFraters2021", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021", "kind": "class", "doc": "Tests inspired by the benchmarks presented in [Fraters & Billen, 2021].
\n"}, "tests.test_simple_shear_3d.TestFraters2021.class_id": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.class_id", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.class_id", "kind": "variable", "doc": "
\n", "default_value": "'Fraters2021'"}, "tests.test_simple_shear_3d.TestFraters2021.run": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.run", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.run", "kind": "function", "doc": "Run simulation with stationary particles in the given velocity gradient.
\n\nThe optional RNG seed is used for the initial pseudorandom orientations.\nA prefix msg will be printed before each timestep log message if given.\nOther keyword args are passed to pydrex.Mineral.update_orientations.
\n\nReturns a tuple containing one olivine (A-type) and one enstatite mineral.\nIf params[\"enstatite_fraction\"] is zero, then the second tuple element will be\nNone instead.
\n", "signature": "(\tcls , \tparams , \ttimestamps , \tget_velocity_gradient_initial , \tget_velocity_gradient_final , \tswitch_time , \tmsg , \tseed = None ): ", "funcdef": "def"}, "tests.test_simple_shear_3d.TestFraters2021.test_direction_change": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.test_direction_change", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.test_direction_change", "kind": "function", "doc": "Test a-axis alignment in simple shear with instantaneous geometry change.
\n\nThe simulation runs for 5 Ma with a strain rate of 1.58e-14/s, resulting in an\naccumulated strain invariant of 2.5.
\n\nThe initial shear has nonzero du/dz and the final shear has nonzero dv/dx where\nu is the velocity along X and v the velocity along Y.
\n", "signature": "(self , outdir , seeds , params_Fraters2021 , switch_time_Ma , ncpus ): ", "funcdef": "def"}, "tests.test_tensors": {"fullname": "tests.test_tensors", "modulename": "tests.test_tensors", "kind": "module", "doc": "\n PyDRex: Tests for tensor operations.
\n \n"}, "tests.test_tensors.test_voigt_decompose": {"fullname": "tests.test_tensors.test_voigt_decompose", "modulename": "tests.test_tensors", "qualname": "test_voigt_decompose", "kind": "function", "doc": "Test decomposition of Voigt 6x6 matrix into distinct contractions.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_tensors.test_voigt_tensor": {"fullname": "tests.test_tensors.test_voigt_tensor", "modulename": "tests.test_tensors", "qualname": "test_voigt_tensor", "kind": "function", "doc": "Test elasticity tensor <-> 6x6 Voigt matrix conversions.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_tensors.test_voigt_to_vector": {"fullname": "tests.test_tensors.test_voigt_to_vector", "modulename": "tests.test_tensors", "qualname": "test_voigt_to_vector", "kind": "function", "doc": "Test Voigt vector construction.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_vortex_2d": {"fullname": "tests.test_vortex_2d", "modulename": "tests.test_vortex_2d", "kind": "module", "doc": "\n PyDRex: tests for CPO stability in 2D vortex and Stokes cell flows.
\n \n"}, "tests.test_vortex_2d.SUBDIR": {"fullname": "tests.test_vortex_2d.SUBDIR", "modulename": "tests.test_vortex_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'2d_vortex'"}, "tests.test_vortex_2d.TestCellOlivineA": {"fullname": "tests.test_vortex_2d.TestCellOlivineA", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA", "kind": "class", "doc": "Tests for A-type olivine polycrystals in a 2D Stokes cell.
\n"}, "tests.test_vortex_2d.TestCellOlivineA.class_id": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.class_id", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'cell_olivineA'"}, "tests.test_vortex_2d.TestCellOlivineA.run": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.run", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.run", "kind": "function", "doc": "Run 2D Stokes cell A-type olivine simulation.
\n", "signature": "(\tcls , \tparams , \tfinal_location , \tget_velocity , \tget_velocity_gradient , \tmin_coords , \tmax_coords , \tmax_strain , \tseed = None ): ", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz_10k": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz_10k", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz_10k", "kind": "function", "doc": "Run 2D cell test with 10000 grains (~14GiB RAM requirement).
\n", "signature": "(self , outdir , seed ): ", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz", "kind": "function", "doc": "Test to check that 5000 grains is \"enough\" to resolve transient features.
\n", "signature": "(self , outdir , seed , n_grains ): ", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz_ensemble": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz_ensemble", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz_ensemble", "kind": "function", "doc": "Test to demonstrate stability of the dip at \u03b5 \u2248 3.75 for 5000+ grains.
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+ /** pdoc search index */const docs = {"version": "0.9.5", "fields": ["qualname", "fullname", "annotation", "default_value", "signature", "bases", "doc"], "ref": "fullname", "documentStore": {"docs": {"pydrex": {"fullname": "pydrex", "modulename": "pydrex", "kind": "module", "doc": "Simulate crystallographic preferred orientation evolution in polycrystals \n\n\n\n
This software is currently in early development (pre-alpha)\nand therefore subject to breaking changes without notice.
\n\n
About \n\nViscoplastic deformation of minerals, e.g. in Earth's mantle, leads to distinct\nsignatures in the mineral texture. Many minerals naturally occur in\npolycrystalline form, which means that they are composed of many grains with\ndifferent volumes and lattice orientations. Preferential alignment of the\naverage lattice orientation is called crystallographic preferred orientation\n(CPO). PyDRex simulates the development and evolution of CPO in deforming\npolycrystals, as well as tracking macroscopic finite strain measures.\nCurrently, the code supports olivine and enstatite mineral phases. The\nfollowing features are provided:
\n\n\nJIT-compiled CPO solver, based on the D-Rex model, which updates the\npolycrystal orientation distribution depending on the macroscopic velocity\ngradients \nMineral class which stores attributes of a distinct mineral phase in the\npolycrystal and its texture snapshotsVoigt averaging to calculate the average elastic tensor of a textured,\nmultiphase polycrystal \nDecomposition of average elastic tensors into components attributed to\nminerals with distinct lattice symmetries \nCrystallographic pole figure visualisation (contouring is a work in progress) \n[work in progress] Texture diagnostics: M-index, bingham average,\nPoint-Girdle-Random symmetry, coaxial a.k.a \"BA\" index, etc. \n[work in progress] Seismic anisotropy diagnostics: % tensorial anisotropy,\nhexagonal symmetry a.k.a transverse isotropy direction, etc. \n \n\nThe core CPO solver is based on the original Fortran 90 implementation by \u00c9douard Kaminski,\nwhich can be downloaded from this link (~90KB) .\nThe reference papers are Kaminski & Ribe (2001) \nand Kaminski & Ribe (2004) ,\nand an open-access paper which discusses the model is Fraters & Billen (2021) .
\n\nInstallation \n\nThe minimum required Python version is set using requires-python in the\npyproject.tomlthe README file.
\n\nDocumentation \n\nThe website menu can be used to discover the public API of this package.\nSome of the tests are also documented and can serve as usage examples.\nTheir docstrings can be viewed in this section .\nDocumentation is also available from the Python REPL via the help() method.
\n\nThe D-Rex kinematic CPO model \n\nThe D-Rex model is used to compute crystallographic preferred orientation (CPO)\nfor polycrystals deforming by plastic deformation and dynamic recrystallization.\nPolycrystals are discretized into \"grains\" which represent fractional volumes\nof the total crystal that are characterised by a particular crystal lattice\norientation. For numerical efficiency, the number of grains in the model does\nnot change, and should only be interpreted as an approximation of the number\nof (unrecrystallised) physical grains. Dynamic recrystallization is modelled using\nstatistical expressions which approximate the interaction of each grain with an\neffective medium based on the averaged dislocation energy of all other grains. Note that\nthe model is not suited to situations where static recrystallization processes are\nsignificant.
\n\nThe primary microphysical mechanism for plastic deformation of the polycrystal\nis dislocation creep, which involves dislocation glide (\"slip\") along symmetry\nplanes of the mineral and dislocation climb, which allows for dislocations to\nannihilate each other so that the number of dislocations reaches a steady-state.\nThe D-Rex model does not simulate dislocation climb, but implicitly assumes that\nthe dislocations are in steady-state so that the dislocation density of the\ncrystal can be described by
\n\n$$\n\u03c1 \u221d b^{-2} \\left(\\frac{\u03c3}{\u03bc}\\right)^{p}\n$$
\n\nwhere $b$ is the length of the Burgers' vector, $\u03c3$ is the stress\nand $\u03bc$ is the shear modulus. The value of the exponent $p$ is given by the\nstress_exponent input parameter. For an overview of available parameters,\nsee [the pydrex.mock source code, for now...]
\n\nThe effects of dynamic recrystallization are twofold. Grains with a higher than\naverage dislocation density may be affected by either grain nucleation, which is\nthe formation of initially small, strain-free sub-grains, or grain boundary\nmigration, by which process other grains of lower strain energy annex a portion\nof its volume. Nucleation occurs mostly in grains oriented favourably for\ndislocation glide, and the new grains also grow by grain boundary migration.\nIf nucleation is too inefficient, the dislocation density in deformation-aligned\ngrains will remain high and these grains will therefore shrink in volume. On the\nother hand, if grain boundaries are too immobile, then nucleated grains will take\nlonger to grow, reducing the speed of CPO development and re-orientation.\nBecause nucleated grains are assumed to inherit the orientation of the parent,\nthey do not affect the model except by reducing the average dislocation density.\nA grain boundary mobility parameter of $M^{\u2217} = 0$ will therefore disable any\nrecrystallization effects. Finally, the process of grain boundary sliding can\nalso be included, which simply disallows rotation of grains with very small volume.\nThis only affects CPO evolution by introducing a latency for the onset of grain\nboundary migration in nucleated grains. It also manifests as an upper bound on\ntexture strength.
\n\nParameter reference \n\nModel parameters will eventually be provided in a .toml file.\nFor now just pass a dictionary to config in the Mineral.update_orientations method.\nA draft of the input file spec is shown below:
\n\n\n
# PyDRex TOML configuration specification. \n# Exactly one valid combination of fields from the [input] section are required, \n# the rest is optional. \n\n# Simulation name is optional but recommended. \nname = "pydrex-spec" \n\n# Input files/options are given in this section: \n[input] \n\n# Input data can be provided in one of three ways: \n# 1. An input mesh with the steady-state numerical velocity gradient field \n# and a plain text SCSV file specifying the FINAL locations of the polycrystals. \n# In this case, polycrystals will first be back-propagated along flow pathlines, \n# and then forward-propagated while the CPO is calculated. \n# The SCSV file should have column names 'X', 'Y', 'Z' for 3D or any two of those for 2D. \n# 2. A built-in (analytical) velocity gradient function from `pydrex.velocity_gradients`, \n# its arguments, and INITIAL locations of the polycrystals. In this case, \n# polycrystals will immediately be forward-advected in the specified field. \n# 3. Pre-computed pathline files with velocity gradients at each point. \n# These can be either plain text SCSV files or binary NPZ files. \n# They should have columns/fields called: 'X_id', 'Y_id', 'Z_id', 'L11_id', 'L12_id', 'L13_id', etc. \n# where 'id' is replaced by an unique identifier of the particle/pathline. \n# If a field called 't' is also present, it will be used for the timestamps. \n# Alternatively, a fixed timestep for all paths can be specified using `timestep`. \n# 4. Names of fields to be read from a geodynamics framework during runtime (not implemented yet). \n\n# Example for method 1, not only .vtu but any format supported by meshio should work: \n# mesh = "filename.vtu" \n# locations_final = "filename.scsv" \n# timestep = 1e9 \n\n# Example for method 2: \nvelocity_gradient = [ "simple_shear_2d" , "Y" , "X" , 5e-6 ] \nlocations_initial = "start.scsv" \ntimestep = 1e9 \n\n# Example for method 3: \n# timestep = 1e9 \n# paths = ["path001.npz", "path002.scsv"] \n\n# In cases where the pathlines do not exit the domain, \n# a maximum strain threshold can bee provided, after which advection is halted. \n# max_strain = 10 \n\n# Output files/options are given in this section: \n[output] \n\n# Optional output directory, will be created if missing. \n# This is also relative to the parent directory of the TOML file, \n# unless an absolute path is given. \ndirectory = "out" \n\n# Optional choice of mineral phases to include in raw output. \n# Raw output means rotation matrices and grain volumes, so 10 floats per grain per mineral. \n# By default, raw output for all supported minerals is saved. \nraw_output = [ "olivine" ] \n\n# Optional choice of mineral phases to include in diagnostic output. \n# Diagnostic output includes texture symmetry, strength and mean angle results. \n# By default, diagnostic output for all supported minerals is saved. \ndiagnostics = [ "olivine" ] \n\n# Should anisotropy postprocessing results be calculated? \n# This uses voigt averaging so the effective values for the multiphase polycrystal are calculated. \nanisotropy = true \n\n# Optional pathline output files (velocity gradients, positions, timestamps, particle ids). \n# Pathline output files use the same format as pathline inputs (by default, they are not produced). \n# They are stored inside the output directory unless absolute paths are given. \n# paths = ["pathline001.scsv"] \n\n# Optional logging level for log files. \n# This sets the log level for all log files, overriding the default value of "WARNING". \n# Supported levels are controlled by Python's logging module. \n# Usually they are "CRITICAL", "ERROR", "WARNING", "INFO" and "DEBUG". \nlog_level = "DEBUG" \n\n# DREX and simulation parameters are given in this section: \n[parameters] \n\n# Optional olivine volume fraction to use for multiphase simulations. \n# If enstatite_fraction is provided, they must sum to 1. \n# Otherwise, the remainder is assumed to be enstatite. \n# olivine_fraction = 1. \n\n# Optional enstatite volume fraction to use for multiphase simulations. \n# If olivine_fraction is provided, they must sum to 1. \n# Otherwise, the remainder is assumed to be olivine. \n# enstatite_fraction = 0. \n\n# Optional initial olivine fabric. A-type by default. \ninitial_olivine_fabric = "A" \n\n# Optional DREX stress_exponent, see documentation for details. \nstress_exponent = 1.5 \n\n# Optional DREX deformation_exponent, see documentation for details. \ndeformation_exponent = 3.5 \n\n# Optional DREX grain boudary mobility, see documentation for details. \ngbm_mobility = 125 \n\n# Optional DREX grain boundary sliding threshold, see documentation for details. \ngbs_threshold = 0.3 \n\n# Optional DREX nucleation efficiency, see documentation for details. \nnucleation_efficiency = 5.0 \n\n# Optional number of (initial) grains per mineral phase per polycrystal. \nnumber_of_grains = 2000 \n\n
\n PyDRex: Custom Matplotlib Axes subclasses.
\n \n"}, "pydrex.axes.PoleFigureAxes": {"fullname": "pydrex.axes.PoleFigureAxes", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes", "kind": "class", "doc": "Axes class designed for crystallographic pole figures.
\n\nThin matplotlib Axes wrapper for crystallographic pole figures.
\n\n\n\n
Projections are not performed automatically using default methods like\nscatter or plot. To actually plot the pole figures, use polefigure.
\n\n
\n", "default_value": "'pydrex.polefigure'"}, "pydrex.axes.PoleFigureAxes.polefigure": {"fullname": "pydrex.axes.PoleFigureAxes.polefigure", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.polefigure", "kind": "function", "doc": "Plot pole figure of crystallographic texture.
\n\nArgs:
\n\n\ndata (array) \u2014 Nx3x3 array of orientation matricesdensity (bool, optional) \u2014 plot contoured pole figures, False by defaultref_axes (string, optional) \u2014 letters specifying the horizontal and vertical\naxes of the pole figure, and respective labelshkl (array, optional) \u2014 crystallographic axis (one of the slip\ndirections of olivine, i.e. [1, 0, 0], [0, 1, 0] or [0, 0, 1])density_kwargs (dict, optional) \u2014 keyword arguments to pass to\npydrex.stats.point_density if density=True \n\nAny additional keyword arguments are passed to either tripcolor if\ndensity=True or scatter if density=False
\n", "signature": "(\tself , \tdata , \tdensity = False , \tref_axes = 'xz' , \thkl = [ 1 , 0 , 0 ] , \tdensity_kwargs = None , \t** kwargs ): ", "funcdef": "def"}, "pydrex.axes.PoleFigureAxes.set": {"fullname": "pydrex.axes.PoleFigureAxes.set", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.set", "kind": "function", "doc": "Set multiple properties at once.
\n\nSupported properties are
\n\nProperties:\n adjustable: {'box', 'datalim'}\n agg_filter: a filter function, which takes a (m, n, 3) float array and a dpi value, and returns a (m, n, 3) array and two offsets from the bottom left corner of the image\n alpha: scalar or None\n anchor: (float, float) or {'C', 'SW', 'S', 'SE', 'E', 'NE', ...}\n animated: bool\n aspect: {'auto', 'equal'} or float\n autoscale_on: bool\n autoscalex_on: unknown\n autoscaley_on: unknown\n axes_locator: Callable[[Axes, Renderer], Bbox]\n axisbelow: bool or 'line'\n box_aspect: float or None\n clip_box: ~matplotlib.transforms.BboxBase or None\n clip_on: bool\n clip_path: Patch or (Path, Transform) or None\n facecolor or fc: color\n figure: ~matplotlib.figure.Figure\n frame_on: bool\n gid: str\n in_layout: bool\n label: object\n mouseover: bool\n navigate: bool\n navigate_mode: unknown\n path_effects: list of .AbstractPathEffect\n picker: None or bool or float or callable\n position: [left, bottom, width, height] or ~matplotlib.transforms.Bbox\n prop_cycle: ~cycler.Cycler\n rasterization_zorder: float or None\n rasterized: bool\n sketch_params: (scale: float, length: float, randomness: float)\n snap: bool or None\n subplotspec: unknown\n title: str\n transform: ~matplotlib.transforms.Transform\n url: str\n visible: bool\n xbound: (lower: float, upper: float)\n xlabel: str\n xlim: (left: float, right: float)\n xmargin: float greater than -0.5\n xscale: unknown\n xticklabels: unknown\n xticks: unknown\n ybound: (lower: float, upper: float)\n ylabel: str\n ylim: (bottom: float, top: float)\n ymargin: float greater than -0.5\n yscale: unknown\n yticklabels: unknown\n yticks: unknown\n zorder: float
\n", "signature": "(\tself , \t* , \tadjustable =< UNSET > , \tagg_filter =< UNSET > , \talpha =< UNSET > , \tanchor =< UNSET > , \tanimated =< UNSET > , \taspect =< UNSET > , \tautoscale_on =< UNSET > , \tautoscalex_on =< UNSET > , \tautoscaley_on =< UNSET > , \taxes_locator =< UNSET > , \taxisbelow =< UNSET > , \tbox_aspect =< UNSET > , \tclip_box =< UNSET > , \tclip_on =< UNSET > , \tclip_path =< UNSET > , \tfacecolor =< UNSET > , \tframe_on =< UNSET > , \tgid =< UNSET > , \tin_layout =< UNSET > , \tlabel =< UNSET > , \tmouseover =< UNSET > , \tnavigate =< UNSET > , \tpath_effects =< UNSET > , \tpicker =< UNSET > , \tposition =< UNSET > , \tprop_cycle =< UNSET > , \trasterization_zorder =< UNSET > , \trasterized =< UNSET > , \tsketch_params =< UNSET > , \tsnap =< UNSET > , \tsubplotspec =< UNSET > , \ttitle =< UNSET > , \ttransform =< UNSET > , \turl =< UNSET > , \tvisible =< UNSET > , \txbound =< UNSET > , \txlabel =< UNSET > , \txlim =< UNSET > , \txmargin =< UNSET > , \txscale =< UNSET > , \txticklabels =< UNSET > , \txticks =< UNSET > , \tybound =< UNSET > , \tylabel =< UNSET > , \tylim =< UNSET > , \tymargin =< UNSET > , \tyscale =< UNSET > , \tyticklabels =< UNSET > , \tyticks =< UNSET > , \tzorder =< UNSET > ): ", "funcdef": "def"}, "pydrex.cli": {"fullname": "pydrex.cli", "modulename": "pydrex.cli", "kind": "module", "doc": "\n PyDRex: Entry points and argument handling for command line tools.
\n \n\nAll CLI handlers should be registered in the CLI_HANDLERS namedtuple,\nwhich ensures that they will be installed as executable scripts alongside the package.
\n"}, "pydrex.cli.NPZFileInspector": {"fullname": "pydrex.cli.NPZFileInspector", "modulename": "pydrex.cli", "qualname": "NPZFileInspector", "kind": "class", "doc": "PyDRex script to show information about serialized CPO data.
\n\nLists the keys that should be used for the postfix in pydrex.Mineral.load and\npydrex.Mineral.from_file.
\n"}, "pydrex.cli.PoleFigureVisualiser": {"fullname": "pydrex.cli.PoleFigureVisualiser", "modulename": "pydrex.cli", "qualname": "PoleFigureVisualiser", "kind": "class", "doc": "PyDRex script to plot pole figures of serialized CPO data.
\n\nProduces [100], [010] and [001] pole figures for serialized pydrex.Minerals.\nIf the range of indices is not specified,\na maximum of 25 of each pole figure will be produced by default.
\n"}, "pydrex.cli.CLI_HANDLERS": {"fullname": "pydrex.cli.CLI_HANDLERS", "modulename": "pydrex.cli", "qualname": "CLI_HANDLERS", "kind": "variable", "doc": "
\n", "default_value": "CLI_HANDLERS(pole_figure_visualiser=PoleFigureVisualiser(), npz_file_inspector=NPZFileInspector())"}, "pydrex.core": {"fullname": "pydrex.core", "modulename": "pydrex.core", "kind": "module", "doc": "\n PyDRex: Core D-Rex functions and enums.
\n \n\nThe function derivatives implements the core D-Rex solver, which computes the\ncrystallographic rotation rate and changes in fractional grain volumes.
\n\nAcronyms:
\n\n\nCRSS = Critical Resolved Shear Stress,\ni.e. threshold stress required to initiate slip on a slip system,\nnormalised to the stress required to initiate slip on the softest slip system \n \n"}, "pydrex.core.PERMUTATION_SYMBOL": {"fullname": "pydrex.core.PERMUTATION_SYMBOL", "modulename": "pydrex.core", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "
\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.core.MineralPhase": {"fullname": "pydrex.core.MineralPhase", "modulename": "pydrex.core", "qualname": "MineralPhase", "kind": "class", "doc": "Supported mineral phases.
\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralPhase.olivine": {"fullname": "pydrex.core.MineralPhase.olivine", "modulename": "pydrex.core", "qualname": "MineralPhase.olivine", "kind": "variable", "doc": "
\n", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.core.MineralPhase.enstatite": {"fullname": "pydrex.core.MineralPhase.enstatite", "modulename": "pydrex.core", "qualname": "MineralPhase.enstatite", "kind": "variable", "doc": "
\n", "default_value": "<MineralPhase.enstatite: 1>"}, "pydrex.core.DeformationRegime": {"fullname": "pydrex.core.DeformationRegime", "modulename": "pydrex.core", "qualname": "DeformationRegime", "kind": "class", "doc": "Deformation mechanism regimes.
\n", "bases": "enum.IntEnum"}, "pydrex.core.DeformationRegime.diffusion": {"fullname": "pydrex.core.DeformationRegime.diffusion", "modulename": "pydrex.core", "qualname": "DeformationRegime.diffusion", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.diffusion: 0>"}, "pydrex.core.DeformationRegime.dislocation": {"fullname": "pydrex.core.DeformationRegime.dislocation", "modulename": "pydrex.core", "qualname": "DeformationRegime.dislocation", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.core.DeformationRegime.byerlee": {"fullname": "pydrex.core.DeformationRegime.byerlee", "modulename": "pydrex.core", "qualname": "DeformationRegime.byerlee", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.byerlee: 2>"}, "pydrex.core.DeformationRegime.max_viscosity": {"fullname": "pydrex.core.DeformationRegime.max_viscosity", "modulename": "pydrex.core", "qualname": "DeformationRegime.max_viscosity", "kind": "variable", "doc": "
\n", "default_value": "<DeformationRegime.max_viscosity: 3>"}, "pydrex.core.MineralFabric": {"fullname": "pydrex.core.MineralFabric", "modulename": "pydrex.core", "qualname": "MineralFabric", "kind": "class", "doc": "Supported mineral fabrics.
\n\nThe following fabric types are supported:
\n\n\n", "bases": "enum.IntEnum"}, "pydrex.core.MineralFabric.olivine_A": {"fullname": "pydrex.core.MineralFabric.olivine_A", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_A", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.core.MineralFabric.olivine_B": {"fullname": "pydrex.core.MineralFabric.olivine_B", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_B", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_B: 1>"}, "pydrex.core.MineralFabric.olivine_C": {"fullname": "pydrex.core.MineralFabric.olivine_C", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_C", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_C: 2>"}, "pydrex.core.MineralFabric.olivine_D": {"fullname": "pydrex.core.MineralFabric.olivine_D", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_D", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_D: 3>"}, "pydrex.core.MineralFabric.olivine_E": {"fullname": "pydrex.core.MineralFabric.olivine_E", "modulename": "pydrex.core", "qualname": "MineralFabric.olivine_E", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.olivine_E: 4>"}, "pydrex.core.MineralFabric.enstatite_AB": {"fullname": "pydrex.core.MineralFabric.enstatite_AB", "modulename": "pydrex.core", "qualname": "MineralFabric.enstatite_AB", "kind": "variable", "doc": "
\n", "default_value": "<MineralFabric.enstatite_AB: 5>"}, "pydrex.core.get_crss": {"fullname": "pydrex.core.get_crss", "modulename": "pydrex.core", "qualname": "get_crss", "kind": "function", "doc": "Get Critical Resolved Shear Stress for the mineral phase and fabric.
\n\nReturns an array of the normalised threshold stresses required to activate slip on\neach slip system. Olivine slip systems are ordered according to the convention used\nfor pydrex.minerals.OLIVINE_SLIP_SYSTEMS.
\n", "signature": "(phase , fabric ): ", "funcdef": "def"}, "pydrex.core.derivatives": {"fullname": "pydrex.core.derivatives", "modulename": "pydrex.core", "qualname": "derivatives", "kind": "function", "doc": "Get derivatives of orientation and volume distribution.
\n\nArgs:
\n\n\nphase (MineralPhase) \u2014 ordinal number of the mineral phasefabric (MineralFabric) \u2014 ordinal number of the fabric typen_grains (int) \u2014 number of \"grains\" i.e. discrete volume segmentsorientations (array) \u2014 n_grainsx3x3 orientations (direction cosines)fractions (array) \u2014 volume fractions of the grains relative to aggregate volumestrain_rate (array) \u2014 3x3 dimensionless macroscopic strain-rate tensorvelocity_gradient (array) \u2014 3x3 dimensionless macroscopic velocity gradientstress_exponent (float) \u2014 p in dislocation_density \u221d shear_stress^pdeformation_exponent (float) \u2014 n in shear_stress \u221d |deformation_rate|^(1/n)nucleation_efficiency (float) \u2014 parameter controlling grain nucleationgmb_mobility (float) \u2014 grain boundary mobility parametervolume_fraction (float) \u2014 volume fraction of the mineral phase relative to\nother phases (multiphase simulations) \n\nReturns a tuple with the rotation rates and grain volume fraction changes.
\n", "signature": "(\tphase , \tfabric , \tn_grains , \torientations , \tfractions , \tstrain_rate , \tvelocity_gradient , \tstress_exponent , \tdeformation_exponent , \tnucleation_efficiency , \tgbm_mobility , \tvolume_fraction ): ", "funcdef": "def"}, "pydrex.diagnostics": {"fullname": "pydrex.diagnostics", "modulename": "pydrex.diagnostics", "kind": "module", "doc": "\n PyDRex: Methods to calculate texture and strain diagnostics.
\n \n\n\n\n
Calculations expect orientation matrices $a$ to represent passive\n(i.e. alias) rotations, which are defined in terms of the extrinsic ZXZ\neuler angles $\u03d5, \u03b8, \u03c6$ as\n$$\na = \\begin{bmatrix}\n \\cos\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\sin\u03c6 & \\cos\u03b8\\cos\u03d5\\sin\u03c6 + \\cos\u03c6\\sin\u03d5 & \\sin\u03c6\\sin\u03b8 \\cr\n -\\sin\u03c6\\cos\u03d5 - \\cos\u03b8\\sin\u03d5\\cos\u03c6 & \\cos\u03b8\\cos\u03d5\\cos\u03c6 - \\sin\u03c6\\sin\u03d5 & \\cos\u03c6\\sin\u03b8 \\cr\n \\sin\u03b8\\sin\u03d5 & -\\sin\u03b8\\cos\u03d5 & \\cos\u03b8\n \\end{bmatrix}\n$$\nsuch that a[i, j] gives the direction cosine of the angle between the i-th\ngrain axis and the j-th external axis (in the global Eulerian frame).
\n\n
Calculate elasticity decompositions for the given elasticity tensors.
\n\nArgs:
\n\n\nvoigt_matrices (array) \u2014 the Nx6x6 Voigt matrix representations of the averaged\nelasticity tensors for a series of polycrystal textures \n\nReturns a dictionary with the following data series:
\n\n\n'bulk_modulus' \u2014 the computed bulk modulus for each Voigt matrix C'shear_modulus' \u2014 the computed shear modulus for each Voigt matrix C'percent_anisotropy' \u2014 for each Voigt matrix C, the total percentage of the\nnorm of the elastic tensor ||C|| that deviates from the norm of the \"closest\"\nisotropic elasticity tensor'percent_hexagonal' \u2014 for each C, the percentage of ||C|| attributed to\nhexagonally symmetric minerals'percent_tetragonal' \u2014 for each C, the percentage of ||C|| attributed to\ntetragonally symmetric minerals'percent_orthorhombic' \u2014 for each C, the percentage of ||C|| attributed to\northorhombically symmetric minerals'percent_monoclinic' \u2014 for each C, the percentage of ||C|| attributed to\nmonoclinically symmetric minerals'percent_triclinic' \u2014 for each C, the percentage of ||C|| attributed to\ntriclinically \"symmetric\" minerals (no mirror planes)'hexagonal_axis' \u2014 for each C, the axis of hexagonal symmetry for the \"closest\"\nhexagonally symmetric approximation to C, a.k.a. the \"transverse isotropy\" axis \n\n\n\n
Only 5 symmetry classes are relevant for elasticity decomposition,\ncompared to the usual 6 used to describe crystal families.\nCrystals with cubic symmetry contribute to the isotropic elasticity tensor,\nbecause the lattice spacing is identical in all orthogonal directions.\nNote also that the trigonal crystal system is not a crystal family\n(it belongs to the hexagonal family).
\n\n
(voigt_matrices ): ", "funcdef": "def"}, "pydrex.diagnostics.bingham_average": {"fullname": "pydrex.diagnostics.bingham_average", "modulename": "pydrex.diagnostics", "qualname": "bingham_average", "kind": "function", "doc": "Compute Bingham average of orientation matrices.
\n\nReturns the antipodally symmetric average orientation\nof the given crystallographic axis, or the a-axis by default.\nValid axis specifiers are \"a\" for [100], \"b\" for [010] and \"c\" for [001].
\n\nSee also: Watson (1966) ,\nMardia & Jupp, \u201cDirectional Statistics\u201d .
\n", "signature": "(orientations , axis = 'a' ): ", "funcdef": "def"}, "pydrex.diagnostics.finite_strain": {"fullname": "pydrex.diagnostics.finite_strain", "modulename": "pydrex.diagnostics", "qualname": "finite_strain", "kind": "function", "doc": "Extract measures of finite strain from the deformation gradient.
\n\nExtracts the largest principal strain value and the vector defining the axis of\nmaximum extension (longest semiaxis of the finite strain ellipsoid) from the 3x3\ndeformation gradient tensor.
\n", "signature": "(deformation_gradient , driver = 'ev' ): ", "funcdef": "def"}, "pydrex.diagnostics.symmetry_pgr": {"fullname": "pydrex.diagnostics.symmetry_pgr", "modulename": "pydrex.diagnostics", "qualname": "symmetry_pgr", "kind": "function", "doc": "Compute texture symmetry eigenvalue diagnostics from grain orientation matrices.
\n\nCompute Point, Girdle and Random symmetry diagnostics\nfor ternary texture classification.\nReturns the tuple (P, G, R) where\n$$\n\\begin{align*}\nP &= (\u03bb_{1} - \u03bb_{2}) / N \\cr\nG &= 2 (\u03bb_{2} - \u03bb_{3}) / N \\cr\nR &= 3 \u03bb_{3} / N\n\\end{align*}\n$$\nwith $N$ the sum of the eigenvalues $\u03bb_{1} \u2265 \u03bb_{2} \u2265 \u03bb_{3}$\nof the scatter (inertia) matrix.
\n\nSee e.g. Vollmer (1990) .
\n", "signature": "(orientations , axis = 'a' ): ", "funcdef": "def"}, "pydrex.diagnostics.misorientation_indices": {"fullname": "pydrex.diagnostics.misorientation_indices", "modulename": "pydrex.diagnostics", "qualname": "misorientation_indices", "kind": "function", "doc": "Calculate M-indices for a series of polycrystal textures.
\n\nCalculate M-index using misorientation_index for a series of texture snapshots.\nThe orientation_stack is a NxMx3x3 array of orientations where N is the number of\ntexture snapshots and M is the number of grains.
\n\nUses the multiprocessing library to calculate texture indices for multiple snapshots\nsimultaneously. If ncpus is None the number of CPU cores to use is chosen\nautomatically based on the maximum number available to the Python interpreter,\notherwise the specified number of cores is requested. Alternatively, an existing\ninstance of multiprocessing.Pool can be provided.
\n\nSee misorientation_index for documentation of the remaining arguments.
\n", "signature": "(\torientation_stack , \tsystem : pydrex . geometry . LatticeSystem , \tbins = None , \tncpus = None , \tpool = None ): ", "funcdef": "def"}, "pydrex.diagnostics.misorientation_index": {"fullname": "pydrex.diagnostics.misorientation_index", "modulename": "pydrex.diagnostics", "qualname": "misorientation_index", "kind": "function", "doc": "Calculate M-index for polycrystal orientations.
\n\nThe bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.
\n\n\n\n
This method must be able to allocate an array of shape\n$ \\frac{N!}{2(N-2)!}\u00d7 M^{2} $\nfor N the length of orientations and M the number of symmetry operations for\nthe given system.
\n\n
See Skemer et al. (2005) .
\n", "signature": "(orientations , system : pydrex . geometry . LatticeSystem , bins = None ): ", "funcdef": "def"}, "pydrex.diagnostics.coaxial_index": {"fullname": "pydrex.diagnostics.coaxial_index", "modulename": "pydrex.diagnostics", "qualname": "coaxial_index", "kind": "function", "doc": "Calculate coaxial \u201cBA\u201d index for a combination of two crystal axes.
\n\nThe BA index of Mainprice et al. (2015) \nis derived from the eigenvalue symmetry diagnostics and measures point vs girdle\nsymmetry in the aggregate. $BA \u2208 [0, 1]$ where $BA = 0$ corresponds to a perfect\naxial girdle texture and $BA = 1$ represents a point symmetry texture assuming that\nthe random component $R$ is negligible. May be less susceptible to random\nfluctuations compared to the raw eigenvalue diagnostics.
\n", "signature": "(orientations , axis1 = 'b' , axis2 = 'a' ): ", "funcdef": "def"}, "pydrex.diagnostics.smallest_angle": {"fullname": "pydrex.diagnostics.smallest_angle", "modulename": "pydrex.diagnostics", "qualname": "smallest_angle", "kind": "function", "doc": "Get smallest angle between a unit vector and a bidirectional axis.
\n\nThe axis is specified using either of its two parallel unit vectors.\nOptionally project the vector onto the plane (given by its unit normal)\nbefore calculating the angle.
\n", "signature": "(vector , axis , plane = None ): ", "funcdef": "def"}, "pydrex.exceptions": {"fullname": "pydrex.exceptions", "modulename": "pydrex.exceptions", "kind": "module", "doc": "\n PyDRex: Custom exceptions (subclasses of pydrex.Error).
\n \n"}, "pydrex.exceptions.Error": {"fullname": "pydrex.exceptions.Error", "modulename": "pydrex.exceptions", "qualname": "Error", "kind": "class", "doc": "Base class for exceptions in PyDRex.
\n", "bases": "builtins.Exception"}, "pydrex.exceptions.ConfigError": {"fullname": "pydrex.exceptions.ConfigError", "modulename": "pydrex.exceptions", "qualname": "ConfigError", "kind": "class", "doc": "Exception raised for errors in the input configuration.
\n\nAttributes:\n message \u2014 explanation of the error
\n", "bases": "Error"}, "pydrex.exceptions.ConfigError.__init__": {"fullname": "pydrex.exceptions.ConfigError.__init__", "modulename": "pydrex.exceptions", "qualname": "ConfigError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.ConfigError.message": {"fullname": "pydrex.exceptions.ConfigError.message", "modulename": "pydrex.exceptions", "qualname": "ConfigError.message", "kind": "variable", "doc": "
\n"}, "pydrex.exceptions.MeshError": {"fullname": "pydrex.exceptions.MeshError", "modulename": "pydrex.exceptions", "qualname": "MeshError", "kind": "class", "doc": "Exception raised for errors in the input mesh.
\n\nAttributes:\n message \u2014 explanation of the error
\n", "bases": "Error"}, "pydrex.exceptions.MeshError.__init__": {"fullname": "pydrex.exceptions.MeshError.__init__", "modulename": "pydrex.exceptions", "qualname": "MeshError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.MeshError.message": {"fullname": "pydrex.exceptions.MeshError.message", "modulename": "pydrex.exceptions", "qualname": "MeshError.message", "kind": "variable", "doc": "
\n"}, "pydrex.exceptions.IterationError": {"fullname": "pydrex.exceptions.IterationError", "modulename": "pydrex.exceptions", "qualname": "IterationError", "kind": "class", "doc": "Exception raised for errors in numerical iteration schemes.
\n\nAttributes:\n message \u2014 explanation of the error
\n", "bases": "Error"}, "pydrex.exceptions.IterationError.__init__": {"fullname": "pydrex.exceptions.IterationError.__init__", "modulename": "pydrex.exceptions", "qualname": "IterationError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.IterationError.message": {"fullname": "pydrex.exceptions.IterationError.message", "modulename": "pydrex.exceptions", "qualname": "IterationError.message", "kind": "variable", "doc": "
\n"}, "pydrex.exceptions.SCSVError": {"fullname": "pydrex.exceptions.SCSVError", "modulename": "pydrex.exceptions", "qualname": "SCSVError", "kind": "class", "doc": "Exception raised for errors in SCSV file I/O.
\n\nAttributes:
\n\n\nmessage \u2014 explanation of the error \n \n", "bases": "Error"}, "pydrex.exceptions.SCSVError.__init__": {"fullname": "pydrex.exceptions.SCSVError.__init__", "modulename": "pydrex.exceptions", "qualname": "SCSVError.__init__", "kind": "function", "doc": "
\n", "signature": "(message "}, "pydrex.exceptions.SCSVError.message": {"fullname": "pydrex.exceptions.SCSVError.message", "modulename": "pydrex.exceptions", "qualname": "SCSVError.message", "kind": "variable", "doc": "
\n"}, "pydrex.geometry": {"fullname": "pydrex.geometry", "modulename": "pydrex.geometry", "kind": "module", "doc": "\n PyDRex: Functions for geometric coordinate conversions and projections.
\n \n"}, "pydrex.geometry.LatticeSystem": {"fullname": "pydrex.geometry.LatticeSystem", "modulename": "pydrex.geometry", "qualname": "LatticeSystem", "kind": "class", "doc": "Crystallographic lattice systems supported by postprocessing methods.
\n\nThe value of a member is (a, b) with a and b as given in the table below.\nThe additional row lists the maximum misorientation angle between two crystallites\nfor the given lattice system.
\n\n triclinic monoclinic orthorhombic rhombohedral tetragonal hexagonal\n------------------------------------------------------------------------------\na 1 2 2 3 4 6\nb 1 2 4 6 8 12\n\u03b8max 180\u00b0 180\u00b0 120\u00b0 120\u00b0 90\u00b0 90\u00b0\nThis is identically Table 1 in Grimmer (1979) .
\n", "bases": "enum.Enum"}, "pydrex.geometry.LatticeSystem.triclinic": {"fullname": "pydrex.geometry.LatticeSystem.triclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.triclinic", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.triclinic: (1, 1)>"}, "pydrex.geometry.LatticeSystem.monoclinic": {"fullname": "pydrex.geometry.LatticeSystem.monoclinic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.monoclinic", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.monoclinic: (2, 2)>"}, "pydrex.geometry.LatticeSystem.orthorhombic": {"fullname": "pydrex.geometry.LatticeSystem.orthorhombic", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.orthorhombic", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.orthorhombic: (2, 4)>"}, "pydrex.geometry.LatticeSystem.rhombohedral": {"fullname": "pydrex.geometry.LatticeSystem.rhombohedral", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.rhombohedral", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.rhombohedral: (3, 6)>"}, "pydrex.geometry.LatticeSystem.tetragonal": {"fullname": "pydrex.geometry.LatticeSystem.tetragonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.tetragonal", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.tetragonal: (4, 8)>"}, "pydrex.geometry.LatticeSystem.hexagonal": {"fullname": "pydrex.geometry.LatticeSystem.hexagonal", "modulename": "pydrex.geometry", "qualname": "LatticeSystem.hexagonal", "kind": "variable", "doc": "
\n", "default_value": "<LatticeSystem.hexagonal: (6, 12)>"}, "pydrex.geometry.to_cartesian": {"fullname": "pydrex.geometry.to_cartesian", "modulename": "pydrex.geometry", "qualname": "to_cartesian", "kind": "function", "doc": "Convert spherical to cartesian coordinates in \u211d\u00b3.
\n\nSpherical coordinate convention:
\n\n\n\u03d5 is the longitude (\u201cazimuth\u201d) \u2208 [0, 2\u03c0) \n\u03b8 is the colatitude (\u201cinclination\u201d) \u2208 [0, \u03c0) \n \n\nBy default, a radius of r = 1 is used for the sphere.\nReturns a tuple containing arrays of x, y, and z values.
\n", "signature": "(\u03c6 , \u03b8 , r = 1 ): ", "funcdef": "def"}, "pydrex.geometry.to_spherical": {"fullname": "pydrex.geometry.to_spherical", "modulename": "pydrex.geometry", "qualname": "to_spherical", "kind": "function", "doc": "Convert cartesian coordinates in \u211d\u00b3 to spherical coordinates.
\n\nSpherical coordinate convention:
\n\n\n\u03d5 is the longitude (\u201cazimuth\u201d) \u2208 [0, 2\u03c0) \n\u03b8 is the colatitude (\u201cinclination\u201d) \u2208 [0, \u03c0) \n \n\nReturns a tuple containing arrays of r, \u03d5 and \u03b8 values.
\n", "signature": "(x , y , z ): ", "funcdef": "def"}, "pydrex.geometry.misorientation_angles": {"fullname": "pydrex.geometry.misorientation_angles", "modulename": "pydrex.geometry", "qualname": "misorientation_angles", "kind": "function", "doc": "Calculate minimum misorientation angles for collections of rotation quaternions.
\n\nCalculate the smallest angular distance between any quaternions q1_array[:, i] and\nq2_array[:, j], where i == j and the first dimensions of q1_array and q2_array\nare of equal length (the output will also be this long):
\n\nq1_array.shape q2_array.shape len(output)\n---------------------------------------------------\nNxAx4 NxBx4 N\n\n\n
This method must be able to allocate a floating point array of shape Nx(A*B)
\n\n
Uses ~25% less memory than the same operation with rotation matrices.
\n\nSee also:
\n\n\n", "signature": "(q1_array , q2_array ): ", "funcdef": "def"}, "pydrex.geometry.symmetry_operations": {"fullname": "pydrex.geometry.symmetry_operations", "modulename": "pydrex.geometry", "qualname": "symmetry_operations", "kind": "function", "doc": "Get sequence of symmetry operations for the given LatticeSystem.
\n\nReturned transforms are either quaternions (for rotations of the lattice) or 4x4\nmatrices which pre-multiply a quaternion to give a reflected variant (reflections\nare improper rotations and cannot be represented as quaternions or SciPy rotation\nmatrices).
\n", "signature": "(system : pydrex . geometry . LatticeSystem ): ", "funcdef": "def"}, "pydrex.geometry.poles": {"fullname": "pydrex.geometry.poles", "modulename": "pydrex.geometry", "qualname": "poles", "kind": "function", "doc": "Extract 3D vectors of crystallographic directions from orientation matrices.
\n\nExpects orientations to be an array with shape (N, 3, 3).\nThe optional arguments ref_axes and hkl can be used to change\nthe global reference axes and the crystallographic direction respectively.\nThe reference axes should be given as a string of two letters,\ne.g. \"xz\" (default), which specify the second and third axes\nof the global right-handed reference frame. The third letter in the set \"xyz\"\ndetermines the first axis. The ref_axes will therefore become the\nhorizontal and vertical axes of pole figures used to plot the directions.
\n", "signature": "(orientations , ref_axes = 'xz' , hkl = [ 1 , 0 , 0 ] ): ", "funcdef": "def"}, "pydrex.geometry.lambert_equal_area": {"fullname": "pydrex.geometry.lambert_equal_area", "modulename": "pydrex.geometry", "qualname": "lambert_equal_area", "kind": "function", "doc": "Project axial data from a 3D sphere onto a 2D disk.
\n\nProject points from a 3D sphere of radius 1, given in Cartesian coordinates,\nto points on a 2D disk using a Lambert equal area azimuthal projection.\nReturns arrays of the X and Y coordinates in the unit disk.
\n\nThis implementation first maps all points onto the same hemisphere,\nand then projects that hemisphere onto the disk.
\n", "signature": "(xvals , yvals , zvals ): ", "funcdef": "def"}, "pydrex.geometry.shirley_concentric_squaredisk": {"fullname": "pydrex.geometry.shirley_concentric_squaredisk", "modulename": "pydrex.geometry", "qualname": "shirley_concentric_squaredisk", "kind": "function", "doc": "Project points from a square onto a disk using the concentric Shirley method.
\n\nThe concentric method of Shirley & Chiu (1997) \nis optimised to preserve area. See also: http://marc-b-reynolds.github.io/math/2017/01/08/SquareDisc.html .
\n\nThis can be used to set up uniform grids on a disk, e.g.
\n\n\n
>>> a = [ x / 5.0 for x in range ( - 5 , 6 )] \n>>> x = [[ x ] * len ( a ) for x in a ] \n>>> y = [ a for _ in a ] \n>>> x_flat = [ j for i in x for j in i ] \n>>> y_flat = [ j for i in y for j in i ] \n>>> x_disk , y_disk = shirley_concentric_squaredisk ( x_flat , y_flat ) \n>>> r = x_disk ** 2 + y_disk ** 2 \n>>> r . reshape (( len ( a ), len ( a ))) \narray([[1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ], \n [1. , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.04, 0. , 0.04, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.04, 0.04, 0.04, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.16, 0.16, 0.16, 0.16, 0.16, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.36, 0.64, 1. ], \n [1. , 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 0.64, 1. ], \n [1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ]]) \n>>> from math import atan2 \n>>> \u03b8 = [ atan2 ( y , x ) for y , x in zip ( y_disk , x_disk )] \n>>> max ( \u03b8 ) \n3.141592653589793 \n>>> min ( \u03b8 ) \n-2.9845130209101467 \n\n
(xvals , yvals ): ", "funcdef": "def"}, "pydrex.io": {"fullname": "pydrex.io", "modulename": "pydrex.io", "kind": "module", "doc": "\n PyDRex: Mesh, configuration and supporting data Input/Output functions.
\n \n\nPyDRex can read/write three kinds of plain text files:
\n\n\nPyDRex configuration files, which specify simulation parameters and initial conditions \n'SCSV' files, CSV files with YAML frontmatter for (small) scientific datasets \nMesh files via meshio, to set up final mineral positions in steady flows. \n \n\nSCSV files are our custom CSV files with a YAML header. The header is used for data\nattribution and metadata, as well as a column type spec. There is no official spec for\nSCSV files at the moment but they should follow the format of existing SCSV files in\nthe data/ folder of the source repository. For supported cell types, see\nSCSV_TYPEMAP.
\n"}, "pydrex.io.DEFAULT_PARAMS": {"fullname": "pydrex.io.DEFAULT_PARAMS", "modulename": "pydrex.io", "qualname": "DEFAULT_PARAMS", "kind": "variable", "doc": "Default simulation parameters.
\n", "default_value": "{'olivine_fraction': 1.0, 'enstatite_fraction': 0.0, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5.0, 'number_of_grains': 3500, 'initial_olivine_fabric': 'A'}"}, "pydrex.io.SCSV_TYPEMAP": {"fullname": "pydrex.io.SCSV_TYPEMAP", "modulename": "pydrex.io", "qualname": "SCSV_TYPEMAP", "kind": "variable", "doc": "Mapping of supported SCSV field types to corresponding Python types.
\n", "default_value": "{'string': <class 'str'>, 'integer': <class 'int'>, 'float': <class 'float'>, 'boolean': <class 'bool'>, 'complex': <class 'complex'>}"}, "pydrex.io.read_scsv": {"fullname": "pydrex.io.read_scsv", "modulename": "pydrex.io", "qualname": "read_scsv", "kind": "function", "doc": "Read data from an SCSV file.
\n\nPrints the YAML header section to output and returns a NamedTuple with columns of\nthe csv data. See also save_scsv.
\n", "signature": "(file ): ", "funcdef": "def"}, "pydrex.io.write_scsv_header": {"fullname": "pydrex.io.write_scsv_header", "modulename": "pydrex.io", "qualname": "write_scsv_header", "kind": "function", "doc": "Write YAML header to an SCSV stream.
\n\nArgs:
\n\n\nstream \u2014 open output stream (e.g. file handle) where data should be writtenschema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keyscomments (optional) \u2014 array of comments to be written above the schema, each on\na new line with an '#' prefix \n\nSee also read_scsv, save_scsv.
\n", "signature": "(stream , schema , comments = None ): ", "funcdef": "def"}, "pydrex.io.save_scsv": {"fullname": "pydrex.io.save_scsv", "modulename": "pydrex.io", "qualname": "save_scsv", "kind": "function", "doc": "Save data to SCSV file.
\n\nArgs:
\n\n\nfile \u2014 path to the file where the data should be writtenschema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keysdata \u2014 data arrays (columns) of equal length \n\nOptional keyword arguments are passed to write_scsv_header. See also read_scsv.
\n", "signature": "(file , schema , data , ** kwargs ): ", "funcdef": "def"}, "pydrex.io.parse_config": {"fullname": "pydrex.io.parse_config", "modulename": "pydrex.io", "qualname": "parse_config", "kind": "function", "doc": "Parse a TOML file containing PyDRex configuration.
\n", "signature": "(path ): ", "funcdef": "def"}, "pydrex.io.resolve_path": {"fullname": "pydrex.io.resolve_path", "modulename": "pydrex.io", "qualname": "resolve_path", "kind": "function", "doc": "Resolve relative paths and create parent directories if necessary.
\n\nRelative paths are interpreted with respect to the current working directory,\ni.e. the directory from whith the current Python process was executed,\nunless a specific reference directory is provided with refdir.
\n", "signature": "(path , refdir = None ): ", "funcdef": "def"}, "pydrex.io.stringify": {"fullname": "pydrex.io.stringify", "modulename": "pydrex.io", "qualname": "stringify", "kind": "function", "doc": "Return a cleaned version of a string for use in filenames, etc.
\n", "signature": "(s ): ", "funcdef": "def"}, "pydrex.io.data": {"fullname": "pydrex.io.data", "modulename": "pydrex.io", "qualname": "data", "kind": "function", "doc": "Get resolved path to a pydrex data directory.
\n", "signature": "(directory ): ", "funcdef": "def"}, "pydrex.logger": {"fullname": "pydrex.logger", "modulename": "pydrex.logger", "kind": "module", "doc": "\n PyDRex: logger settings and boilerplate.
\n \n\nPython's logging module is weird and its methods don't allow us to specify\nwhich logger to use, so just using logging.debug for example always uses\nthe \"root\" logger, which spams a bunch of messages from other imports/modules.\nInstead, the methods in this module are thin wrappers that use custom\nlogging objects (pydrex.logger.LOGGER and pydrex.logger.CONSOLE_LOGGER).\nThe method quiet_aliens can be invoked to suppress most messages\nfrom third-party modules, except critical errors and warnings from Numba.
\n\nBy default, PyDRex emits INFO level messages to the console.\nThis can be changed globally by setting the new level with CONSOLE_LOGGER.setLevel:
\n\n\n
from pydrex import logger as _log \n_log . info ( "this message will be printed to the console" ) \n\n_log . CONSOLE_LOGGER . setLevel ( "ERROR" ) \n_log . info ( "this message will NOT be printed to the console" ) \n_log . error ( "this message will be printed to the console" ) \n\n
To change the console logging level for a particular local context,\nuse the handler_level context manager:
\n\n\n
_log . CONSOLE_LOGGER . setLevel ( "INFO" ) \n_log . info ( "this message will be printed to the console" ) \n\nwith handler_level ( "ERROR" ): \n _log . info ( "this message will NOT be printed to the console" ) \n\n_log . info ( "this message will be printed to the console" ) \n\n
To save debug logs to a file, the logfile_enable context manager is recommended.\nAlways use the old printf style formatting for log messages, not fstrings,\notherwise compute time will be wasted on string conversions when logging is disabled:
\n\n\n
_log . quiet_aliens () # Suppress third-party log messages except CRITICAL from Numba. \nwith _log . logfile_enable ( "my_log_file.log" ): # Overwrite existing file unless mode="a". \n value = 42 \n _log . critical ( "critical error with value: %s " , value ) \n _log . error ( "runtime error with value: %s " , value ) \n _log . warning ( "warning with value: %s " , value ) \n _log . info ( "information message with value: %s " , value ) \n _log . debug ( "verbose debugging message with value: %s " , value ) \n ... # Construct Minerals, update orientations, etc. \n\n
Log formatter that uses terminal color codes.
\n", "bases": "logging.Formatter"}, "pydrex.logger.ConsoleFormatter.colorfmt": {"fullname": "pydrex.logger.ConsoleFormatter.colorfmt", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.colorfmt", "kind": "function", "doc": "
\n", "signature": "(self , code ): ", "funcdef": "def"}, "pydrex.logger.ConsoleFormatter.format": {"fullname": "pydrex.logger.ConsoleFormatter.format", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter.format", "kind": "function", "doc": "Format the specified record as text.
\n\nThe record's attribute dictionary is used as the operand to a\nstring formatting operation which yields the returned string.\nBefore formatting the dictionary, a couple of preparatory steps\nare carried out. The message attribute of the record is computed\nusing LogRecord.getMessage(). If the formatting string uses the\ntime (as determined by a call to usesTime(), formatTime() is\ncalled to format the event time. If there is exception information,\nit is formatted using formatException() and appended to the message.
\n", "signature": "(self , record ): ", "funcdef": "def"}, "pydrex.logger.LOGGER": {"fullname": "pydrex.logger.LOGGER", "modulename": "pydrex.logger", "qualname": "LOGGER", "kind": "variable", "doc": "
\n", "default_value": "<Logger pydrex (DEBUG)>"}, "pydrex.logger.CONSOLE_LOGGER": {"fullname": "pydrex.logger.CONSOLE_LOGGER", "modulename": "pydrex.logger", "qualname": "CONSOLE_LOGGER", "kind": "variable", "doc": "
\n", "default_value": "<StreamHandler (INFO)>"}, "pydrex.logger.handle_exception": {"fullname": "pydrex.logger.handle_exception", "modulename": "pydrex.logger", "qualname": "handle_exception", "kind": "function", "doc": "
\n", "signature": "(exec_type , exec_value , exec_traceback ): ", "funcdef": "def"}, "pydrex.logger.handler_level": {"fullname": "pydrex.logger.handler_level", "modulename": "pydrex.logger", "qualname": "handler_level", "kind": "function", "doc": "Set logging handler level for current context.
\n\nArgs:
\n\n\nlevel (string) \u2014 logging level name e.g. \"DEBUG\", \"ERROR\", etc.\nSee Python's logging module for details.handler (optional, logging.Handler) \u2014 alternative handler to control instead\nof the default, CONSOLE_LOGGER. \n", "signature": "(level , handler =< StreamHandler ( INFO ) > ): ", "funcdef": "def"}, "pydrex.logger.logfile_enable": {"fullname": "pydrex.logger.logfile_enable", "modulename": "pydrex.logger", "qualname": "logfile_enable", "kind": "function", "doc": "Enable logging to a file at path with given level.
\n", "signature": "(path , level = 10 , mode = 'w' ): ", "funcdef": "def"}, "pydrex.logger.critical": {"fullname": "pydrex.logger.critical", "modulename": "pydrex.logger", "qualname": "critical", "kind": "function", "doc": "Log a CRITICAL message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.error": {"fullname": "pydrex.logger.error", "modulename": "pydrex.logger", "qualname": "error", "kind": "function", "doc": "Log an ERROR message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.warning": {"fullname": "pydrex.logger.warning", "modulename": "pydrex.logger", "qualname": "warning", "kind": "function", "doc": "Log a WARNING message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.info": {"fullname": "pydrex.logger.info", "modulename": "pydrex.logger", "qualname": "info", "kind": "function", "doc": "Log an INFO message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.debug": {"fullname": "pydrex.logger.debug", "modulename": "pydrex.logger", "qualname": "debug", "kind": "function", "doc": "Log a DEBUG message in PyDRex.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.exception": {"fullname": "pydrex.logger.exception", "modulename": "pydrex.logger", "qualname": "exception", "kind": "function", "doc": "Log a message with level ERROR but retain exception information.
\n\nThis function should only be called from an exception handler.
\n", "signature": "(msg , * args , ** kwargs ): ", "funcdef": "def"}, "pydrex.logger.quiet_aliens": {"fullname": "pydrex.logger.quiet_aliens", "modulename": "pydrex.logger", "qualname": "quiet_aliens", "kind": "function", "doc": "Restrict alien loggers \ud83d\udc7d because I'm trying to find MY bugs, thanks.
\n", "signature": "(): ", "funcdef": "def"}, "pydrex.minerals": {"fullname": "pydrex.minerals", "modulename": "pydrex.minerals", "kind": "module", "doc": "\n PyDRex: Computations of mineral texture and elasticity.
\n \n\nAcronyms:
\n\n\nCPO = Crystallographic preferred orientation,\ni.e. preferential clustering of polycrystal grain orientations in SO(3),\nleading to an overall anisotropic orientation distribution \n \n"}, "pydrex.minerals.OLIVINE_STIFFNESS": {"fullname": "pydrex.minerals.OLIVINE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_STIFFNESS", "kind": "variable", "doc": "Stiffness tensor for olivine (Voigt representation), with units of GPa.
\n\nThe source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz \n[88K download]
\n", "default_value": "array([[320.71, 69.84, 71.22, 0. , 0. , 0. ],\n [ 69.84, 197.25, 74.8 , 0. , 0. , 0. ],\n [ 71.22, 74.8 , 234.32, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 63.77, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 77.67, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 78.36]])"}, "pydrex.minerals.ENSTATITE_STIFFNESS": {"fullname": "pydrex.minerals.ENSTATITE_STIFFNESS", "modulename": "pydrex.minerals", "qualname": "ENSTATITE_STIFFNESS", "kind": "variable", "doc": "Stiffness tensor for enstatite (Voigt representation), with units of GPa.
\n\nThe source of the values used here is unknown, but they are copied\nfrom the original DRex code: http://www.ipgp.fr/~kaminski/web_doudoud/DRex.tar.gz \n[88K download]
\n", "default_value": "array([[236.9, 79.6, 63.2, 0. , 0. , 0. ],\n [ 79.6, 180.5, 56.8, 0. , 0. , 0. ],\n [ 63.2, 56.8, 230.4, 0. , 0. , 0. ],\n [ 0. , 0. , 0. , 84.3, 0. , 0. ],\n [ 0. , 0. , 0. , 0. , 79.4, 0. ],\n [ 0. , 0. , 0. , 0. , 0. , 80.1]])"}, "pydrex.minerals.OLIVINE_PRIMARY_AXIS": {"fullname": "pydrex.minerals.OLIVINE_PRIMARY_AXIS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_PRIMARY_AXIS", "kind": "variable", "doc": "Primary slip axis name for for the given olivine fabric.
\n", "default_value": "{<MineralFabric.olivine_A: 0>: 'a', <MineralFabric.olivine_B: 1>: 'c', <MineralFabric.olivine_C: 2>: 'c', <MineralFabric.olivine_D: 3>: 'a', <MineralFabric.olivine_E: 4>: 'a'}"}, "pydrex.minerals.OLIVINE_SLIP_SYSTEMS": {"fullname": "pydrex.minerals.OLIVINE_SLIP_SYSTEMS", "modulename": "pydrex.minerals", "qualname": "OLIVINE_SLIP_SYSTEMS", "kind": "variable", "doc": "Slip systems for olivine in conventional order.
\n\nTuples contain the slip plane normal and slip direction vectors.\nThe order of slip systems returned matches the order of critical shear stresses\nreturned by pydrex.core.get_crss.
\n", "default_value": "(([0, 1, 0], [1, 0, 0]), ([0, 0, 1], [1, 0, 0]), ([0, 1, 0], [0, 0, 1]), ([1, 0, 0], [0, 0, 1]))"}, "pydrex.minerals.voigt_averages": {"fullname": "pydrex.minerals.voigt_averages", "modulename": "pydrex.minerals", "qualname": "voigt_averages", "kind": "function", "doc": "Calculate elastic tensors as the Voigt averages of a collection of minerals.
\n\nArgs:
\n\n\nminerals \u2014 list of pydrex.minerals.Mineral instances storing orientations and\nfractional volumes of the grains within each distinct mineral phaseweights (dict) \u2014 dictionary containing weights of each mineral\nphase, as a fraction of 1, in keys named \"_fraction\",\ne.g. \"olivine_fraction\" \n\nRaises a ValueError if the minerals contain an unequal number of grains or stored\ntexture results.
\n", "signature": "(minerals , weights ): ", "funcdef": "def"}, "pydrex.minerals.Mineral": {"fullname": "pydrex.minerals.Mineral", "modulename": "pydrex.minerals", "qualname": "Mineral", "kind": "class", "doc": "Class for storing polycrystal texture for a single mineral phase.
\n\nA Mineral stores texture data for an aggregate of grains*.\nAdditionally, mineral fabric type and deformation regime are also tracked.\nTo provide an initial texture for the mineral, use the constructor arguments\nfractions_init and orientations_init. By default,\na uniform volume distribution of random orientations is generated.
\n\nThe update_orientations method computes new orientations and grain volumes\nfor a given velocity gradient. These results are stored in the .orientations and\n.fractions attributes of the Mineral instance. The method also returns the\nupdated macroscopic deformation gradient based on the provided initial deformation\ngradient.
\n\n*Note that the \"number of grains\" is a static integer value that\ndoes not track the actual number of physical grains in the deforming polycrystal.\nInstead, this number acts as a \"number of bins\" for the statistical resolution of\nthe crystallographic orientation distribution. The value is roughly equivalent to\n(a multiple of) the number of initial, un-recrystallised grains in the polycrystal.\nIt is assumed that recrystallised grains do not grow large enough to require\nrotation tracking.
\n\nExamples:
\n\nMineral with isotropic initial texture:
\n\n\n
>>> import pydrex \n>>> olA = pydrex . Mineral ( \n... phase = pydrex . MineralPhase . olivine , \n... fabric = pydrex . MineralFabric . olivine_A , \n... regime = pydrex . DeformationRegime . dislocation , \n... n_grains = 2000 \n... ) \n>>> olA . phase \n<MineralPhase.olivine: 0> \n>>> olA . fabric \n<MineralFabric.olivine_A: 0> \n>>> olA . regime \n<DeformationRegime.dislocation: 1> \n>>> olA . n_grains \n2000 \n\n
Mineral with specified initial texture and default phase, fabric and regime settings\nwhich are for an olivine A-type mineral in the dislocation creep regime.\nThe initial grain volume fractions should be normalised.
\n\n\n
>>> import numpy as np \n>>> from scipy.spatial.transform import Rotation \n>>> import pydrex \n>>> rng = np . random . default_rng () \n>>> n_grains = 2000 \n>>> olA = pydrex . Mineral ( \n... n_grains = n_grains , \n... fractions_init = np . full ( n_grains , 1 / n_grains ), \n... orientations_init = Rotation . from_euler ( \n... "zxz" , [ \n... [ x * np . pi / 2 , np . pi / 2 , np . pi / 2 ] for x in rng . random ( n_grains ) \n... ] \n... ) . inv () . as_matrix (), \n... ) \n>>> len ( olA . orientations ) \n1 \n>>> type ( olA . orientations ) \n<class 'list'> \n>>> olA . orientations [ 0 ] . shape \n(2000, 3, 3) \n>>> olA . fractions [ 0 ] . shape \n(2000,) \n\n
Note that minerals can also be constructed from serialized data,\nsee Mineral.load and Mineral.from_file.
\n\nAttributes:
\n\n\nphase (pydrex.core.MineralPhase) \u2014 ordinal number of the mineral phasefabric (pydrex.core.MineralFabric) \u2014 ordinal number of the fabric typeregime (pydrex.core.DeformationRegime) \u2014 ordinal number of the deformation\nregimen_grains (int) \u2014 number of grains in the aggregatefractions (list of arrays) \u2014 grain volume fractions for each texture snapshotorientations (list of arrays) \u2014 grain orientation matrices for each texture\nsnapshotseed (int) \u2014 seed used by the random number generator to set up the isotropic\ninitial condition when fractions_init or orientations_init are not providedlband (int) \u2014 passed to the scipy.integrate.LSODA solveruband (int) \u2014 passed to the scipy.integrate.LSODA solver \n"}, "pydrex.minerals.Mineral.__init__": {"fullname": "pydrex.minerals.Mineral.__init__", "modulename": "pydrex.minerals", "qualname": "Mineral.__init__", "kind": "function", "doc": "
\n", "signature": "(\tphase : int = < MineralPhase . olivine : 0 > , \tfabric : int = < MineralFabric . olivine_A : 0 > , \tregime : int = < DeformationRegime . dislocation : 1 > , \tn_grains : int = 3500 , \tfractions_init : numpy . ndarray = None , \torientations_init : numpy . ndarray = None , \tfractions : list = < factory > , \torientations : list = < factory > , \tseed : int = None , \tlband : int = None , \tuband : int = None ) "}, "pydrex.minerals.Mineral.phase": {"fullname": "pydrex.minerals.Mineral.phase", "modulename": "pydrex.minerals", "qualname": "Mineral.phase", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "<MineralPhase.olivine: 0>"}, "pydrex.minerals.Mineral.fabric": {"fullname": "pydrex.minerals.Mineral.fabric", "modulename": "pydrex.minerals", "qualname": "Mineral.fabric", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "<MineralFabric.olivine_A: 0>"}, "pydrex.minerals.Mineral.regime": {"fullname": "pydrex.minerals.Mineral.regime", "modulename": "pydrex.minerals", "qualname": "Mineral.regime", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "<DeformationRegime.dislocation: 1>"}, "pydrex.minerals.Mineral.n_grains": {"fullname": "pydrex.minerals.Mineral.n_grains", "modulename": "pydrex.minerals", "qualname": "Mineral.n_grains", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "3500"}, "pydrex.minerals.Mineral.fractions_init": {"fullname": "pydrex.minerals.Mineral.fractions_init", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions_init", "kind": "variable", "doc": "
\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.orientations_init": {"fullname": "pydrex.minerals.Mineral.orientations_init", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations_init", "kind": "variable", "doc": "
\n", "annotation": ": numpy.ndarray", "default_value": "None"}, "pydrex.minerals.Mineral.fractions": {"fullname": "pydrex.minerals.Mineral.fractions", "modulename": "pydrex.minerals", "qualname": "Mineral.fractions", "kind": "variable", "doc": "
\n", "annotation": ": list"}, "pydrex.minerals.Mineral.orientations": {"fullname": "pydrex.minerals.Mineral.orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.orientations", "kind": "variable", "doc": "
\n", "annotation": ": list"}, "pydrex.minerals.Mineral.seed": {"fullname": "pydrex.minerals.Mineral.seed", "modulename": "pydrex.minerals", "qualname": "Mineral.seed", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.lband": {"fullname": "pydrex.minerals.Mineral.lband", "modulename": "pydrex.minerals", "qualname": "Mineral.lband", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.uband": {"fullname": "pydrex.minerals.Mineral.uband", "modulename": "pydrex.minerals", "qualname": "Mineral.uband", "kind": "variable", "doc": "
\n", "annotation": ": int", "default_value": "None"}, "pydrex.minerals.Mineral.update_orientations": {"fullname": "pydrex.minerals.Mineral.update_orientations", "modulename": "pydrex.minerals", "qualname": "Mineral.update_orientations", "kind": "function", "doc": "Update orientations and volume distribution for the Mineral.
\n\nUpdate crystalline orientations and grain volume distribution\nfor minerals undergoing plastic deformation. Return the updated deformation\ngradient measuring the corresponding macroscopic deformation.
\n\nArgs:
\n\n\nconfig (dict) \u2014 PyDRex configuration dictionarydeformation_gradient (array) \u2014 3x3 initial deformation gradient tensorget_velocity_gradient (function) \u2014 callable with signature f(x) that returns\na 3x3 velocity gradient matrix at position x (vector)pathline (tuple) \u2014 tuple consisting of:\n\nthe time at which to start the CPO integration (t_start) \nthe time at which to stop the CPO integration (t_end) \ncallable with signature f(t) that returns the position of the mineral at\ntime t \u2208 [t_start, t_end] \n \n\nAny additional (optional) keyword arguments are passed to\nscipy.integrate.LSODA.
\n\nArray values must provide a NumPy-compatible interface:\nhttps://numpy.org/doc/stable/user/whatisnumpy.html
\n", "signature": "(\tself , \tconfig , \tdeformation_gradient , \tget_velocity_gradient , \tpathline , \t** kwargs ): ", "funcdef": "def"}, "pydrex.minerals.Mineral.save": {"fullname": "pydrex.minerals.Mineral.save", "modulename": "pydrex.minerals", "qualname": "Mineral.save", "kind": "function", "doc": "Save CPO data for all stored timesteps to a numpy NPZ file.
\n\nIf postfix is not None, the data is appended to the NPZ file\nin fields ending with \"_postfix\".
\n\nRaises a ValueError if the data shapes are not compatible.
\n\nSee also: numpy.savez, Mineral.load, Mineral.from_file.
\n", "signature": "(self , filename , postfix = None ): ", "funcdef": "def"}, "pydrex.minerals.Mineral.load": {"fullname": "pydrex.minerals.Mineral.load", "modulename": "pydrex.minerals", "qualname": "Mineral.load", "kind": "function", "doc": "Load CPO data from a numpy NPZ file.
\n\nIf postfix is not None, data is read from fields ending with \"_postfix\".
\n\nSee also: Mineral.save, Mineral.from_file.
\n", "signature": "(self , filename , postfix = None ): ", "funcdef": "def"}, "pydrex.minerals.Mineral.from_file": {"fullname": "pydrex.minerals.Mineral.from_file", "modulename": "pydrex.minerals", "qualname": "Mineral.from_file", "kind": "function", "doc": "Construct a Mineral instance using data from a numpy NPZ file.
\n\nIf postfix is not None, data is read from fields ending with \u201c_postfix\u201d.
\n\nSee also: Mineral.save, Mineral.load.
\n", "signature": "(cls , filename , postfix = None ): ", "funcdef": "def"}, "pydrex.mock": {"fullname": "pydrex.mock", "modulename": "pydrex.mock", "kind": "module", "doc": "\n PyDRex: Mock objects for testing and reproducibility.
\n \n"}, "pydrex.mock.PARAMS_FRATERS2021": {"fullname": "pydrex.mock.PARAMS_FRATERS2021", "modulename": "pydrex.mock", "qualname": "PARAMS_FRATERS2021", "kind": "variable", "doc": "Values used for tests 1, 2 and 4 in https://doi.org/10.1029/2021gc009846 .
\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.3, 'nucleation_efficiency': 5, 'number_of_grains': 5000}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SOLID", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SOLID", "kind": "variable", "doc": "Values used for the M*=0 test in https://doi.org/10.1016/s0012-821x(01)00356-9 .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 0, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_SHORTDASH", "kind": "variable", "doc": "Values used for the M*=50 test in https://doi.org/10.1016/s0012-821x(01)00356-9 .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 50, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2001_FIG5_LONGDASH", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2001_FIG5_LONGDASH", "kind": "variable", "doc": "Values used for the M*=200 test in https://doi.org/10.1016/s0012-821x(01)00356-9 .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 200, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 3375}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_TRIANGLES", "kind": "variable", "doc": "Values used for the \u03c7=0.4 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.4, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_SQUARES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_SQUARES", "kind": "variable", "doc": "Values used for the \u03c7=0.2 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES": {"fullname": "pydrex.mock.PARAMS_KAMINSKI2004_FIG4_CIRCLES", "modulename": "pydrex.mock", "qualname": "PARAMS_KAMINSKI2004_FIG4_CIRCLES", "kind": "variable", "doc": "Values used for the \u03c7=0 test in https://doi.org/10.1111/j.1365-246x.2004.02308.x .
\n", "default_value": "{'olivine_fraction': 1, 'enstatite_fraction': 0, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 125, 'gbs_threshold': 0, 'nucleation_efficiency': 5, 'number_of_grains': 4394}"}, "pydrex.mock.PARAMS_HEDJAZIAN2017": {"fullname": "pydrex.mock.PARAMS_HEDJAZIAN2017", "modulename": "pydrex.mock", "qualname": "PARAMS_HEDJAZIAN2017", "kind": "variable", "doc": "Values used for the MOR model in https://doi.org/10.1016/j.epsl.2016.12.004 .
\n", "default_value": "{'olivine_fraction': 0.7, 'enstatite_fraction': 0.3, 'initial_olivine_fabric': <MineralFabric.olivine_A: 0>, 'stress_exponent': 1.5, 'deformation_exponent': 3.5, 'gbm_mobility': 10, 'gbs_threshold': 0.2, 'nucleation_efficiency': 5, 'number_of_grains': 2197}"}, "pydrex.pathlines": {"fullname": "pydrex.pathlines", "modulename": "pydrex.pathlines", "kind": "module", "doc": "\n PyDRex: Functions for pathline construction.
\n \n"}, "pydrex.pathlines.get_pathline": {"fullname": "pydrex.pathlines.get_pathline", "modulename": "pydrex.pathlines", "qualname": "get_pathline", "kind": "function", "doc": "Determine the pathline for a particle in a steady state flow.
\n\nThe pathline will terminate at the given final_location and follow a curve\ndetermined by the velocity gradient. It works for both 2D (rectangular) and 3D\n(orthopiped\u00b9) domains, so long as the provided callables expect/return arrays of the\nappropriate dimension.
\n\n\n\n
The pathline is calculated backwards in time (t < 0) from the given endpoint.\nTherefore, the returned position callable should be evaluated at negative times.
\n\n
Args:
\n\n\nfinal_location (array) \u2014 coordinates of the final locationget_velocity (callable) \u2014 returns velocity vector at a pointget_velocity_gradient (callable) \u2014 returns velocity gradient matrix at a pointmin_coords (array) \u2014 lower bound coordinates of the boxmax_coords (array) \u2014 upper bound coordinates of the boxmax_strain (float) \u2014 target strain (given as \u201ctensorial\u201d strain \u03b5) at the final\nlocation, useful if the pathline never inflows into the domain (the pathline will\nonly be traced backwards until a strain of 0 is reached, unless a domain boundary\nis reached first)regular_steps (float, optional) \u2014 number of time steps to use for regular\nresampling between the start (t << 0) and end (t <= 0) of the pathline\n(if None, which is the default, then the timestamps obtained from\nscipy.integrate.solve_ivp are returned instead) \n\nOptional keyword arguments will be passed to scipy.integrate.solve_ivp. However,\nsome of the arguments to the solve_ivp call may not be modified, and a warning\nwill be raised if they are provided.
\n\nReturns a tuple containing the time points and an interpolant that can be used\nto evaluate the pathline position (see scipy.integrate.OdeSolution).
\n\n\u00b9An \u201corthopiped\u201d is a 3D rectangle (called a \u201cbox\u201d when we are in a hurry), see\nhttps://www.whatistoday.net/2020/04/cuboid-dilemma.html .
\n", "signature": "(\tfinal_location , \tget_velocity , \tget_velocity_gradient , \tmin_coords , \tmax_coords , \tmax_strain , \tregular_steps = None , \t** kwargs ): ", "funcdef": "def"}, "pydrex.stats": {"fullname": "pydrex.stats", "modulename": "pydrex.stats", "kind": "module", "doc": "\n PyDRex: Statistical methods for orientation and elasticity data.
\n \n"}, "pydrex.stats.resample_orientations": {"fullname": "pydrex.stats.resample_orientations", "modulename": "pydrex.stats", "qualname": "resample_orientations", "kind": "function", "doc": "Return new samples from orientations weighted by the volume distribution.
\n\nArgs:
\n\n\norientations (array) \u2014 NxMx3x3 array of orientationsfractions (array) \u2014 NxM array of grain volume fractionsn_samples (int) \u2014 optional number of samples to return, default is Mseed (int) \u2014 optional seed for the random number generator, which is used to\npick random grain volume samples from the discrete distribution \n\nReturns the Nxn_samplesx3x3 orientations and associated sorted (ascending) grain\nvolumes.
\n", "signature": "(orientations , fractions , n_samples = None , seed = None ): ", "funcdef": "def"}, "pydrex.stats.misorientation_hist": {"fullname": "pydrex.stats.misorientation_hist", "modulename": "pydrex.stats", "qualname": "misorientation_hist", "kind": "function", "doc": "Calculate misorientation histogram for polycrystal orientations.
\n\nThe bins argument is passed to numpy.histogram.\nIf left as None, 1\u00b0 bins will be used as recommended by the reference paper.\nThe symmetry argument specifies the lattice system which determines intrinsic\nsymmetry degeneracies and the maximum allowable misorientation angle.\nSee _geo.LatticeSystem for supported systems.
\n\n\n\n
This method must be able to allocate an array of shape\n$ \\frac{N!}{2(N-2)!}\u00d7 M^{2} $\nfor N the length of orientations and M the number of symmetry operations for\nthe given system.
\n\n
See Skemer et al. (2005) .
\n", "signature": "(orientations , system : pydrex . geometry . LatticeSystem , bins = None ): ", "funcdef": "def"}, "pydrex.stats.misorientations_random": {"fullname": "pydrex.stats.misorientations_random", "modulename": "pydrex.stats", "qualname": "misorientations_random", "kind": "function", "doc": "Get expected count of misorientation angles for an isotropic aggregate.
\n\nEstimate the expected number of misorientation angles between grains\nthat would fall within $($low, high$)$ in degrees for an aggregate\nwith randomly oriented grains, where low $\u2208 [0, $high$)$,\nand high is bounded by the maximum theoretical misorientation angle\nfor the given lattice symmetry system.\nSee _geo.LatticeSystem for supported systems.
\n", "signature": "(low , high , system : pydrex . geometry . LatticeSystem ): ", "funcdef": "def"}, "pydrex.stats.point_density": {"fullname": "pydrex.stats.point_density", "modulename": "pydrex.stats", "qualname": "point_density", "kind": "function", "doc": "Estimate point density of orientation data on the unit sphere.
\n\nEstimates the density of orientations on the unit sphere by counting the input data\nthat falls within small areas around a uniform grid of spherical counting locations.\nThe input data is expected in cartesian coordinates, and the contouring is performed\nusing kernel functions defined in Vollmer 1995 .\nThe following optional parameters control the contouring method:
\n\n\ngridsteps (int) \u2014 the number of steps, i.e. number of points along a diameter of\nthe spherical counting gridweights (array) \u2014 auxiliary weights for each data pointkernel (string) \u2014 the name of the kernel function to use, see\nSPHERICAL_COUNTING_KERNELSaxial (bool) \u2014 toggle axial versions of the kernel functions\n(for crystallographic data this should normally be kept as True) \n\nAny other keyword arguments are passed to the kernel function calls.\nMost kernels accept a parameter \u03c3 to control the degree of smoothing.
\n", "signature": "(\tx_data , \ty_data , \tz_data , \tgridsteps = 101 , \tweights = 1 , \tkernel = 'linear_inverse_kamb' , \taxial = True , \t** kwargs ): ", "funcdef": "def"}, "pydrex.stats.exponential_kamb": {"fullname": "pydrex.stats.exponential_kamb", "modulename": "pydrex.stats", "qualname": "exponential_kamb", "kind": "function", "doc": "Kernel function from Vollmer 1995 for exponential smoothing.
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.linear_inverse_kamb": {"fullname": "pydrex.stats.linear_inverse_kamb", "modulename": "pydrex.stats", "qualname": "linear_inverse_kamb", "kind": "function", "doc": "Kernel function from Vollmer 1995 for linear smoothing.
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.square_inverse_kamb": {"fullname": "pydrex.stats.square_inverse_kamb", "modulename": "pydrex.stats", "qualname": "square_inverse_kamb", "kind": "function", "doc": "Kernel function from Vollmer 1995 for inverse square smoothing.
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.kamb_count": {"fullname": "pydrex.stats.kamb_count", "modulename": "pydrex.stats", "qualname": "kamb_count", "kind": "function", "doc": "Original Kamb 1959 kernel function (raw count within radius).
\n", "signature": "(cos_dist , \u03c3 = 10 , axial = True ): ", "funcdef": "def"}, "pydrex.stats.schmidt_count": {"fullname": "pydrex.stats.schmidt_count", "modulename": "pydrex.stats", "qualname": "schmidt_count", "kind": "function", "doc": "Schmidt (a.k.a. 1%) counting kernel function.
\n", "signature": "(cos_dist , axial = None ): ", "funcdef": "def"}, "pydrex.stats.SPHERICAL_COUNTING_KERNELS": {"fullname": "pydrex.stats.SPHERICAL_COUNTING_KERNELS", "modulename": "pydrex.stats", "qualname": "SPHERICAL_COUNTING_KERNELS", "kind": "variable", "doc": "Kernel functions that return an un-summed distribution and a normalization factor.
\n\nSupported kernel functions are based on the discussion in\nVollmer 1995 .\nKamb methods accept the parameter \u03c3 (default: 10) to control the degree of smoothing.\nValues lower than 3 and higher than 20 are not recommended.
\n", "default_value": "{'kamb_count': <function kamb_count>, 'schmidt_count': <function schmidt_count>, 'exponential_kamb': <function exponential_kamb>, 'linear_inverse_kamb': <function linear_inverse_kamb>, 'square_inverse_kamb': <function square_inverse_kamb>}"}, "pydrex.tensors": {"fullname": "pydrex.tensors", "modulename": "pydrex.tensors", "kind": "module", "doc": "\n PyDRex: Tensor operation functions and helpers.
\n \n\nFor Voigt notation, the symmetric 6x6 matrix representation is used,\nwhich assumes that the fourth order tensor being represented as such is also symmetric.\nThe vectorial notation uses 21 components which are the independent components of the\nsymmetric 6x6 matrix.
\n"}, "pydrex.tensors.PERMUTATION_SYMBOL": {"fullname": "pydrex.tensors.PERMUTATION_SYMBOL", "modulename": "pydrex.tensors", "qualname": "PERMUTATION_SYMBOL", "kind": "variable", "doc": "
\n", "default_value": "array([[[ 0., 0., 0.],\n [ 0., 0., 1.],\n [ 0., -1., 0.]],\n\n [[ 0., 0., -1.],\n [ 0., 0., 0.],\n [ 1., 0., 0.]],\n\n [[ 0., 1., 0.],\n [-1., 0., 0.],\n [ 0., 0., 0.]]])"}, "pydrex.tensors.voigt_decompose": {"fullname": "pydrex.tensors.voigt_decompose", "modulename": "pydrex.tensors", "qualname": "voigt_decompose", "kind": "function", "doc": "Decompose elastic tensor (as 6x6 Voigt matrix) into distinct contractions.
\n\nReturn the only two independent contractions of the elastic tensor given as a 6x6\nVoigt matrix. With reference to the full 4-th order elastic tensor, the\ncontractions are defined as:
\n\n\n$d_{ij} = C_{ijkk}$ (dilatational stiffness tensor) \n$v_{ij} = C_{ijkj}$ (deviatoric stiffness tensor) \n \n\nAny vector which is an eigenvector of both $d_{ij}$ and $v_{ij}$ is always normal to\na symmetry plane of the elastic medium.
\n\nSee Equations 3.4 & 3.5 in Browaeys & Chevrot (2004) .
\n", "signature": "(matrix ): ", "funcdef": "def"}, "pydrex.tensors.mono_project": {"fullname": "pydrex.tensors.mono_project", "modulename": "pydrex.tensors", "qualname": "mono_project", "kind": "function", "doc": "Project 21-component voigt_vector onto monoclinic symmetry subspace.
\n\nMonoclinic symmetry is characterised by 13 independent elasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.ortho_project": {"fullname": "pydrex.tensors.ortho_project", "modulename": "pydrex.tensors", "qualname": "ortho_project", "kind": "function", "doc": "Project 21-component voigt_vector onto orthorhombic symmetry subspace.
\n\nOrthorhombic symmetry is characterised by 9 independent elasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.tetr_project": {"fullname": "pydrex.tensors.tetr_project", "modulename": "pydrex.tensors", "qualname": "tetr_project", "kind": "function", "doc": "Project 21-component voigt_vector onto tetragonal symmetry subspace.
\n\nTetragonal symmetry is characterised by 6 independent elasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.hex_project": {"fullname": "pydrex.tensors.hex_project", "modulename": "pydrex.tensors", "qualname": "hex_project", "kind": "function", "doc": "Project 21-component voigt_vector onto hexagonal symmetry subspace.
\n\nHexagonal symmetry (a.k.a. transverse isotropy) is characterised by 5 independent\nelasticity components.
\n\nSee Browaeys & Chevrot (2004) .
\n", "signature": "(voigt_vector ): ", "funcdef": "def"}, "pydrex.tensors.upper_tri_to_symmetric": {"fullname": "pydrex.tensors.upper_tri_to_symmetric", "modulename": "pydrex.tensors", "qualname": "upper_tri_to_symmetric", "kind": "function", "doc": "Create symmetric array using upper triangle of input array.
\n\n\n
>>> import numpy as np \n>>> upper_tri_to_symmetric ( np . array ([ \n... [ 1. , 2. , 3. , 4. ], \n... [ 0. , 5. , 6. , 7. ], \n... [ 0. , 0. , 8. , 9. ], \n... [ 9. , 0. , 0. , 10. ] \n... ])) \narray([[ 1., 2., 3., 4.], \n [ 2., 5., 6., 7.], \n [ 3., 6., 8., 9.], \n [ 4., 7., 9., 10.]]) \n\n
(arr ): ", "funcdef": "def"}, "pydrex.tensors.voigt_to_elastic_tensor": {"fullname": "pydrex.tensors.voigt_to_elastic_tensor", "modulename": "pydrex.tensors", "qualname": "voigt_to_elastic_tensor", "kind": "function", "doc": "Create 4-th order elastic tensor from an equivalent Voigt matrix.
\n\nSee also: elastic_tensor_to_voigt.
\n", "signature": "(matrix ): ", "funcdef": "def"}, "pydrex.tensors.elastic_tensor_to_voigt": {"fullname": "pydrex.tensors.elastic_tensor_to_voigt", "modulename": "pydrex.tensors", "qualname": "elastic_tensor_to_voigt", "kind": "function", "doc": "Create a 6x6 Voigt matrix from an equivalent 4-th order elastic tensor.
\n", "signature": "(tensor ): ", "funcdef": "def"}, "pydrex.tensors.voigt_matrix_to_vector": {"fullname": "pydrex.tensors.voigt_matrix_to_vector", "modulename": "pydrex.tensors", "qualname": "voigt_matrix_to_vector", "kind": "function", "doc": "Create the 21-component Voigt vector equivalent to the 6x6 Voigt matrix.
\n", "signature": "(matrix ): ", "funcdef": "def"}, "pydrex.tensors.voigt_vector_to_matrix": {"fullname": "pydrex.tensors.voigt_vector_to_matrix", "modulename": "pydrex.tensors", "qualname": "voigt_vector_to_matrix", "kind": "function", "doc": "Create the 6x6 matrix representation of the 21-component Voigt vector.
\n\nSee also: voigt_matrix_to_vector.
\n", "signature": "(vector ): ", "funcdef": "def"}, "pydrex.tensors.rotate": {"fullname": "pydrex.tensors.rotate", "modulename": "pydrex.tensors", "qualname": "rotate", "kind": "function", "doc": "Rotate 4-th order tensor using a 3x3 rotation matrix.
\n", "signature": "(tensor , rotation ): ", "funcdef": "def"}, "pydrex.utils": {"fullname": "pydrex.utils", "modulename": "pydrex.utils", "kind": "module", "doc": "\n PyDRex: Miscellaneous utility methods.
\n \n"}, "pydrex.utils.strain_increment": {"fullname": "pydrex.utils.strain_increment", "modulename": "pydrex.utils", "qualname": "strain_increment", "kind": "function", "doc": "Calculate strain increment for a given time increment and velocity gradient.
\n\nReturns \u201ctensorial\u201d strain increment \u03b5, which is equal to \u03b3/2 where \u03b3 is the\n\u201c(engineering) shear strain\u201d increment.
\n", "signature": "(dt , velocity_gradient ): ", "funcdef": "def"}, "pydrex.utils.apply_gbs": {"fullname": "pydrex.utils.apply_gbs", "modulename": "pydrex.utils", "qualname": "apply_gbs", "kind": "function", "doc": "Apply grain boundary sliding for small grains.
\n", "signature": "(orientations , fractions , gbs_threshold , orientations_prev , n_grains ): ", "funcdef": "def"}, "pydrex.utils.extract_vars": {"fullname": "pydrex.utils.extract_vars", "modulename": "pydrex.utils", "qualname": "extract_vars", "kind": "function", "doc": "Extract deformation gradient, orientation matrices and grain sizes from y.
\n", "signature": "(y , n_grains ): ", "funcdef": "def"}, "pydrex.utils.remove_nans": {"fullname": "pydrex.utils.remove_nans", "modulename": "pydrex.utils", "qualname": "remove_nans", "kind": "function", "doc": "Remove NaN values from array.
\n", "signature": "(a ): ", "funcdef": "def"}, "pydrex.utils.default_ncpus": {"fullname": "pydrex.utils.default_ncpus", "modulename": "pydrex.utils", "qualname": "default_ncpus", "kind": "function", "doc": "Get a safe default number of CPUs available for multiprocessing.
\n\nOn Linux platforms that support it, the method os.sched_getaffinity() is used.\nOn Mac OS, the command sysctl -n hw.ncpu is used.\nOn Windows, the environment variable NUMBER_OF_PROCESSORS is queried.\nIf any of these fail, a fallback of 1 is used and a warning is logged.
\n", "signature": "(): ", "funcdef": "def"}, "pydrex.utils.diff_like": {"fullname": "pydrex.utils.diff_like", "modulename": "pydrex.utils", "qualname": "diff_like", "kind": "function", "doc": "Get forward difference of 2D array a, with repeated last elements.
\n\nThe repeated last elements ensure that output and input arrays have equal shape.
\n\nExamples:
\n\n\n
>>> diff_like ( np . array ([ 1 , 2 , 3 , 4 , 5 ])) \narray([[1, 1, 1, 1, 1]]) \n\n
\n
>>> diff_like ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ]])) \narray([[1, 1, 1, 1, 1], \n [2, 3, 3, 1, 1]]) \n\n
\n
>>> diff_like ( np . array ([[ 1 , 2 , 3 , 4 , 5 ], [ 1 , 3 , 6 , 9 , 10 ], [ 1 , 0 , 0 , 0 , np . inf ]])) \narray([[ 1., 1., 1., 1., 1.], \n [ 2., 3., 3., 1., 1.], \n [-1., 0., 0., inf, nan]]) \n\n
(a ): ", "funcdef": "def"}, "pydrex.utils.angle_fse_simpleshear": {"fullname": "pydrex.utils.angle_fse_simpleshear", "modulename": "pydrex.utils", "qualname": "angle_fse_simpleshear", "kind": "function", "doc": "Get angle of FSE long axis anticlockwise from the X axis in simple shear.
\n", "signature": "(strain ): ", "funcdef": "def"}, "pydrex.utils.lag_2d_corner_flow": {"fullname": "pydrex.utils.lag_2d_corner_flow", "modulename": "pydrex.utils", "qualname": "lag_2d_corner_flow", "kind": "function", "doc": "Get predicted grain orientation lag for 2D corner flow.
\n\nSee eq. 11 in Kaminski & Ribe (2002) .
\n", "signature": "(\u03b8 ): ", "funcdef": "def"}, "pydrex.utils.quat_product": {"fullname": "pydrex.utils.quat_product", "modulename": "pydrex.utils", "qualname": "quat_product", "kind": "function", "doc": "Quaternion product, q1, q2 and output are in scalar-last (x,y,z,w) format.
\n", "signature": "(q1 , q2 ): ", "funcdef": "def"}, "pydrex.utils.redraw_legend": {"fullname": "pydrex.utils.redraw_legend", "modulename": "pydrex.utils", "qualname": "redraw_legend", "kind": "function", "doc": "Redraw legend on matplotlib axis or figure.
\n\nTransparency is removed from legend symbols.\nIf fig is not None and remove_all is True,\nall legends are first removed from the parent figure.\nOptional keyword arguments are passed to matplotlib.axes.Axes.legend by default,\nor matplotlib.figure.Figure.legend if fig is not None.
\n\nIf legendax is not None, the axis legend will be redrawn using the legendax axes\ninstead of taking up space in the original axes. This option requires fig=None.
\n\n\n\n
Note that if fig is not None, the legend may be cropped from the saved\nfigure due to a Matplotlib bug. In this case, it is required to add the\narguments bbox_extra_artists=(legend,) and bbox_inches=\"tight\" to savefig,\nwhere legend is the object returned by this function. To prevent the legend\nfrom consuming axes/subplot space, it is further required to add the lines:\nlegend.set_in_layout(False), fig.canvas.draw(), legend.set_layout(True)\nand fig.set_layout_engine(\"none\") before saving the figure.
\n\n
(ax , fig = None , legendax = None , remove_all = True , ** kwargs ): ", "funcdef": "def"}, "pydrex.utils.add_subplot_labels": {"fullname": "pydrex.utils.add_subplot_labels", "modulename": "pydrex.utils", "qualname": "add_subplot_labels", "kind": "function", "doc": "Add subplot labels to axes mosaic.
\n\nUse labelmap to specify a dictionary that maps keys in mosaic to subplot labels.\nIf labelmap is None, the keys in axs will be used as the labels by default.
\n\nIf internal is False (default), the axes titles will be used.\nOtherwise, internal labels will be drawn with ax.text,\nin which case loc must be a tuple of floats.
\n\nAny axes in axs corresponding to the special key legend are skipped.
\n", "signature": "(\tmosaic , \tlabelmap = None , \tloc = 'left' , \tfontsize = 'medium' , \tinternal = False , \t** kwargs ): ", "funcdef": "def"}, "pydrex.velocity": {"fullname": "pydrex.velocity", "modulename": "pydrex.velocity", "kind": "module", "doc": "\n PyDRex: Steady-state solutions of velocity (gradients) for various flows.
\n \n\nFor the sake of consistency, all callables returned from methods in this module expect a\n3D position vector as input. They also return 3D tensors in all cases. This means they\ncan be directly used as arguments to e.g. pydrex.minerals.Mineral.update_orientations.
\n"}, "pydrex.velocity.simple_shear_2d": {"fullname": "pydrex.velocity.simple_shear_2d", "modulename": "pydrex.velocity", "qualname": "simple_shear_2d", "kind": "function", "doc": "Return simple shear velocity and velocity gradient callables.
\n\nThe returned callables have signature f(x) where x is a 3D position vector.
\n\nArgs:
\n\n\ndirection (one of {\"X\", \"Y\", \"Z\"}) \u2014 velocity vector directiondeformation_plane (one of {\"X\", \"Y\", \"Z\"}) \u2014 direction of velocity gradientstrain_rate (float) \u2014 1/2 \u00d7 magnitude of the largest eigenvalue of the velocity\ngradient \n\n\n\n
Input arrays to the returned callables must have homogeneous element types.\nArrays with e.g. both floating point and integer values are not supported.
\n\n
Examples:
\n\n\n
>>> import numpy as np \n>>> u , L = simple_shear_2d ( "X" , "Z" , 1e-4 ) \n>>> u ( np . array ([ 0 , 0 , 0 ])) \narray([0., 0., 0.]) \n>>> u ( np . array ([ 0 , 0 , 1 ])) \narray([0.0001, 0. , 0. ]) \n>>> u ( np . array ([ 0.0 , 0.0 , 2.0 ])) \narray([0.0002, 0. , 0. ]) \n>>> L ( np . array ([ 0 , 0 , 0 ])) \narray([[0. , 0. , 0.0002], \n [0. , 0. , 0. ], \n [0. , 0. , 0. ]]) \n>>> L ( np . array ([ 0.0 , 0.0 , 1.0 ])) \narray([[0. , 0. , 0.0002], \n [0. , 0. , 0. ], \n [0. , 0. , 0. ]]) \n\n
(direction , deformation_plane , strain_rate ): ", "funcdef": "def"}, "pydrex.velocity.cell_2d": {"fullname": "pydrex.velocity.cell_2d", "modulename": "pydrex.velocity", "qualname": "cell_2d", "kind": "function", "doc": "Get velocity and velocity gradient callables for a steady-state 2D Stokes cell.
\n\nThe cell is centered at (0,0) and the velocity field is defined by:\n$$\n\\bm{u} = U\\cos(\u03c0 x/d)\\sin(\u03c0 z/d) \\bm{\\hat{h}} - U\\sin(\u03c0 x/d)\\cos(\u03c0 z/d) \\bm{\\hat{v}}\n$$\nwhere $\\bm{\\hat{h}}$ and $\\bm{\\hat{v}}$ are unit vectors in the chosen horizontal\nand vertical directions, respectively. The velocity at the cell edge has a magnitude\nof $U$ and $d$ is the length of a cell edge.
\n\nThe returned callables have signature f(x) where x is a 3D position vector.
\n\nArgs:
\n\n\nhorizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal directionvertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical directionvelocity_edge (float) \u2014 velocity magnitude at the center of the cell edgeedge_length (float, optional) \u2014 the edge length of the cell (= 2 by default) \n\nExamples:
\n\n\n
>>> import numpy as np \n>>> u , L = cell_2d ( "X" , "Z" , 1 ) \n>>> u ( np . array ([ 0 , 0 , 0 ])) \narray([ 0., 0., -0.]) \n>>> u ( np . array ([ 0 , 0 , 1 ])) \narray([ 1., 0., -0.]) \n>>> u ( np . array ([ 0 , 1 , 0 ])) # Y-value is not used. \narray([ 0., 0., -0.]) \n>>> u ( np . array ([ 0 , 0 , - 1 ])) \narray([-1., 0., -0.]) \n>>> u ( np . array ([ 1 , 0 , 0 ])) \narray([ 0., 0., -1.]) \n>>> u ( np . array ([ - 0.5 , 0.0 , 0.0 ])) \narray([0. , 0. , 0.70710678]) \n>>> L ( np . array ([ 0 , 0 , 0 ])) \narray([[-0. , 0. , 1.57079633], \n [ 0. , 0. , 0. ], \n [ 0. , 0. , -1.57079633]]) \n>>> L ( np . array ([ 0.5 , 0.0 , 0.0 ])) \narray([[-0. , 0. , 1.11072073], \n [ 0. , 0. , 0. ], \n [ 0. , 0. , -1.11072073]]) \n>>> L ( np . array ([ 0 , 0 , 0 ])) == L ( np . array ([ 0 , 1 , 0 ])) # Y-value is not used. \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 1 , 0 , 0 ])) == L ( np . array ([ 0 , 0 , 1 ])) \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 1 , 0 , 0 ])) == L ( np . array ([ - 1 , 0 , 0 ])) \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 1 , 0 , 0 ])) == L ( np . array ([ 0 , 0 , - 1 ])) \narray([[ True, True, True], \n [ True, True, True], \n [ True, True, True]]) \n>>> L ( np . array ([ 0.5 , 0.0 , 0.5 ])) \narray([[-0.78539816, 0. , 0.78539816], \n [ 0. , 0. , 0. ], \n [ 0.78539816, 0. , -0.78539816]]) \n\n
\n
>>> u , L = cell_2d ( "X" , "Z" , 6.3e-10 , 1e5 ) \n>>> u ( np . array ([ 0 , 0 , 0 ])) \narray([ 0., 0., -0.]) \n>>> u ( np . array ([ 0.0 , 0.0 , - 5e4 ])) \narray([-6.3e-10, 0.0e+00, -0.0e+00]) \n>>> u ( np . array ([ 2e2 , 0e0 , 0e0 ])) \narray([ 0.0000000e+00, 0.0000000e+00, -3.9583807e-12]) \n\n
(horizontal , vertical , velocity_edge , edge_length = 2 ): ", "funcdef": "def"}, "pydrex.velocity.corner_2d": {"fullname": "pydrex.velocity.corner_2d", "modulename": "pydrex.velocity", "qualname": "corner_2d", "kind": "function", "doc": "Get velocity and velocity gradient callables for a steady-state 2D corner flow.
\n\nThe velocity field is defined by:\n$$\n\\bm{u} = \\frac{dr}{dt} \\bm{\\hat{r}} + r \\frac{d\u03b8}{dt} \\bm{\\hat{\u03b8}}\n= \\frac{2 U}{\u03c0}(\u03b8\\sin\u03b8 - \\cos\u03b8) \u22c5 \\bm{\\hat{r}} + \\frac{2 U}{\u03c0}\u03b8\\cos\u03b8 \u22c5 \\bm{\\hat{\u03b8}}\n$$\nwhere $\u03b8 = 0$ points vertically downwards along the ridge axis\nand $\u03b8 = \u03c0/2$ points along the surface. $U$ is the half spreading velocity.\nStreamlines for the flow obey:\n$$\n\u03c8 = \\frac{2 U r}{\u03c0}\u03b8\\cos\u03b8\n$$\nand are related to the velocity through:\n$$\n\\bm{u} = -\\frac{1}{r} \u22c5 \\frac{d\u03c8}{d\u03b8} \u22c5 \\bm{\\hat{r}} + \\frac{d\u03c8}{dr}\\bm{\\hat{\u03b8}}\n$$\nConversion to Cartesian ($x,y,z$) coordinates yields:\n$$\n\\bm{u} = \\frac{2U}{\u03c0} \\left[\n\\tan^{-1}\\left(\\frac{x}{-z}\\right) + \\frac{xz}{x^{2} + z^{2}} \\right] \\bm{\\hat{x}} +\n\\frac{2U}{\u03c0} \\frac{z^{2}}{x^{2} + z^{2}} \\bm{\\hat{z}}\n$$\nwhere\n\\begin{align*}\nx &= r \\sin\u03b8 \\cr\nz &= -r \\cos\u03b8\n\\end{align*}\nand the velocity gradient is:\n$$\nL = \\frac{4 U}{\u03c0{(x^{2}+z^{2})}^{2}} \u22c5\n\\begin{bmatrix}\n -x^{2}z & 0 & x^{3} \\cr\n 0 & 0 & 0 \\cr\n -xz^{2} & 0 & x^{2}z\n\\end{bmatrix}\n$$\nSee also Fig. 5 in Kaminski & Ribe, 2002 .
\n\nThe returned callables have signature f(x) where x is a 3D position vector.
\n\nArgs:
\n\n\nhorizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal directionvertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical directionplate_speed (float) \u2014 speed of the \u201cplate\u201d i.e. upper boundary \n", "signature": "(horizontal , vertical , plate_speed ): ", "funcdef": "def"}, "pydrex.visualisation": {"fullname": "pydrex.visualisation", "modulename": "pydrex.visualisation", "kind": "module", "doc": "\n PyDRex: Visualisation functions for test outputs and examples.
\n \n"}, "pydrex.visualisation.polefigures": {"fullname": "pydrex.visualisation.polefigures", "modulename": "pydrex.visualisation", "qualname": "polefigures", "kind": "function", "doc": "Plot pole figures of a series of (Nx3x3) orientation matrix stacks.
\n\nProduces [100], [010] and [001] pole figures for (resampled) orientations.\nFor the argument specification, check the output of pydrex-polefigures --help\non the command line.
\n", "signature": "(\torientations , \tref_axes , \ti_range , \tdensity = False , \tsavefile = 'polefigures.png' , \tstrains = None , \t** kwargs ): ", "funcdef": "def"}, "pydrex.visualisation.pathline_box2d": {"fullname": "pydrex.visualisation.pathline_box2d", "modulename": "pydrex.visualisation", "qualname": "pathline_box2d", "kind": "function", "doc": "Plot pathlines and velocity arrows for a 2D box domain.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nArgs:
\n\n\nget_velocity (callable) \u2014 object with call signature f(x) that returns\nthe 3D velocity vector at a given 3D position vectorref_axes (two letters from {\"x\", \"y\", \"z\"}) \u2014 labels for the horizontal and\nvertical axes (these also define the projection for the 3D velocity/position)colors (array) \u2014 monotonic values along a representative pathline in the flowpositions (Nx3 array) \u2014 3D position vectors along the same pathlinemin_coords (array) \u2014 2D coordinates of the lower left corner of the domainmax_coords (array) \u2014 2D coordinates of the upper right corner of the domainresolution (array) \u2014 2D resolution of the velocity arrow grid (i.e. number of\ngrid points in the horizontal and vertical directions) which can be set to None to\nprevent drawing velocity vectorsaspect (str|float, optional) \u2014 see matplotlib.axes.Axes.set_aspectcmap (Matplotlib color map, optional) \u2014 color map for colorscpo_vectors (array, optional) \u2014 vectors to plot as bars at pathline locationscpo_strengths (array, optional) \u2014 strengths used to scale the cpo barstick_formatter (callable, optional) \u2014 function used to format tick labels \n\nAdditional keyword arguments are passed to the matplotlib.axes.Axes.quiver call\nused to plot the velocity vectors.
\n\nReturns the figure handle, the axes handle, the quiver collection (velocities) and\nthe scatter collection (pathline).
\n", "signature": "(\tax , \tget_velocity , \tref_axes , \tcolors , \tpositions , \tmarker , \tmin_coords , \tmax_coords , \tresolution , \taspect = 'equal' , \tcmap =< matplotlib . colors . ListedColormap object > , \tcpo_vectors = None , \tcpo_strengths = None , \ttick_formatter =< function < lambda >> , \t** kwargs ): ", "funcdef": "def"}, "pydrex.visualisation.alignment": {"fullname": "pydrex.visualisation.alignment", "modulename": "pydrex.visualisation", "qualname": "alignment", "kind": "function", "doc": "Plot angles (in degrees) versus strains on the given axis.
\n\nAlignment angles could be either bingham averages or the a-axis in the hexagonal\nsymmetry projection, measured from e.g. the shear direction. In the first case,\nthey should be calculated from resampled grain orientations. Expects as many\nmarkers and labels as there are data series in angles.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nArgs:
\n\n\nstrains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain seriesangles (array) \u2014 Y-values, may be a 2D array of multiple angle seriesmarkers (sequence) \u2014 MatPlotLib markers to use for the data serieslabels (sequence) \u2014 labels to use for the data serieserr (array, optional) \u2014 standard errors for the angles, shapes must match\u03b8_max (int) \u2014 maximum angle (\u00b0) to show on the plot, should be less than 90\u03b8_fse (array, optional) \u2014 an array of angles from the long axis of the finite\nstrain ellipsoid to the reference direction (e.g. shear direction)colors (array, optional) \u2014 color coordinates for series of anglescmaps (Matplotlib color maps, optional) \u2014 color maps for colors \n\nIf colors and cmaps are used, then angle values are colored individually within\neach angle series.
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tstrains , \tangles , \tmarkers , \tlabels , \terr = None , \t\u03b8_max = 90 , \t\u03b8_fse = None , \tcolors = None , \tcmaps = None ): ", "funcdef": "def"}, "pydrex.visualisation.strengths": {"fullname": "pydrex.visualisation.strengths", "modulename": "pydrex.visualisation", "qualname": "strengths", "kind": "function", "doc": "Plot CPO strengths (e.g. M-indices) versus strains on the given axis.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nArgs:
\n\n\nstrains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain seriesstrengths (array) \u2014 Y-values, may be a 2D array of multiple strength seriesmarkers (sequence) \u2014 MatPlotLib markers to use for the data serieslabels (sequence) \u2014 labels to use for the data serieserr (array, optional) \u2014 standard errors for the strengths, shapes must matchcolors (array, optional) \u2014 color coordinates for series of strengthscpo_threshold (float, optional) \u2014 plot a dashed line at this thresholdcmaps (Matplotlib color maps, optional) \u2014 color maps for colors \n\nIf colors and cmaps are used, then strength values are colored individually\nwithin each strength series.
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tstrains , \tstrengths , \tylabel , \tmarkers , \tlabels , \terr = None , \tcpo_threshold = None , \tcolors = None , \tcmaps = None ): ", "funcdef": "def"}, "pydrex.visualisation.grainsizes": {"fullname": "pydrex.visualisation.grainsizes", "modulename": "pydrex.visualisation", "qualname": "grainsizes", "kind": "function", "doc": "Plot grain volume fractions versus strains on the given axis.
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n", "signature": "(ax , strains , fractions ): ", "funcdef": "def"}, "pydrex.visualisation.show_Skemer2016_ShearStrainAngles": {"fullname": "pydrex.visualisation.show_Skemer2016_ShearStrainAngles", "modulename": "pydrex.visualisation", "qualname": "show_Skemer2016_ShearStrainAngles", "kind": "function", "doc": "Show data from src/pydrex/data/thirdparty/Skemer2016_ShearStrainAngles.scsv.
\n\nPlot data from the Skemer 2016 datafile on the axis given by ax. Select the\nstudies from which to plot the data, which must be a list of strings with exact\nmatches in the study column in the datafile.\nAlso filter the data to select only the given fabric\n(see pydrex.core.MineralFabric).
\n\nIf ax is None, a new figure and axes are created with figure_unless.
\n\nReturns a tuple containing:
\n\n\nthe figure handle \nthe axes handle \nthe set of colors used for the data series plots \nthe Skemer 2016 dataset \nthe indices used to select data according to the \"studies\" and \"fabric\" filters \n \n", "signature": "(ax , studies , markers , colors , fillstyles , labels , fabric ): ", "funcdef": "def"}, "pydrex.visualisation.spin": {"fullname": "pydrex.visualisation.spin", "modulename": "pydrex.visualisation", "qualname": "spin", "kind": "function", "doc": "Plot rotation rates of grains with known, unique initial [100] angles from X.
\n\nIf ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tinitial_angles , \trotation_rates , \ttarget_initial_angles = None , \ttarget_rotation_rates = None , \tlabels = ( 'target' , 'computed' ) , \tshear_axis = None ): ", "funcdef": "def"}, "pydrex.visualisation.growth": {"fullname": "pydrex.visualisation.growth", "modulename": "pydrex.visualisation", "qualname": "growth", "kind": "function", "doc": "Plot grain growth of grains with known, unique initial [100] angles from X.
\n\nIf ax is None, a new figure and axes are created with figure_unless.\nThe default labels (\"target\", \"computed\") can also be overriden.\nIf shear_axis is not None, a dashed line will be drawn at the given x-value\n(and its reflection around 180\u00b0).
\n\nReturns a tuple of the figure handle, the axes handle and the set of colors used for\nthe data series plots.
\n", "signature": "(\tax , \tinitial_angles , \tfractions_diff , \ttarget_initial_angles = None , \ttarget_fractions_diff = None , \tlabels = ( 'target' , 'computed' ) , \tshear_axis = None ): ", "funcdef": "def"}, "pydrex.visualisation.figure_unless": {"fullname": "pydrex.visualisation.figure_unless", "modulename": "pydrex.visualisation", "qualname": "figure_unless", "kind": "function", "doc": "Create figure and axes if ax is None, or return existing figure for ax.
\n\nIf ax is None, a new figure is created for the axes with a few opinionated default\nsettings (grid, constrained layout, high DPI).
\n\nReturns a tuple containing the figure handle and the axes object.
\n", "signature": "(ax ): ", "funcdef": "def"}, "pydrex.visualisation.figure": {"fullname": "pydrex.visualisation.figure", "modulename": "pydrex.visualisation", "qualname": "figure", "kind": "function", "doc": "Create new figure with a few opinionated default settings.
\n\n(e.g. grid, constrained layout, high DPI).
\n\nThe keyword argument figscale can be used to scale the figure width and height\nrelative to the default values by passing a tuple. Any additional keyword arguments\nare passed to matplotlib.pyplot.figure().
\n", "signature": "(figscale = None , ** kwargs ): ", "funcdef": "def"}, "tests": {"fullname": "tests", "modulename": "tests", "kind": "module", "doc": "PyDRex tests \n\nRunning the tests requires pytest .\nFrom the root of the source tree, run pytest.\nTo print more verbose information (including INFO level logging),\nsuch as detailed test progress, use the flag pytest -v.\nThe custom optional flag --outdir=\"OUT\" is recommended\nto produce output figures, data dumps and logs and save them in the directory \"OUT\".\nThe value \".\" can be used to save these in the current directory.
\n\nIn total, the following custom pytest command line flags are defined by PyDRex:
\n\n\n--outdir (described above)--runbig (enable tests which require a large amount of RAM)--runslow (enable slow tests which require HPC resources, implies --runbig)--ncpus (number of CPU cores to use for shared memory multiprocessing, set to one less than the available maximum by default)--fontsize (Matplotlib rcParams[\"font.size\"])--markersize (Matplotlib rcParams[\"lines.markersize\"])--linewidth (Matplotlib rcParams[\"lines.linewidth\"]) \n\nTests which require a \u201csignificant\u201d amount of memory (> ~16GB RAM) are disabled by default.\nTo fully check the functionality of the code, it is recommended to run these locally\nby using the --runbig flag before moving to larger simulations.
\n\nLong tests/examples are also disabled by default and can be enabled with --runslow.\nIt is recommended to run these on a HPC cluster infrastructure (>100GB RAM, >32 cores).\nThe number of cores to use for shared memory multiprocessing can be specified with --ncpus.
\n\nWriting tests \n\nFor quick sanity checks and inline unit tests, use python doctests .\nThese will also appear as inline examples in the generated documentation.\nMore comprehensive unit tests and larger integration tests should be organised\ninto submodules of the test module.
\n\n\nTo mark a test as \u201cbig\u201d (i.e. requiring more than ~16GB RAM), apply the\n@pytest.mark.big decorator to the corresponding method definition.
To mark a test as \u201cslow\u201d (i.e. requiring more than ~32 cores), apply the\n@pytest.mark.slow decorator to the corresponding method definition.
\n\nTests should not produce persistent output by default.\nIf a test method can produce such output for debugging or visualisation,\nit should accept the outdir positional argument,\nand check if its value is not None.\nIf outdir is None then no persistent output should be produced.\nIf outdir is a directory path (string):
\n\n\nlogs can be saved by using the pydrex.logger.logfile_enable context manager,\nwhich accepts a path name and an optional logging level as per Python's logging module\n(the default is logging.DEBUG which implies the most verbose output), \nfigures can be saved by (implementing and) calling a helper from pydrex.visualisation, and \ndata dumps can be saved to outdir, e.g. in .npz format (see the pydrex.minerals.Mineral.save method)\nIn all cases, saving to outdir should handle creation of parent directories.\nTo handle this as well as relative paths, we provide pydrex.io.resolve_path,\nwhich is a thin wrapper around some pathlib methods. \n \n"}, "tests.conftest": {"fullname": "tests.conftest", "modulename": "tests.conftest", "kind": "module", "doc": "\n Configuration and fixtures for PyDRex tests.
\n \n"}, "tests.conftest.pytest_addoption": {"fullname": "tests.conftest.pytest_addoption", "modulename": "tests.conftest", "qualname": "pytest_addoption", "kind": "function", "doc": "
\n", "signature": "(parser ): ", "funcdef": "def"}, "tests.conftest.PytestConsoleLogger": {"fullname": "tests.conftest.PytestConsoleLogger", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger", "kind": "class", "doc": "Pytest plugin that allows linking up a custom console logger.
\n", "bases": "_pytest.logging.LoggingPlugin"}, "tests.conftest.PytestConsoleLogger.__init__": {"fullname": "tests.conftest.PytestConsoleLogger.__init__", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.__init__", "kind": "function", "doc": "Create a new plugin to capture log messages.
\n\nThe formatter can be safely shared across all handlers so\ncreate a single one for the entire test session here.
\n", "signature": "(config , * args , ** kwargs "}, "tests.conftest.PytestConsoleLogger.name": {"fullname": "tests.conftest.PytestConsoleLogger.name", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.name", "kind": "variable", "doc": "
\n", "default_value": "'pytest-console-logger'"}, "tests.conftest.PytestConsoleLogger.log_cli_handler": {"fullname": "tests.conftest.PytestConsoleLogger.log_cli_handler", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.log_cli_handler", "kind": "variable", "doc": "
\n"}, "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown": {"fullname": "tests.conftest.PytestConsoleLogger.pytest_runtest_teardown", "modulename": "tests.conftest", "qualname": "PytestConsoleLogger.pytest_runtest_teardown", "kind": "function", "doc": "
\n", "signature": "(self , item ): ", "funcdef": "def"}, "tests.conftest.pytest_configure": {"fullname": "tests.conftest.pytest_configure", "modulename": "tests.conftest", "qualname": "pytest_configure", "kind": "function", "doc": "
\n", "signature": "(config ): ", "funcdef": "def"}, "tests.conftest.pytest_collection_modifyitems": {"fullname": "tests.conftest.pytest_collection_modifyitems", "modulename": "tests.conftest", "qualname": "pytest_collection_modifyitems", "kind": "function", "doc": "
\n", "signature": "(config , items ): ", "funcdef": "def"}, "tests.conftest.outdir": {"fullname": "tests.conftest.outdir", "modulename": "tests.conftest", "qualname": "outdir", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.ncpus": {"fullname": "tests.conftest.ncpus", "modulename": "tests.conftest", "qualname": "ncpus", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.console_handler": {"fullname": "tests.conftest.console_handler", "modulename": "tests.conftest", "qualname": "console_handler", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.params_Fraters2021": {"fullname": "tests.conftest.params_Fraters2021", "modulename": "tests.conftest", "qualname": "params_Fraters2021", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_solid": {"fullname": "tests.conftest.params_Kaminski2001_fig5_solid", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_solid", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_shortdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_shortdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_shortdash", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2001_fig5_longdash": {"fullname": "tests.conftest.params_Kaminski2001_fig5_longdash", "modulename": "tests.conftest", "qualname": "params_Kaminski2001_fig5_longdash", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_triangles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_triangles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_triangles", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_squares": {"fullname": "tests.conftest.params_Kaminski2004_fig4_squares", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_squares", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Kaminski2004_fig4_circles": {"fullname": "tests.conftest.params_Kaminski2004_fig4_circles", "modulename": "tests.conftest", "qualname": "params_Kaminski2004_fig4_circles", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.params_Hedjazian2017": {"fullname": "tests.conftest.params_Hedjazian2017", "modulename": "tests.conftest", "qualname": "params_Hedjazian2017", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.n_grains": {"fullname": "tests.conftest.n_grains", "modulename": "tests.conftest", "qualname": "n_grains", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.hkl": {"fullname": "tests.conftest.hkl", "modulename": "tests.conftest", "qualname": "hkl", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.ref_axes": {"fullname": "tests.conftest.ref_axes", "modulename": "tests.conftest", "qualname": "ref_axes", "kind": "function", "doc": "
\n", "signature": "(request ): ", "funcdef": "def"}, "tests.conftest.seeds": {"fullname": "tests.conftest.seeds", "modulename": "tests.conftest", "qualname": "seeds", "kind": "function", "doc": "1000 unique seeds for ensemble runs that need an RNG seed.
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.seed": {"fullname": "tests.conftest.seed", "modulename": "tests.conftest", "qualname": "seed", "kind": "function", "doc": "Default seed for test RNG.
\n", "signature": "(): ", "funcdef": "def"}, "tests.conftest.seeds_nearX45": {"fullname": "tests.conftest.seeds_nearX45", "modulename": "tests.conftest", "qualname": "seeds_nearX45", "kind": "function", "doc": "41 seeds which have the initial hexagonal symmetry axis near 45\u00b0 from X.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_config": {"fullname": "tests.test_config", "modulename": "tests.test_config", "kind": "module", "doc": "\n PyDRex: tests for configuration file format.
\n \n"}, "tests.test_config.test_specfile": {"fullname": "tests.test_config.test_specfile", "modulename": "tests.test_config", "qualname": "test_specfile", "kind": "function", "doc": "Test TOML spec file parsing.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_core": {"fullname": "tests.test_core", "modulename": "tests.test_core", "kind": "module", "doc": "\n PyDRex: Tests for core D-Rex routines.
\n \n"}, "tests.test_core.SUBDIR": {"fullname": "tests.test_core.SUBDIR", "modulename": "tests.test_core", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'core'"}, "tests.test_core.TestDislocationCreepOPX": {"fullname": "tests.test_core.TestDislocationCreepOPX", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX", "kind": "class", "doc": "Single-grain orthopyroxene crystallographic rotation rate tests.
\n"}, "tests.test_core.TestDislocationCreepOPX.class_id": {"fullname": "tests.test_core.TestDislocationCreepOPX.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.class_id", "kind": "variable", "doc": "
\n", "default_value": "'dislocation_creep_OPX'"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dudz": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dudz", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dudz", "kind": "function", "doc": "
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx": {"fullname": "tests.test_core.TestDislocationCreepOPX.test_shear_dvdx", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOPX.test_shear_dvdx", "kind": "function", "doc": "
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA": {"fullname": "tests.test_core.TestDislocationCreepOlivineA", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA", "kind": "class", "doc": "Single-grain A-type olivine analytical rotation rate tests.
\n"}, "tests.test_core.TestDislocationCreepOlivineA.class_id": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.class_id", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'dislocation_creep_OlA'"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdx_slip_010_100", "kind": "function", "doc": "Single grain of A-type olivine, slip on (010)[100].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dudz_slip_001_100", "kind": "function", "doc": "Single grain of A-type olivine, slip on (001)[100].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 2 \\cr 0 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dwdx_slip_001_100", "kind": "function", "doc": "Single grain of A-type olivine, slip on (001)[100].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 0 \\cr 2 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001": {"fullname": "tests.test_core.TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "modulename": "tests.test_core", "qualname": "TestDislocationCreepOlivineA.test_shear_dvdz_slip_010_001", "kind": "function", "doc": "Single grain of A-type olivine, slip on (010)[001].
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 0 & 0 & 2 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D": {"fullname": "tests.test_core.TestRecrystallisation2D", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D", "kind": "class", "doc": "Basic recrystallisation tests for 2D simple shear.
\n"}, "tests.test_core.TestRecrystallisation2D.class_id": {"fullname": "tests.test_core.TestRecrystallisation2D.class_id", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.class_id", "kind": "variable", "doc": "
\n", "default_value": "'recrystallisation_2D'"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_inplane", "kind": "function", "doc": "360000 grains of A-type olivine with uniform spread of a-axes on a circle.
\n\nGrain growth rates are compared to analytical calculations.\nThe a-axes are distributed in the YX plane (i.e.\\ rotated around Z).
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane": {"fullname": "tests.test_core.TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "modulename": "tests.test_core", "qualname": "TestRecrystallisation2D.test_shear_dvdx_circle_shearplane", "kind": "function", "doc": "360000 grains of A-type olivine with uniform spread of a-axes on a circle.
\n\nUnlike test_shear_dvdx_circle_inplane, two slip systems are active here,\nwith cyclical variety in which one is dominant depending on grain orientation.\nThe a-axes are distributed in the YZ plane\n(i.e.\\ extrinsic rotation around Z by 90\u00b0 and then around X).
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(self , outdir ): ", "funcdef": "def"}, "tests.test_corner_flow_2d": {"fullname": "tests.test_corner_flow_2d", "modulename": "tests.test_corner_flow_2d", "kind": "module", "doc": "\n PyDRex: 2D corner flow tests.
\n \n"}, "tests.test_corner_flow_2d.SUBDIR": {"fullname": "tests.test_corner_flow_2d.SUBDIR", "modulename": "tests.test_corner_flow_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'2d_cornerflow'"}, "tests.test_corner_flow_2d.TestCornerOlivineA": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA", "kind": "class", "doc": "Tests for pure A-type olivine polycrystals in 2D corner flows.
\n"}, "tests.test_corner_flow_2d.TestCornerOlivineA.class_id": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA.class_id", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'corner_olivineA'"}, "tests.test_corner_flow_2d.TestCornerOlivineA.run": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA.run", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA.run", "kind": "function", "doc": "Run 2D corner flow A-type olivine simulation.
\n", "signature": "(\tcls , \tparams , \tseed , \tget_velocity , \tget_velocity_gradient , \tmin_coords , \tmax_coords , \tmax_strain , \tn_timesteps , \tfinal_location ): ", "funcdef": "def"}, "tests.test_corner_flow_2d.TestCornerOlivineA.test_prescribed": {"fullname": "tests.test_corner_flow_2d.TestCornerOlivineA.test_prescribed", "modulename": "tests.test_corner_flow_2d", "qualname": "TestCornerOlivineA.test_prescribed", "kind": "function", "doc": "Test CPO evolution in prescribed 2D corner flow.
\n\nInitial condition: random orientations and uniform volumes in all Minerals.
\n\nPlate velocity: 2 cm/yr
\n\n\n\n
This example takes about 11 CPU hours to run and uses around 60GB of RAM.\nIt is recommended to only use ncpus=4 which matches the number of\npathlines, because higher numbers can lead to redundant cross-core\ncommunication.
\n\n
(self , outdir , seed , ncpus ): ", "funcdef": "def"}, "tests.test_diagnostics": {"fullname": "tests.test_diagnostics", "modulename": "tests.test_diagnostics", "kind": "module", "doc": "\n PyDRex: tests for texture diagnostics.
\n \n"}, "tests.test_diagnostics.TestElasticityComponents": {"fullname": "tests.test_diagnostics.TestElasticityComponents", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents", "kind": "class", "doc": "Test symmetry decomposition of elastic tensors.
\n"}, "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_olivine_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_olivine_Browaeys2004", "kind": "function", "doc": "
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004": {"fullname": "tests.test_diagnostics.TestElasticityComponents.test_enstatite_Browaeys2004", "modulename": "tests.test_diagnostics", "qualname": "TestElasticityComponents.test_enstatite_Browaeys2004", "kind": "function", "doc": "
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR": {"fullname": "tests.test_diagnostics.TestSymmetryPGR", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR", "kind": "class", "doc": "Test Point-Girdle-Random (eigenvalue) symmetry diagnostics.
\n"}, "tests.test_diagnostics.TestSymmetryPGR.test_pointX": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_pointX", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_pointX", "kind": "function", "doc": "Test diagnostics of point symmetry aligned to the X axis.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_random": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_random", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_random", "kind": "function", "doc": "Test diagnostics of random grain orientations.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestSymmetryPGR.test_girdle": {"fullname": "tests.test_diagnostics.TestSymmetryPGR.test_girdle", "modulename": "tests.test_diagnostics", "qualname": "TestSymmetryPGR.test_girdle", "kind": "function", "doc": "Test diagnostics of girdled orientations.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting": {"fullname": "tests.test_diagnostics.TestVolumeWeighting", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting", "kind": "class", "doc": "Tests for volumetric resampling of orientation data.
\n"}, "tests.test_diagnostics.TestVolumeWeighting.test_output_shape": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_output_shape", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_output_shape", "kind": "function", "doc": "Test that we get the correct output shape.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_upsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_upsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_upsample", "kind": "function", "doc": "Test upsampling of the raw orientation data.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_downsample": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_downsample", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_downsample", "kind": "function", "doc": "Test downsampling of orientation data.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors": {"fullname": "tests.test_diagnostics.TestVolumeWeighting.test_common_input_errors", "modulename": "tests.test_diagnostics", "qualname": "TestVolumeWeighting.test_common_input_errors", "kind": "function", "doc": "Test that exceptions are raised for bad input data.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats": {"fullname": "tests.test_diagnostics.TestBinghamStats", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats", "kind": "class", "doc": "Tests for antipodally symmetric (bingham) statistics.
\n"}, "tests.test_diagnostics.TestBinghamStats.test_average_0": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_0", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_0", "kind": "function", "doc": "Test bingham average of vectors aligned to the reference frame.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_twopoles90Z", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_twopoles90Z", "kind": "function", "doc": "Test bingham average of vectors rotated by \u00b190\u00b0 around Z.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestBinghamStats.test_average_spread10X": {"fullname": "tests.test_diagnostics.TestBinghamStats.test_average_spread10X", "modulename": "tests.test_diagnostics", "qualname": "TestBinghamStats.test_average_spread10X", "kind": "function", "doc": "Test bingham average of vectors spread within 10\u00b0 of the \u00b1X-axis.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex": {"fullname": "tests.test_diagnostics.TestMIndex", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex", "kind": "class", "doc": "Tests for the M-index texture strength diagnostic.
\n"}, "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_uniform_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_uniform_ortho", "kind": "function", "doc": "Test with random (uniform distribution) orthorhombic grain orientations.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread10X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread10X_ortho", "kind": "function", "doc": "Test for orthorhombic grains spread within 10\u00b0 of the \u00b1X axis.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_spread45X_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_spread45X_ortho", "kind": "function", "doc": "Test for orthorhombic grains spread within 45\u00b0 of the \u00b1X axis.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_textures_increasing_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_textures_increasing_ortho", "kind": "function", "doc": "Test M-index for textures of increasing strength.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho": {"fullname": "tests.test_diagnostics.TestMIndex.test_texture_girdle_ortho", "modulename": "tests.test_diagnostics", "qualname": "TestMIndex.test_texture_girdle_ortho", "kind": "function", "doc": "Test M-index for girdled texture.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_doctests": {"fullname": "tests.test_doctests", "modulename": "tests.test_doctests", "kind": "module", "doc": "\n PyDRex: Run doctests for all submodules.
\n \n"}, "tests.test_doctests.test_doctests": {"fullname": "tests.test_doctests.test_doctests", "modulename": "tests.test_doctests", "qualname": "test_doctests", "kind": "function", "doc": "Run doctests for all submodules.
\n", "signature": "(module ): ", "funcdef": "def"}, "tests.test_geometry": {"fullname": "tests.test_geometry", "modulename": "tests.test_geometry", "kind": "module", "doc": "\n PyDRex: Tests for geometric conversions and projections.
\n \n"}, "tests.test_geometry.test_poles_example": {"fullname": "tests.test_geometry.test_poles_example", "modulename": "tests.test_geometry", "qualname": "test_poles_example", "kind": "function", "doc": "Test poles (directions of crystallographic axes) of example data.
\n", "signature": "(hkl , ref_axes ): ", "funcdef": "def"}, "tests.test_geometry.test_lambert_equal_area": {"fullname": "tests.test_geometry.test_lambert_equal_area", "modulename": "tests.test_geometry", "qualname": "test_lambert_equal_area", "kind": "function", "doc": "Test Lambert equal area projection.
\n", "signature": "(seed ): ", "funcdef": "def"}, "tests.test_scsv": {"fullname": "tests.test_scsv", "modulename": "tests.test_scsv", "kind": "module", "doc": "\n PyDRex: tests for the SCSV plain text file format.
\n \n"}, "tests.test_scsv.test_validate_schema": {"fullname": "tests.test_scsv.test_validate_schema", "modulename": "tests.test_scsv", "qualname": "test_validate_schema", "kind": "function", "doc": "Test SCSV schema validation.
\n", "signature": "(console_handler ): ", "funcdef": "def"}, "tests.test_scsv.test_read_specfile": {"fullname": "tests.test_scsv.test_read_specfile", "modulename": "tests.test_scsv", "qualname": "test_read_specfile", "kind": "function", "doc": "Test SCSV spec file parsing.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_save_specfile": {"fullname": "tests.test_scsv.test_save_specfile", "modulename": "tests.test_scsv", "qualname": "test_save_specfile", "kind": "function", "doc": "Test SCSV spec file reproduction.
\n", "signature": "(outdir ): ", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2002": {"fullname": "tests.test_scsv.test_read_Kaminski2002", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2002", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_save_scsv_errors": {"fullname": "tests.test_scsv.test_save_scsv_errors", "modulename": "tests.test_scsv", "qualname": "test_save_scsv_errors", "kind": "function", "doc": "Check that we raise errors when attempting to write bad SCSV data.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_read_Kaminski2004": {"fullname": "tests.test_scsv.test_read_Kaminski2004", "modulename": "tests.test_scsv", "qualname": "test_read_Kaminski2004", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_scsv.test_read_Skemer2016": {"fullname": "tests.test_scsv.test_read_Skemer2016", "modulename": "tests.test_scsv", "qualname": "test_read_Skemer2016", "kind": "function", "doc": "
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_simple_shear_2d": {"fullname": "tests.test_simple_shear_2d", "modulename": "tests.test_simple_shear_2d", "kind": "module", "doc": "\n PyDRex: 2D simple shear tests.
\n \n"}, "tests.test_simple_shear_2d.SUBDIR": {"fullname": "tests.test_simple_shear_2d.SUBDIR", "modulename": "tests.test_simple_shear_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'2d_simple_shear'"}, "tests.test_simple_shear_2d.TestPreliminaries": {"fullname": "tests.test_simple_shear_2d.TestPreliminaries", "modulename": "tests.test_simple_shear_2d", "qualname": "TestPreliminaries", "kind": "class", "doc": "Preliminary tests to check that various auxiliary routines are working.
\n"}, "tests.test_simple_shear_2d.TestPreliminaries.test_strain_increment": {"fullname": "tests.test_simple_shear_2d.TestPreliminaries.test_strain_increment", "modulename": "tests.test_simple_shear_2d", "qualname": "TestPreliminaries.test_strain_increment", "kind": "function", "doc": "Test for accumulating strain via strain increment calculations.
\n", "signature": "(self ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA": {"fullname": "tests.test_simple_shear_2d.TestOlivineA", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA", "kind": "class", "doc": "Tests for stationary A-type olivine polycrystals in 2D simple shear.
\n"}, "tests.test_simple_shear_2d.TestOlivineA.class_id": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.class_id", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'olivineA'"}, "tests.test_simple_shear_2d.TestOlivineA.run": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.run", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.run", "kind": "function", "doc": "Reusable logic for 2D olivine (A-type) simple shear tests.
\n\nReturns a tuple with the mineral and the FSE angle (or None if return_fse is\nNone).
\n", "signature": "(\tcls , \tparams , \ttimestamps , \tstrain_rate , \tget_velocity_gradient , \tshear_direction , \tseed = None , \treturn_fse = None , \tget_position =< function TestOlivineA .< lambda >> ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_Kaminski2001", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_Kaminski2001", "kind": "function", "doc": "Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBM_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBM_FortranDRex", "kind": "function", "doc": "Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_FortranDRex", "kind": "function", "doc": "Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_long_FortranDRex", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_long_FortranDRex", "kind": "function", "doc": "Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.interp_GBS_Kaminski2004", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.interp_GBS_Kaminski2004", "kind": "function", "doc": "Interpolate Kaminski & Ribe, 2001 data to get target angles at strains.
\n", "signature": "(cls , strains ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_zero_recrystallisation", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_zero_recrystallisation", "kind": "function", "doc": "Check that M*=0 is a reliable switch to turn off recrystallisation.
\n", "signature": "(self , seed ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_grainsize_median", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_grainsize_median", "kind": "function", "doc": "Check that M={50,100,150}, \u03bb =5 causes decreasing grain size median.
\n", "signature": "(self , seed , gbm_mobility ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_ensemble", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_ensemble", "kind": "function", "doc": "Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).
\n\nVelocity gradient:\n$$\\bm{L} = \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}$$
\n", "signature": "(\tself , \toutdir , \tseeds_nearX45 , \tncpus , \tgbs_threshold , \tnucleation_efficiency ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dvdx_GBM", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dvdx_GBM", "kind": "function", "doc": "Test a-axis alignment to shear in Y direction (init. SCCS near 45\u00b0 from X).
\n\nVelocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$
\n\nResults are compared to the Fortran 90 output.
\n", "signature": "(self , outdir , seeds_nearX45 , ncpus ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_GBM_calibration", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_GBM_calibration", "kind": "function", "doc": "Compare results for various values of $$M^\u2217$$ to A-type olivine data.
\n\nVelocity gradient:\n$$\n\\bm{L} = 10^{-4} \u00d7\n \\begin{bmatrix} 0 & 0 & 0 \\cr 2 & 0 & 0 \\cr 0 & 0 & 0 \\end{bmatrix}\n$$
\n\nUnlike test_dvdx_GBM,\ngrain boudary sliding is enabled here (see _io.DEFAULT_PARAMS).\nData are provided by Skemer & Hansen, 2016 .
\n", "signature": "(self , outdir , seeds , ncpus ): ", "funcdef": "def"}, "tests.test_simple_shear_2d.TestOlivineA.test_dudz_pathline": {"fullname": "tests.test_simple_shear_2d.TestOlivineA.test_dudz_pathline", "modulename": "tests.test_simple_shear_2d", "qualname": "TestOlivineA.test_dudz_pathline", "kind": "function", "doc": "Test alignment of olivine a-axis for a polycrystal advected on a pathline.
\n", "signature": "(self , outdir , seed ): ", "funcdef": "def"}, "tests.test_simple_shear_3d": {"fullname": "tests.test_simple_shear_3d", "modulename": "tests.test_simple_shear_3d", "kind": "module", "doc": "\n PyDRex: Simple shear 3D tests.
\n \n"}, "tests.test_simple_shear_3d.SUBDIR": {"fullname": "tests.test_simple_shear_3d.SUBDIR", "modulename": "tests.test_simple_shear_3d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'3d_simple_shear'"}, "tests.test_simple_shear_3d.TestFraters2021": {"fullname": "tests.test_simple_shear_3d.TestFraters2021", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021", "kind": "class", "doc": "Tests inspired by the benchmarks presented in [Fraters & Billen, 2021].
\n"}, "tests.test_simple_shear_3d.TestFraters2021.class_id": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.class_id", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.class_id", "kind": "variable", "doc": "
\n", "default_value": "'Fraters2021'"}, "tests.test_simple_shear_3d.TestFraters2021.run": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.run", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.run", "kind": "function", "doc": "Run simulation with stationary particles in the given velocity gradient.
\n\nThe optional RNG seed is used for the initial pseudorandom orientations.\nA prefix msg will be printed before each timestep log message if given.\nOther keyword args are passed to pydrex.Mineral.update_orientations.
\n\nReturns a tuple containing one olivine (A-type) and one enstatite mineral.\nIf params[\"enstatite_fraction\"] is zero, then the second tuple element will be\nNone instead.
\n", "signature": "(\tcls , \tparams , \ttimestamps , \tget_velocity_gradient_initial , \tget_velocity_gradient_final , \tswitch_time , \tmsg , \tseed = None ): ", "funcdef": "def"}, "tests.test_simple_shear_3d.TestFraters2021.test_direction_change": {"fullname": "tests.test_simple_shear_3d.TestFraters2021.test_direction_change", "modulename": "tests.test_simple_shear_3d", "qualname": "TestFraters2021.test_direction_change", "kind": "function", "doc": "Test a-axis alignment in simple shear with instantaneous geometry change.
\n\nThe simulation runs for 5 Ma with a strain rate of 1.58e-14/s, resulting in an\naccumulated strain invariant of 2.5.
\n\nThe initial shear has nonzero du/dz and the final shear has nonzero dv/dx where\nu is the velocity along X and v the velocity along Y.
\n", "signature": "(self , outdir , seeds , params_Fraters2021 , switch_time_Ma , ncpus ): ", "funcdef": "def"}, "tests.test_tensors": {"fullname": "tests.test_tensors", "modulename": "tests.test_tensors", "kind": "module", "doc": "\n PyDRex: Tests for tensor operations.
\n \n"}, "tests.test_tensors.test_voigt_decompose": {"fullname": "tests.test_tensors.test_voigt_decompose", "modulename": "tests.test_tensors", "qualname": "test_voigt_decompose", "kind": "function", "doc": "Test decomposition of Voigt 6x6 matrix into distinct contractions.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_tensors.test_voigt_tensor": {"fullname": "tests.test_tensors.test_voigt_tensor", "modulename": "tests.test_tensors", "qualname": "test_voigt_tensor", "kind": "function", "doc": "Test elasticity tensor <-> 6x6 Voigt matrix conversions.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_tensors.test_voigt_to_vector": {"fullname": "tests.test_tensors.test_voigt_to_vector", "modulename": "tests.test_tensors", "qualname": "test_voigt_to_vector", "kind": "function", "doc": "Test Voigt vector construction.
\n", "signature": "(): ", "funcdef": "def"}, "tests.test_vortex_2d": {"fullname": "tests.test_vortex_2d", "modulename": "tests.test_vortex_2d", "kind": "module", "doc": "\n PyDRex: tests for CPO stability in 2D vortex and Stokes cell flows.
\n \n"}, "tests.test_vortex_2d.SUBDIR": {"fullname": "tests.test_vortex_2d.SUBDIR", "modulename": "tests.test_vortex_2d", "qualname": "SUBDIR", "kind": "variable", "doc": "
\n", "default_value": "'2d_vortex'"}, "tests.test_vortex_2d.TestCellOlivineA": {"fullname": "tests.test_vortex_2d.TestCellOlivineA", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA", "kind": "class", "doc": "Tests for A-type olivine polycrystals in a 2D Stokes cell.
\n"}, "tests.test_vortex_2d.TestCellOlivineA.class_id": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.class_id", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.class_id", "kind": "variable", "doc": "
\n", "default_value": "'cell_olivineA'"}, "tests.test_vortex_2d.TestCellOlivineA.run": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.run", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.run", "kind": "function", "doc": "Run 2D Stokes cell A-type olivine simulation.
\n", "signature": "(\tcls , \tparams , \tfinal_location , \tget_velocity , \tget_velocity_gradient , \tmin_coords , \tmax_coords , \tmax_strain , \tseed = None ): ", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz_10k": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz_10k", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz_10k", "kind": "function", "doc": "Run 2D cell test with 10000 grains (~14GiB RAM requirement).
\n", "signature": "(self , outdir , seed ): ", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz", "kind": "function", "doc": "Test to check that 5000 grains is \"enough\" to resolve transient features.
\n", "signature": "(self , outdir , seed , n_grains ): ", "funcdef": "def"}, "tests.test_vortex_2d.TestCellOlivineA.test_xz_ensemble": {"fullname": "tests.test_vortex_2d.TestCellOlivineA.test_xz_ensemble", "modulename": "tests.test_vortex_2d", "qualname": "TestCellOlivineA.test_xz_ensemble", "kind": "function", "doc": "Test to demonstrate stability of the dip at \u03b5 \u2248 3.75 for 5000+ grains.
\n", "signature": "(self , outdir , seeds_nearX45 , ncpus , n_grains ): ", "funcdef": "def"}}, "docInfo": {"pydrex": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 2230}, "pydrex.axes": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 12}, "pydrex.axes.PoleFigureAxes": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 4, "doc": 54}, "pydrex.axes.PoleFigureAxes.name": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "pydrex.axes.PoleFigureAxes.polefigure": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 92, "bases": 0, "doc": 148}, "pydrex.axes.PoleFigureAxes.set": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 833, "bases": 0, "doc": 267}, "pydrex.cli": {"qualname": 0, "fullname": 2, "annotation": 0, 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// mirrored in build-search-index.js (part 1)
// Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/tests/test_corner_flow_2d.html b/tests/test_corner_flow_2d.html
index 9957694f..c5cd0fd6 100644
--- a/tests/test_corner_flow_2d.html
+++ b/tests/test_corner_flow_2d.html
@@ -147,15 +147,15 @@
52 seed = seed ,
53 )
54 deformation_gradient = np . eye ( 3 )
- 55 timestamps_back , get_position = _path . get_pathline (
+ 55 timestamps , get_position = _path . get_pathline (
56 final_location ,
57 get_velocity ,
58 get_velocity_gradient ,
59 min_coords ,
60 max_coords ,
61 max_strain ,
- 62 )
- 63 timestamps = np . linspace ( timestamps_back [ - 1 ], timestamps_back [ 0 ], n_timesteps )
+ 62 regular_steps = n_timesteps ,
+ 63 )
64 positions = [ get_position ( t ) for t in timestamps ]
65 velocity_gradients = [ get_velocity_gradient ( np . asarray ( x )) for x in positions ]
66 strains = np . empty_like ( timestamps )
@@ -402,15 +402,15 @@
53 seed = seed ,
54 )
55 deformation_gradient = np . eye ( 3 )
- 56 timestamps_back , get_position = _path . get_pathline (
+ 56 timestamps , get_position = _path . get_pathline (
57 final_location ,
58 get_velocity ,
59 get_velocity_gradient ,
60 min_coords ,
61 max_coords ,
62 max_strain ,
- 63 )
- 64 timestamps = np . linspace ( timestamps_back [ - 1 ], timestamps_back [ 0 ], n_timesteps )
+ 63 regular_steps = n_timesteps ,
+ 64 )
65 positions = [ get_position ( t ) for t in timestamps ]
66 velocity_gradients = [ get_velocity_gradient ( np . asarray ( x )) for x in positions ]
67 strains = np . empty_like ( timestamps )
@@ -656,15 +656,15 @@
53 seed = seed ,
54 )
55 deformation_gradient = np . eye ( 3 )
-56 timestamps_back , get_position = _path . get_pathline (
+56 timestamps , get_position = _path . get_pathline (
57 final_location ,
58 get_velocity ,
59 get_velocity_gradient ,
60 min_coords ,
61 max_coords ,
62 max_strain ,
-63 )
-64 timestamps = np . linspace ( timestamps_back [ - 1 ], timestamps_back [ 0 ], n_timesteps )
+63 regular_steps = n_timesteps ,
+64 )
65 positions = [ get_position ( t ) for t in timestamps ]
66 velocity_gradients = [ get_velocity_gradient ( np . asarray ( x )) for x in positions ]
67 strains = np . empty_like ( timestamps )
diff --git a/tests/test_simple_shear_2d.html b/tests/test_simple_shear_2d.html
index a20d072f..4d3955f8 100644
--- a/tests/test_simple_shear_2d.html
+++ b/tests/test_simple_shear_2d.html
@@ -54,13 +54,19 @@ API Documentation
SUBDIR
- TestOlivineA
+ TestPreliminaries
+
+
+
+ TestOlivineA
+
@@ -132,697 +141,870 @@
7 8 import numpy as np
9 import pytest
- 10 from numpy import testing as nt
- 11 from scipy.interpolate import PchipInterpolator
- 12 13 from pydrex import core as _core
- 14 from pydrex import diagnostics as _diagnostics
- 15 from pydrex import io as _io
- 16 from pydrex import logger as _log
- 17 from pydrex import minerals as _minerals
- 18 from pydrex import utils as _utils
- 19 from pydrex import velocity as _velocity
- 20 from pydrex import visualisation as _vis
- 21 22 # Subdirectory of `outdir` used to store outputs from these tests.
- 23 SUBDIR = "2d_simple_shear"
- 24 10 from numpy import asarray as Ŋ
+ 11 from numpy import testing as nt
+ 12 from scipy.interpolate import PchipInterpolator
+ 13 14 from pydrex import core as _core
+ 15 from pydrex import diagnostics as _diagnostics
+ 16 from pydrex import geometry as _geo
+ 17 from pydrex import io as _io
+ 18 from pydrex import logger as _log
+ 19 from pydrex import minerals as _minerals
+ 20 from pydrex import pathlines as _paths
+ 21 from pydrex import stats as _stats
+ 22 from pydrex import utils as _utils
+ 23 from pydrex import velocity as _velocity
+ 24 from pydrex import visualisation as _vis
25 26 class TestOlivineA :
- 27 """Tests for stationary A-type olivine polycrystals in 2D simple shear."""
+ 26 # Subdirectory of `outdir` used to store outputs from these tests.
+ 27 SUBDIR = "2d_simple_shear"
28 29 class_id = "olivineA"
- 30 31 @classmethod
- 32 def get_position ( cls , t ):
- 33 return np . zeros ( 3 ) # These crystals are stationary.
- 34 35 @classmethod
- 36 def run (
- 37 cls ,
- 38 params ,
- 39 timestamps ,
- 40 strain_rate ,
- 41 get_velocity_gradient ,
- 42 shear_direction ,
- 43 seed = None ,
- 44 return_fse = None ,
- 45 ):
- 46 """Reusable logic for 2D olivine (A-type) simple shear tests.
- 47 48 Returns a tuple with the mineral and the FSE angle (or `None` if `return_fse` is
- 49 `None`).
- 50 51 """
- 52 mineral = _minerals . Mineral (
- 53 phase = _core . MineralPhase . olivine ,
- 54 fabric = _core . MineralFabric . olivine_A ,
- 55 regime = _core . DeformationRegime . dislocation ,
- 56 n_grains = params [ "number_of_grains" ],
- 57 seed = seed ,
- 58 )
- 59 deformation_gradient = np . eye ( 3 ) # Undeformed initial state.
- 60 θ_fse = np . empty_like ( timestamps )
- 61 θ_fse [ 0 ] = 45
- 62 63 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
- 64 # Set up logging message depending on dynamic parameter and seeds.
- 65 msg_start = (
- 66 f "N = { params [ 'number_of_grains' ] } ; "
- 67 + f "λ∗ = { params [ 'nucleation_efficiency' ] } ; "
- 68 + f "X = { params [ 'gbs_threshold' ] } ; "
- 69 + f "M∗ = { params [ 'gbm_mobility' ] } ; "
- 70 )
- 71 if seed is not None :
- 72 msg_start += f "# { seed } ; "
+ 29 30 class TestPreliminaries :
+ 31 """Preliminary tests to check that various auxiliary routines are working."""
+ 32 33 def test_strain_increment ( self ):
+ 34 """Test for accumulating strain via strain increment calculations."""
+ 35 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "X" , "Z" , 1 )
+ 36 timestamps = np . linspace ( 0 , 1 , 10 ) # Solve until D₀t=1 (tensorial strain).
+ 37 strains_inc = np . zeros_like ( timestamps )
+ 38 L = get_velocity_gradient ( Ŋ ([ 0e0 , 0e0 , 0e0 ]))
+ 39 for i , ε in enumerate ( strains_inc [ 1 :]):
+ 40 strains_inc [ i + 1 ] = strains_inc [ i ] + _utils . strain_increment (
+ 41 timestamps [ 1 ] - timestamps [ 0 ],
+ 42 L ,
+ 43 )
+ 44 # For constant timesteps, check strains == positive_timestamps * strain_rate.
+ 45 nt . assert_allclose ( strains_inc , timestamps , atol = 6e-16 , rtol = 0 )
+ 46 47 # Same thing, but for strain rate similar to experiments.
+ 48 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , 1e-5 )
+ 49 timestamps = np . linspace ( 0 , 1e6 , 10 ) # Solve until D₀t=10 (tensorial strain).
+ 50 strains_inc = np . zeros_like ( timestamps )
+ 51 L = get_velocity_gradient ( Ŋ ([ 0e0 , 0e0 , 0e0 ]))
+ 52 for i , ε in enumerate ( strains_inc [ 1 :]):
+ 53 strains_inc [ i + 1 ] = strains_inc [ i ] + _utils . strain_increment (
+ 54 timestamps [ 1 ] - timestamps [ 0 ],
+ 55 L ,
+ 56 )
+ 57 nt . assert_allclose ( strains_inc , timestamps * 1e-5 , atol = 5e-15 , rtol = 0 )
+ 58 59 # Again, but this time the particle will move (using get_pathline).
+ 60 # We use a 400km x 400km box and a strain rate of 1e-15 s⁻¹.
+ 61 get_velocity , get_velocity_gradient = _velocity . simple_shear_2d ( "X" , "Z" , 1e-15 )
+ 62 timestamps , get_position = _paths . get_pathline (
+ 63 Ŋ ([ 1e5 , 0e0 , 1e5 ]),
+ 64 get_velocity ,
+ 65 get_velocity_gradient ,
+ 66 Ŋ ([ - 2e5 , 0e0 , - 2e5 ]),
+ 67 Ŋ ([ 2e5 , 0e0 , 2e5 ]),
+ 68 2 ,
+ 69 regular_steps = 10 ,
+ 70 )
+ 71 positions = [ get_position ( t ) for t in timestamps ]
+ 72 velocity_gradients = [ get_velocity_gradient ( Ŋ ( x )) for x in positions ]
73 74 _log . info ( msg_start + "step %s / %s (t = %s )" , t , len ( timestamps ) - 1 , time )
- 75 76 deformation_gradient = mineral . update_orientations (
- 77 params ,
- 78 deformation_gradient ,
- 79 get_velocity_gradient ,
- 80 pathline = ( time , timestamps [ t ], cls . get_position ),
- 81 )
- 82 _log . debug (
- 83 "› velocity gradient = %s " ,
- 84 get_velocity_gradient ( None ) . flatten (),
- 85 )
- 86 _log . debug ( "› strain D₀t = %.2f " , strain_rate * timestamps [ t ])
- 87 _log . debug (
- 88 "› grain fractions: median = %s , max = %s , min = %s " ,
- 89 np . median ( mineral . fractions [ - 1 ]),
- 90 np . max ( mineral . fractions [ - 1 ]),
- 91 np . min ( mineral . fractions [ - 1 ]),
- 92 )
- 93 if return_fse :
- 94 _ , fse_v = _diagnostics . finite_strain ( deformation_gradient )
- 95 θ_fse [ t ] = _diagnostics . smallest_angle ( fse_v , shear_direction )
- 96 else :
- 97 θ_fse = None
- 98 99 return mineral , θ_fse
-100 101 @classmethod
-102 def interp_GBM_Kaminski2001 ( cls , strains ):
-103 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
-104 _log . info ( "interpolating target CPO angles..." )
-105 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2001_GBMshear.scsv" )
-106 cs_M0 = PchipInterpolator (
-107 _utils . remove_nans ( data . equivalent_strain_M0 ) / 200 ,
-108 _utils . remove_nans ( data . angle_M0 ),
-109 )
-110 cs_M50 = PchipInterpolator (
-111 _utils . remove_nans ( data . equivalent_strain_M50 ) / 200 ,
-112 _utils . remove_nans ( data . angle_M50 ),
-113 )
-114 cs_M200 = PchipInterpolator (
-115 _utils . remove_nans ( data . equivalent_strain_M200 ) / 200 ,
-116 _utils . remove_nans ( data . angle_M200 ),
-117 )
-118 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
-119 120 @classmethod
-121 def interp_GBM_FortranDRex ( cls , strains ):
-122 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-123 _log . info ( "interpolating target CPO angles..." )
-124 data = _io . read_scsv ( _io . data ( "drexF90" ) / "olA_D1E4_dt50_X0_L5.scsv" )
-125 data_strains = np . linspace ( 0 , 1 , 200 )
-126 cs_M0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M0_angle ))
-127 cs_M50 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M50_angle ))
-128 cs_M200 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M200_angle ))
-129 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
-130 131 @classmethod
-132 def interp_GBS_FortranDRex ( cls , strains ):
-133 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-134 _log . info ( "interpolating target CPO angles..." )
-135 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_fortran.scsv" )
-136 data_strains = np . linspace ( 0 , 1 , 200 )
-137 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
-138 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
-139 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
-140 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
-141 142 @classmethod
-143 def interp_GBS_long_FortranDRex ( cls , strains ):
-144 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-145 _log . info ( "interpolating target CPO angles..." )
-146 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_long_fortran.scsv" )
-147 data_strains = np . linspace ( 0 , 2.5 , 500 )
-148 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
-149 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
-150 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
-151 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
-152 153 @classmethod
-154 def interp_GBS_Kaminski2004 ( cls , strains ):
-155 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
-156 _log . info ( "interpolating target CPO angles..." )
-157 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2004_GBSshear.scsv" )
-158 cs_X0 = PchipInterpolator (
-159 _utils . remove_nans ( data . dimensionless_time_X0 ),
-160 45 + _utils . remove_nans ( data . angle_X0 ),
-161 )
-162 cs_X0d2 = PchipInterpolator (
-163 _utils . remove_nans ( data . dimensionless_time_X0d2 ),
-164 45 + _utils . remove_nans ( data . angle_X0d2 ),
-165 )
-166 cs_X0d4 = PchipInterpolator (
-167 _utils . remove_nans ( data . dimensionless_time_X0d4 ),
-168 45 + _utils . remove_nans ( data . angle_X0d4 ),
-169 )
-170 return [ cs_X0 ( strains ), cs_X0d2 ( strains ), cs_X0d4 ( strains )]
-171 172 def test_zero_recrystallisation ( self , seed ):
-173 """Check that M*=0 is a reliable switch to turn off recrystallisation."""
-174 params = _io . DEFAULT_PARAMS
-175 params [ "gbm_mobility" ] = 0
-176 strain_rate = 1
-177 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
-178 shear_direction = [ 0 , 1 , 0 ]
-179 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-180 mineral , _ = self . run (
-181 params ,
-182 timestamps ,
-183 strain_rate ,
-184 get_velocity_gradient ,
-185 shear_direction ,
-186 seed = seed ,
-187 )
-188 for fractions in mineral . fractions [ 1 :]:
-189 nt . assert_allclose ( fractions , mineral . fractions [ 0 ], atol = 1e-15 , rtol = 0 )
-190 191 @pytest . mark . parametrize ( "gbm_mobility" , [ 50 , 100 , 150 ])
-192 def test_grainsize_median ( self , seed , gbm_mobility ):
-193 """Check that M*={50,100,150}, λ*=5 causes decreasing grain size median."""
-194 params = _io . DEFAULT_PARAMS
-195 params [ "gbm_mobility" ] = gbm_mobility
-196 params [ "nucleation_efficiency" ] = 5
-197 strain_rate = 1
-198 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
-199 n_timestamps = len ( timestamps )
-200 shear_direction = [ 0 , 1 , 0 ]
-201 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-202 mineral , _ = self . run (
-203 params ,
-204 timestamps ,
-205 strain_rate ,
-206 get_velocity_gradient ,
-207 shear_direction ,
-208 seed = seed ,
-209 )
-210 medians = np . empty ( n_timestamps )
-211 for i , fractions in enumerate ( mineral . fractions ):
-212 medians [ i ] = np . median ( fractions )
-213 214 # The first diff is positive (~1e-6) before nucleation sets in.
-215 nt . assert_array_less ( np . diff ( medians )[ 1 :], np . full ( n_timestamps - 2 , 0 ))
-216 217 @pytest . mark . slow
-218 @pytest . mark . parametrize ( "gbs_threshold" , [ 0 , 0.2 , 0.4 ])
-219 @pytest . mark . parametrize ( "nucleation_efficiency" , [ 3 , 5 , 10 ])
-220 def test_dvdx_ensemble (
-221 self , outdir , seeds_nearX45 , ncpus , gbs_threshold , nucleation_efficiency
-222 ):
-223 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
-224 225 Velocity gradient:
-226 $$\bm{L} = \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}$$
-227 228 """
-229 strain_rate = 1
-230 timestamps = np . linspace ( 0 , 1 , 201 ) # Solve until D₀t=1 ('shear' γ=2).
-231 n_timestamps = len ( timestamps )
-232 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
-233 _seeds = seeds_nearX45
-234 n_seeds = len ( _seeds )
-235 236 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-237 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-238 239 gbm_mobilities = [ 0 , 50 , 125 , 200 ]
-240 markers = ( "x" , "*" , "d" , "s" )
-241 242 _id = f "X { _io . stringify ( gbs_threshold ) } _L { _io . stringify ( nucleation_efficiency ) } "
-243 # Output setup with optional logging and data series labels.
-244 θ_fse = np . empty_like ( timestamps )
-245 angles = np . empty (( len ( gbm_mobilities ), n_seeds , n_timestamps ))
-246 optional_logging = cl . nullcontext ()
-247 if outdir is not None :
-248 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _dvdx_ensemble_ { _id } "
-249 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-250 labels = []
-251 252 with optional_logging :
-253 clock_start = process_time ()
-254 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-255 if m == 0 :
-256 return_fse = True
-257 else :
-258 return_fse = False
-259 260 params = {
-261 "olivine_fraction" : 1.0 ,
-262 "enstatite_fraction" : 0.0 ,
-263 "stress_exponent" : 1.5 ,
-264 "deformation_exponent" : 3.5 ,
-265 "gbm_mobility" : gbm_mobility ,
-266 "gbs_threshold" : gbs_threshold ,
-267 "nucleation_efficiency" : nucleation_efficiency ,
-268 "number_of_grains" : 5000 ,
-269 "initial_olivine_fabric" : "A" ,
-270 }
+ 74 # Check that polycrystal is experiencing steady velocity gradient.
+ 75 nt . assert_array_equal (
+ 76 velocity_gradients , np . full_like ( velocity_gradients , velocity_gradients [ 0 ])
+ 77 )
+ 78 # Check that positions are changing as expected.
+ 79 xdiff = np . diff ( Ŋ ([ x [ 0 ] for x in positions ]))
+ 80 zdiff = np . diff ( Ŋ ([ x [ 2 ] for x in positions ]))
+ 81 assert xdiff [ 0 ] > 0
+ 82 assert zdiff [ 0 ] == 0
+ 83 nt . assert_allclose ( xdiff , np . full_like ( xdiff , xdiff [ 0 ]), rtol = 0 , atol = 1e-10 )
+ 84 nt . assert_allclose ( zdiff , np . full_like ( zdiff , zdiff [ 0 ]), rtol = 0 , atol = 1e-10 )
+ 85 strains_inc = np . zeros_like ( timestamps )
+ 86 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+ 87 strains_inc [ t ] = strains_inc [ t - 1 ] + (
+ 88 _utils . strain_increment ( timestamps [ t ] - time , velocity_gradients [ t ])
+ 89 )
+ 90 # fig, ax, _, _ = _vis.pathline_box2d(
+ 91 # None,
+ 92 # get_velocity,
+ 93 # "xz",
+ 94 # strains_inc,
+ 95 # positions,
+ 96 # ".",
+ 97 # Ŋ([-2e5, -2e5]),
+ 98 # Ŋ([2e5, 2e5]),
+ 99 # [20, 20],
+100 # )
+101 # fig.savefig("/tmp/fig.png")
+102 nt . assert_allclose (
+103 strains_inc ,
+104 ( timestamps - timestamps [ 0 ]) * 1e-15 ,
+105 atol = 5e-15 ,
+106 rtol = 0 ,
+107 )
+108 109 110 class TestOlivineA :
+111 """Tests for stationary A-type olivine polycrystals in 2D simple shear."""
+112 113 class_id = "olivineA"
+114 115 @classmethod
+116 def run (
+117 cls ,
+118 params ,
+119 timestamps ,
+120 strain_rate ,
+121 get_velocity_gradient ,
+122 shear_direction ,
+123 seed = None ,
+124 return_fse = None ,
+125 get_position = lambda t : np . zeros ( 3 ), # Stationary particles by default.
+126 ):
+127 """Reusable logic for 2D olivine (A-type) simple shear tests.
+128 129 Returns a tuple with the mineral and the FSE angle (or `None` if `return_fse` is
+130 `None`).
+131 132 """
+133 mineral = _minerals . Mineral (
+134 phase = _core . MineralPhase . olivine ,
+135 fabric = _core . MineralFabric . olivine_A ,
+136 regime = _core . DeformationRegime . dislocation ,
+137 n_grains = params [ "number_of_grains" ],
+138 seed = seed ,
+139 )
+140 deformation_gradient = np . eye ( 3 ) # Undeformed initial state.
+141 θ_fse = np . empty_like ( timestamps )
+142 θ_fse [ 0 ] = 45
+143 144 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+145 # Set up logging message depending on dynamic parameter and seeds.
+146 msg_start = (
+147 f "N = { params [ 'number_of_grains' ] } ; "
+148 + f "λ∗ = { params [ 'nucleation_efficiency' ] } ; "
+149 + f "X = { params [ 'gbs_threshold' ] } ; "
+150 + f "M∗ = { params [ 'gbm_mobility' ] } ; "
+151 )
+152 if seed is not None :
+153 msg_start += f "# { seed } ; "
+154 155 _log . info ( msg_start + "step %s / %s (t = %s )" , t , len ( timestamps ) - 1 , time )
+156 157 deformation_gradient = mineral . update_orientations (
+158 params ,
+159 deformation_gradient ,
+160 get_velocity_gradient ,
+161 pathline = ( time , timestamps [ t ], get_position ),
+162 )
+163 _log . debug (
+164 "› velocity gradient = %s " ,
+165 get_velocity_gradient ( None ) . flatten (),
+166 )
+167 _log . debug ( "› strain D₀t = %.2f " , strain_rate * timestamps [ t ])
+168 _log . debug (
+169 "› grain fractions: median = %s , max = %s , min = %s " ,
+170 np . median ( mineral . fractions [ - 1 ]),
+171 np . max ( mineral . fractions [ - 1 ]),
+172 np . min ( mineral . fractions [ - 1 ]),
+173 )
+174 if return_fse :
+175 _ , fse_v = _diagnostics . finite_strain ( deformation_gradient )
+176 θ_fse [ t ] = _diagnostics . smallest_angle ( fse_v , shear_direction )
+177 else :
+178 θ_fse = None
+179 180 return mineral , θ_fse
+181 182 @classmethod
+183 def interp_GBM_Kaminski2001 ( cls , strains ):
+184 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
+185 _log . info ( "interpolating target CPO angles..." )
+186 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2001_GBMshear.scsv" )
+187 cs_M0 = PchipInterpolator (
+188 _utils . remove_nans ( data . equivalent_strain_M0 ) / 200 ,
+189 _utils . remove_nans ( data . angle_M0 ),
+190 )
+191 cs_M50 = PchipInterpolator (
+192 _utils . remove_nans ( data . equivalent_strain_M50 ) / 200 ,
+193 _utils . remove_nans ( data . angle_M50 ),
+194 )
+195 cs_M200 = PchipInterpolator (
+196 _utils . remove_nans ( data . equivalent_strain_M200 ) / 200 ,
+197 _utils . remove_nans ( data . angle_M200 ),
+198 )
+199 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
+200 201 @classmethod
+202 def interp_GBM_FortranDRex ( cls , strains ):
+203 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+204 _log . info ( "interpolating target CPO angles..." )
+205 data = _io . read_scsv ( _io . data ( "drexF90" ) / "olA_D1E4_dt50_X0_L5.scsv" )
+206 data_strains = np . linspace ( 0 , 1 , 200 )
+207 cs_M0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M0_angle ))
+208 cs_M50 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M50_angle ))
+209 cs_M200 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M200_angle ))
+210 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
+211 212 @classmethod
+213 def interp_GBS_FortranDRex ( cls , strains ):
+214 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+215 _log . info ( "interpolating target CPO angles..." )
+216 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_fortran.scsv" )
+217 data_strains = np . linspace ( 0 , 1 , 200 )
+218 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
+219 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
+220 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
+221 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
+222 223 @classmethod
+224 def interp_GBS_long_FortranDRex ( cls , strains ):
+225 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+226 _log . info ( "interpolating target CPO angles..." )
+227 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_long_fortran.scsv" )
+228 data_strains = np . linspace ( 0 , 2.5 , 500 )
+229 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
+230 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
+231 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
+232 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
+233 234 @classmethod
+235 def interp_GBS_Kaminski2004 ( cls , strains ):
+236 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
+237 _log . info ( "interpolating target CPO angles..." )
+238 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2004_GBSshear.scsv" )
+239 cs_X0 = PchipInterpolator (
+240 _utils . remove_nans ( data . dimensionless_time_X0 ),
+241 45 + _utils . remove_nans ( data . angle_X0 ),
+242 )
+243 cs_X0d2 = PchipInterpolator (
+244 _utils . remove_nans ( data . dimensionless_time_X0d2 ),
+245 45 + _utils . remove_nans ( data . angle_X0d2 ),
+246 )
+247 cs_X0d4 = PchipInterpolator (
+248 _utils . remove_nans ( data . dimensionless_time_X0d4 ),
+249 45 + _utils . remove_nans ( data . angle_X0d4 ),
+250 )
+251 return [ cs_X0 ( strains ), cs_X0d2 ( strains ), cs_X0d4 ( strains )]
+252 253 def test_zero_recrystallisation ( self , seed ):
+254 """Check that M*=0 is a reliable switch to turn off recrystallisation."""
+255 params = _io . DEFAULT_PARAMS
+256 params [ "gbm_mobility" ] = 0
+257 strain_rate = 1
+258 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
+259 shear_direction = [ 0 , 1 , 0 ]
+260 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+261 mineral , _ = self . run (
+262 params ,
+263 timestamps ,
+264 strain_rate ,
+265 get_velocity_gradient ,
+266 shear_direction ,
+267 seed = seed ,
+268 )
+269 for fractions in mineral . fractions [ 1 :]:
+270 nt . assert_allclose ( fractions , mineral . fractions [ 0 ], atol = 1e-15 , rtol = 0 )
271 272 _run = ft . partial (
-273 self . run ,
-274 params ,
-275 timestamps ,
-276 strain_rate ,
-277 get_velocity_gradient ,
-278 shear_direction ,
-279 return_fse = return_fse ,
-280 )
-281 with Pool ( processes = ncpus ) as pool :
-282 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-283 mineral , fse_angles = out
-284 angles [ m , s , :] = [
-285 _diagnostics . smallest_angle ( v , shear_direction )
-286 for v in _diagnostics . elasticity_components (
-287 _minerals . voigt_averages ([ mineral ], params )
-288 )[ "hexagonal_axis" ]
-289 ]
-290 # Save the whole mineral for the first seed only.
-291 if outdir is not None and s == 0 :
-292 postfix = (
-293 f "M { _io . stringify ( gbm_mobility ) } "
-294 + f "_X { _io . stringify ( gbs_threshold ) } "
-295 + f "_L { _io . stringify ( nucleation_efficiency ) } "
-296 )
-297 mineral . save ( f " { out_basepath } .npz" , postfix = postfix )
-298 if return_fse :
-299 θ_fse += fse_angles
-300 301 if return_fse :
-302 θ_fse /= n_seeds
-303 304 if outdir is not None :
-305 labels . append ( f "$M^∗$ = { gbm_mobility } " )
-306 307 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+272 @pytest . mark . parametrize ( "gbm_mobility" , [ 50 , 100 , 150 ])
+273 def test_grainsize_median ( self , seed , gbm_mobility ):
+274 """Check that M*={50,100,150}, λ*=5 causes decreasing grain size median."""
+275 params = _io . DEFAULT_PARAMS
+276 params [ "gbm_mobility" ] = gbm_mobility
+277 params [ "nucleation_efficiency" ] = 5
+278 strain_rate = 1
+279 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
+280 n_timestamps = len ( timestamps )
+281 shear_direction = [ 0 , 1 , 0 ]
+282 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+283 mineral , _ = self . run (
+284 params ,
+285 timestamps ,
+286 strain_rate ,
+287 get_velocity_gradient ,
+288 shear_direction ,
+289 seed = seed ,
+290 )
+291 medians = np . empty ( n_timestamps )
+292 for i , fractions in enumerate ( mineral . fractions ):
+293 medians [ i ] = np . median ( fractions )
+294 295 # The first diff is positive (~1e-6) before nucleation sets in.
+296 nt . assert_array_less ( np . diff ( medians )[ 1 :], np . full ( n_timestamps - 2 , 0 ))
+297 298 @pytest . mark . slow
+299 @pytest . mark . parametrize ( "gbs_threshold" , [ 0 , 0.2 , 0.4 ])
+300 @pytest . mark . parametrize ( "nucleation_efficiency" , [ 3 , 5 , 10 ])
+301 def test_dvdx_ensemble (
+302 self , outdir , seeds_nearX45 , ncpus , gbs_threshold , nucleation_efficiency
+303 ):
+304 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
+305 306 Velocity gradient:
+307 $$\bm{L} = \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}$$
308 309 # Take ensemble means and optionally plot figure.
-310 strains = timestamps * strain_rate
-311 _log . info ( "postprocessing results for %s " , _id )
-312 result_angles = angles . mean ( axis = 1 )
-313 result_angles_err = angles . std ( axis = 1 )
-314 315 if outdir is not None :
-316 schema = {
-317 "delimiter" : "," ,
-318 "missing" : "-" ,
-319 "fields" : [
-320 {
-321 "name" : "strain" ,
-322 "type" : "integer" ,
-323 "unit" : "percent" ,
-324 "fill" : 999999 ,
-325 }
-326 ],
-327 }
-328 np . savez (
-329 f " { out_basepath } .npz" ,
-330 angles = result_angles ,
-331 angles_err = result_angles_err ,
-332 )
-333 _io . save_scsv (
-334 f " { out_basepath } _strains.scsv" ,
-335 schema ,
-336 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-337 )
-338 fig , ax , colors = _vis . alignment (
-339 None ,
-340 strains ,
-341 result_angles ,
-342 markers ,
-343 labels ,
-344 err = result_angles_err ,
-345 θ_max = 60 ,
-346 θ_fse = θ_fse ,
-347 )
-348 fig . savefig ( _io . resolve_path ( f " { out_basepath } .pdf" ))
-349 350 @pytest . mark . slow
-351 def test_dvdx_GBM ( self , outdir , seeds_nearX45 , ncpus ):
-352 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
-353 354 Velocity gradient:
-355 $$
-356 \bm{L} = 10^{-4} ×
-357 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
-358 $$
-359 360 Results are compared to the Fortran 90 output.
-361 362 """
-363 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-364 strain_rate = 1e-4
-365 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-366 timestamps = np . linspace ( 0 , 1e4 , 51 ) # Solve until D₀t=1 ('shear' γ=2).
-367 i_strain_40p = 10 # Index of 40% strain, lower strains are not relevant here.
-368 i_strain_100p = 25 # Index of 100% strain, when M*=0 matches FSE.
-369 params = _io . DEFAULT_PARAMS
-370 params [ "gbs_threshold" ] = 0 # No GBS, to match the Fortran parameters.
-371 gbm_mobilities = ( 0 , 10 , 50 , 125 , 200 ) # Must be in ascending order.
-372 markers = ( "x" , "." , "*" , "d" , "s" )
-373 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
-374 _seeds = seeds_nearX45
-375 n_seeds = len ( _seeds )
-376 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
-377 θ_fse = np . zeros_like ( timestamps )
-378 strains = timestamps * strain_rate
-379 M0_drexF90 , M50_drexF90 , M200_drexF90 = self . interp_GBM_FortranDRex ( strains )
-380 381 optional_logging = cl . nullcontext ()
-382 if outdir is not None :
-383 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _mobility"
-384 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-385 labels = []
-386 387 with optional_logging :
-388 clock_start = process_time ()
-389 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-390 if m == 0 :
-391 return_fse = True
-392 else :
-393 return_fse = False
-394 params [ "gbm_mobility" ] = gbm_mobility
+309 """
+310 strain_rate = 1
+311 timestamps = np . linspace ( 0 , 1 , 201 ) # Solve until D₀t=1 ('shear' γ=2).
+312 n_timestamps = len ( timestamps )
+313 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
+314 _seeds = seeds_nearX45
+315 n_seeds = len ( _seeds )
+316 317 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+318 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+319 320 gbm_mobilities = [ 0 , 50 , 125 , 200 ]
+321 markers = ( "x" , "*" , "d" , "s" )
+322 323 _id = f "X { _io . stringify ( gbs_threshold ) } _L { _io . stringify ( nucleation_efficiency ) } "
+324 # Output setup with optional logging and data series labels.
+325 θ_fse = np . empty_like ( timestamps )
+326 angles = np . empty (( len ( gbm_mobilities ), n_seeds , n_timestamps ))
+327 optional_logging = cl . nullcontext ()
+328 if outdir is not None :
+329 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _dvdx_ensemble_ { _id } "
+330 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+331 labels = []
+332 333 with optional_logging :
+334 clock_start = process_time ()
+335 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+336 if m == 0 :
+337 return_fse = True
+338 else :
+339 return_fse = False
+340 341 params = {
+342 "olivine_fraction" : 1.0 ,
+343 "enstatite_fraction" : 0.0 ,
+344 "stress_exponent" : 1.5 ,
+345 "deformation_exponent" : 3.5 ,
+346 "gbm_mobility" : gbm_mobility ,
+347 "gbs_threshold" : gbs_threshold ,
+348 "nucleation_efficiency" : nucleation_efficiency ,
+349 "number_of_grains" : 5000 ,
+350 "initial_olivine_fabric" : "A" ,
+351 }
+352 353 _run = ft . partial (
+354 self . run ,
+355 params ,
+356 timestamps ,
+357 strain_rate ,
+358 get_velocity_gradient ,
+359 shear_direction ,
+360 return_fse = return_fse ,
+361 )
+362 with Pool ( processes = ncpus ) as pool :
+363 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+364 mineral , fse_angles = out
+365 angles [ m , s , :] = [
+366 _diagnostics . smallest_angle ( v , shear_direction )
+367 for v in _diagnostics . elasticity_components (
+368 _minerals . voigt_averages ([ mineral ], params )
+369 )[ "hexagonal_axis" ]
+370 ]
+371 # Save the whole mineral for the first seed only.
+372 if outdir is not None and s == 0 :
+373 postfix = (
+374 f "M { _io . stringify ( gbm_mobility ) } "
+375 + f "_X { _io . stringify ( gbs_threshold ) } "
+376 + f "_L { _io . stringify ( nucleation_efficiency ) } "
+377 )
+378 mineral . save ( f " { out_basepath } .npz" , postfix = postfix )
+379 if return_fse :
+380 θ_fse += fse_angles
+381 382 if return_fse :
+383 θ_fse /= n_seeds
+384 385 if outdir is not None :
+386 labels . append ( f "$M^∗$ = { gbm_mobility } " )
+387 388 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+389 390 # Take ensemble means and optionally plot figure.
+391 strains = timestamps * strain_rate
+392 _log . info ( "postprocessing results for %s " , _id )
+393 result_angles = angles . mean ( axis = 1 )
+394 result_angles_err = angles . std ( axis = 1 )
395 396 _run = ft . partial (
-397 self . run ,
-398 params ,
-399 timestamps ,
-400 strain_rate ,
-401 get_velocity_gradient ,
-402 shear_direction ,
-403 return_fse = True ,
-404 )
-405 with Pool ( processes = ncpus ) as pool :
-406 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-407 mineral , fse_angles = out
-408 angles [ m , s , :] = [
-409 _diagnostics . smallest_angle ( v , shear_direction )
-410 for v in _diagnostics . elasticity_components (
-411 _minerals . voigt_averages ([ mineral ], params )
-412 )[ "hexagonal_axis" ]
-413 ]
-414 # Save the whole mineral for the first seed only.
-415 if outdir is not None and s == 0 :
-416 mineral . save (
-417 f " { out_basepath } .npz" ,
-418 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
-419 )
-420 if return_fse :
-421 θ_fse += fse_angles
-422 423 if return_fse :
-424 θ_fse /= n_seeds
-425 426 if outdir is not None :
-427 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
-428 429 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+396 if outdir is not None :
+397 schema = {
+398 "delimiter" : "," ,
+399 "missing" : "-" ,
+400 "fields" : [
+401 {
+402 "name" : "strain" ,
+403 "type" : "integer" ,
+404 "unit" : "percent" ,
+405 "fill" : 999999 ,
+406 }
+407 ],
+408 }
+409 np . savez (
+410 f " { out_basepath } .npz" ,
+411 angles = result_angles ,
+412 angles_err = result_angles_err ,
+413 )
+414 _io . save_scsv (
+415 f " { out_basepath } _strains.scsv" ,
+416 schema ,
+417 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+418 )
+419 fig , ax , colors = _vis . alignment (
+420 None ,
+421 strains ,
+422 result_angles ,
+423 markers ,
+424 labels ,
+425 err = result_angles_err ,
+426 θ_max = 60 ,
+427 θ_fse = θ_fse ,
+428 )
+429 fig . savefig ( _io . resolve_path ( f " { out_basepath } .pdf" ))
430 431 # Take ensemble means and optionally plot figure.
-432 _log . info ( "postprocessing results..." )
-433 result_angles = angles . mean ( axis = 1 )
-434 result_angles_err = angles . std ( axis = 1 )
-435 436 if outdir is not None :
-437 schema = {
-438 "delimiter" : "," ,
-439 "missing" : "-" ,
-440 "fields" : [
-441 {
-442 "name" : "strain" ,
-443 "type" : "integer" ,
-444 "unit" : "percent" ,
-445 "fill" : 999999 ,
-446 }
-447 ],
-448 }
-449 _io . save_scsv (
-450 f " { out_basepath } _strains.scsv" ,
-451 schema ,
-452 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-453 )
-454 np . savez (
-455 f " { out_basepath } _angles.npz" ,
-456 angles = result_angles ,
-457 err = result_angles_err ,
-458 )
-459 fig , ax , colors = _vis . alignment (
-460 None ,
-461 strains ,
-462 result_angles ,
-463 markers ,
-464 labels ,
-465 err = result_angles_err ,
-466 θ_max = 60 ,
-467 θ_fse = θ_fse ,
-468 )
-469 ax . plot ( strains , M0_drexF90 , c = colors [ 0 ])
-470 ax . plot ( strains , M50_drexF90 , c = colors [ 2 ])
-471 ax . plot ( strains , M200_drexF90 , c = colors [ 4 ])
-472 _vis . show_Skemer2016_ShearStrainAngles (
-473 ax ,
-474 [ "Z&K 1200 C" , "Z&K 1300 C" ],
-475 [ "v" , "^" ],
-476 [ "k" , "k" ],
-477 [ "none" , None ],
-478 [
-479 "Zhang & Karato, 1995 \n (1473 K)" ,
-480 "Zhang & Karato, 1995 \n (1573 K)" ,
-481 ],
-482 _core . MineralFabric . olivine_A ,
-483 )
-484 # There is a lot of stuff on this legend, so put it outside the axes.
-485 # These values might need to be tweaked depending on the font size, etc.
-486 _legend = _utils . redraw_legend ( ax , fig = fig , bbox_to_anchor = ( 1.66 , 0.99 ))
-487 fig . savefig (
-488 _io . resolve_path ( f " { out_basepath } .pdf" ),
-489 bbox_extra_artists = ( _legend ,),
-490 bbox_inches = "tight" ,
-491 )
-492 493 # Check that GBM speeds up the alignment between 40% and 100% strain.
-494 _log . info ( "checking grain orientations..." )
-495 for i , θ in enumerate ( result_angles [: - 1 ], start = 1 ):
-496 nt . assert_array_less (
-497 result_angles [ i ][ i_strain_40p : i_strain_100p ],
-498 θ [ i_strain_40p : i_strain_100p ],
-499 )
-500 501 # Check that M*=0 matches FSE (±1°) past 100% strain.
-502 nt . assert_allclose (
-503 result_angles [ 0 ][ i_strain_100p :],
-504 θ_fse [ i_strain_100p :],
-505 atol = 1 ,
-506 rtol = 0 ,
-507 )
-508 509 # Check that results match Fortran output past 40% strain.
-510 nt . assert_allclose (
-511 result_angles [ 0 ][ i_strain_40p :],
-512 M0_drexF90 [ i_strain_40p :],
-513 atol = 0 ,
-514 rtol = 0.1 , # At 40% strain the match is worse than at higher strain.
-515 )
-516 nt . assert_allclose (
-517 result_angles [ 2 ][ i_strain_40p :],
-518 M50_drexF90 [ i_strain_40p :],
-519 atol = 1 ,
-520 rtol = 0 ,
-521 )
-522 nt . assert_allclose (
-523 result_angles [ 4 ][ i_strain_40p :],
-524 M200_drexF90 [ i_strain_40p :],
-525 atol = 1.5 ,
-526 rtol = 0 ,
-527 )
-528 529 @pytest . mark . slow
-530 def test_GBM_calibration ( self , outdir , seeds , ncpus ):
-531 r """Compare results for various values of $$M^∗$$ to A-type olivine data.
-532 533 Velocity gradient:
-534 $$
-535 \bm{L} = 10^{-4} ×
-536 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
-537 $$
-538 539 Unlike `test_dvdx_GBM`,
-540 grain boudary sliding is enabled here (see `_io.DEFAULT_PARAMS`).
-541 Data are provided by [Skemer & Hansen, 2016](http://dx.doi.org/10.1016/j.tecto.2015.12.003).
-542 543 """
-544 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-545 strain_rate = 1
-546 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-547 timestamps = np . linspace ( 0 , 3.2 , 65 ) # Solve until D₀t=3.2 ('shear' γ=6.4).
-548 params = _io . DEFAULT_PARAMS
-549 params [ "number_of_grains" ] = 5000
-550 gbm_mobilities = ( 0 , 10 , 50 , 125 ) # Must be in ascending order.
-551 markers = ( "x" , "*" , "1" , "." )
-552 # Uses 100 seeds by default; use all 1000 if you have more RAM and CPU time.
-553 _seeds = seeds [: 100 ]
-554 n_seeds = len ( _seeds )
-555 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
-556 θ_fse = np . zeros_like ( timestamps )
-557 strains = timestamps * strain_rate
-558 559 optional_logging = cl . nullcontext ()
-560 if outdir is not None :
-561 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _calibration"
-562 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-563 labels = []
-564 565 with optional_logging :
-566 clock_start = process_time ()
-567 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-568 return_fse = True if m == 0 else False
-569 params [ "gbm_mobility" ] = gbm_mobility
-570 _run = ft . partial (
-571 self . run ,
-572 params ,
-573 timestamps ,
-574 strain_rate ,
-575 get_velocity_gradient ,
-576 shear_direction ,
-577 return_fse = return_fse ,
-578 )
-579 with Pool ( processes = ncpus ) as pool :
-580 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-581 mineral , fse_angles = out
-582 angles [ m , s , :] = [
-583 _diagnostics . smallest_angle ( v , shear_direction )
-584 for v in _diagnostics . elasticity_components (
-585 _minerals . voigt_averages ([ mineral ], params )
-586 )[ "hexagonal_axis" ]
-587 ]
-588 # Save the whole mineral for the first seed only.
-589 if outdir is not None and s == 0 :
-590 mineral . save (
-591 f " { out_basepath } .npz" ,
-592 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
-593 )
-594 if return_fse :
-595 θ_fse += fse_angles
-596 597 if return_fse :
-598 θ_fse /= n_seeds
-599 600 if outdir is not None :
-601 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
-602 603 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
-604 605 # Take ensemble means and optionally plot figure.
-606 _log . info ( "postprocessing results..." )
-607 result_angles = angles . mean ( axis = 1 )
-608 result_angles_err = angles . std ( axis = 1 )
+431 @pytest . mark . slow
+432 def test_dvdx_GBM ( self , outdir , seeds_nearX45 , ncpus ):
+433 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
+434 435 Velocity gradient:
+436 $$
+437 \bm{L} = 10^{-4} ×
+438 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
+439 $$
+440 441 Results are compared to the Fortran 90 output.
+442 443 """
+444 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+445 strain_rate = 1e-4
+446 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+447 timestamps = np . linspace ( 0 , 1e4 , 51 ) # Solve until D₀t=1 ('shear' γ=2).
+448 i_strain_40p = 10 # Index of 40% strain, lower strains are not relevant here.
+449 i_strain_100p = 25 # Index of 100% strain, when M*=0 matches FSE.
+450 params = _io . DEFAULT_PARAMS
+451 params [ "gbs_threshold" ] = 0 # No GBS, to match the Fortran parameters.
+452 gbm_mobilities = ( 0 , 10 , 50 , 125 , 200 ) # Must be in ascending order.
+453 markers = ( "x" , "." , "*" , "d" , "s" )
+454 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
+455 _seeds = seeds_nearX45
+456 n_seeds = len ( _seeds )
+457 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
+458 θ_fse = np . zeros_like ( timestamps )
+459 strains = timestamps * strain_rate
+460 M0_drexF90 , M50_drexF90 , M200_drexF90 = self . interp_GBM_FortranDRex ( strains )
+461 462 optional_logging = cl . nullcontext ()
+463 if outdir is not None :
+464 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _mobility"
+465 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+466 labels = []
+467 468 with optional_logging :
+469 clock_start = process_time ()
+470 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+471 if m == 0 :
+472 return_fse = True
+473 else :
+474 return_fse = False
+475 params [ "gbm_mobility" ] = gbm_mobility
+476 477 _run = ft . partial (
+478 self . run ,
+479 params ,
+480 timestamps ,
+481 strain_rate ,
+482 get_velocity_gradient ,
+483 shear_direction ,
+484 return_fse = True ,
+485 )
+486 with Pool ( processes = ncpus ) as pool :
+487 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+488 mineral , fse_angles = out
+489 angles [ m , s , :] = [
+490 _diagnostics . smallest_angle ( v , shear_direction )
+491 for v in _diagnostics . elasticity_components (
+492 _minerals . voigt_averages ([ mineral ], params )
+493 )[ "hexagonal_axis" ]
+494 ]
+495 # Save the whole mineral for the first seed only.
+496 if outdir is not None and s == 0 :
+497 mineral . save (
+498 f " { out_basepath } .npz" ,
+499 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
+500 )
+501 if return_fse :
+502 θ_fse += fse_angles
+503 504 if return_fse :
+505 θ_fse /= n_seeds
+506 507 if outdir is not None :
+508 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
+509 510 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+511 512 # Take ensemble means and optionally plot figure.
+513 _log . info ( "postprocessing results..." )
+514 result_angles = angles . mean ( axis = 1 )
+515 result_angles_err = angles . std ( axis = 1 )
+516 517 if outdir is not None :
+518 schema = {
+519 "delimiter" : "," ,
+520 "missing" : "-" ,
+521 "fields" : [
+522 {
+523 "name" : "strain" ,
+524 "type" : "integer" ,
+525 "unit" : "percent" ,
+526 "fill" : 999999 ,
+527 }
+528 ],
+529 }
+530 _io . save_scsv (
+531 f " { out_basepath } _strains.scsv" ,
+532 schema ,
+533 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+534 )
+535 np . savez (
+536 f " { out_basepath } _angles.npz" ,
+537 angles = result_angles ,
+538 err = result_angles_err ,
+539 )
+540 fig , ax , colors = _vis . alignment (
+541 None ,
+542 strains ,
+543 result_angles ,
+544 markers ,
+545 labels ,
+546 err = result_angles_err ,
+547 θ_max = 60 ,
+548 θ_fse = θ_fse ,
+549 )
+550 ax . plot ( strains , M0_drexF90 , c = colors [ 0 ])
+551 ax . plot ( strains , M50_drexF90 , c = colors [ 2 ])
+552 ax . plot ( strains , M200_drexF90 , c = colors [ 4 ])
+553 _vis . show_Skemer2016_ShearStrainAngles (
+554 ax ,
+555 [ "Z&K 1200 C" , "Z&K 1300 C" ],
+556 [ "v" , "^" ],
+557 [ "k" , "k" ],
+558 [ "none" , None ],
+559 [
+560 "Zhang & Karato, 1995 \n (1473 K)" ,
+561 "Zhang & Karato, 1995 \n (1573 K)" ,
+562 ],
+563 _core . MineralFabric . olivine_A ,
+564 )
+565 # There is a lot of stuff on this legend, so put it outside the axes.
+566 # These values might need to be tweaked depending on the font size, etc.
+567 _legend = _utils . redraw_legend ( ax , fig = fig , bbox_to_anchor = ( 1.66 , 0.99 ))
+568 fig . savefig (
+569 _io . resolve_path ( f " { out_basepath } .pdf" ),
+570 bbox_extra_artists = ( _legend ,),
+571 bbox_inches = "tight" ,
+572 )
+573 574 # Check that GBM speeds up the alignment between 40% and 100% strain.
+575 _log . info ( "checking grain orientations..." )
+576 for i , θ in enumerate ( result_angles [: - 1 ], start = 1 ):
+577 nt . assert_array_less (
+578 result_angles [ i ][ i_strain_40p : i_strain_100p ],
+579 θ [ i_strain_40p : i_strain_100p ],
+580 )
+581 582 # Check that M*=0 matches FSE (±1°) past 100% strain.
+583 nt . assert_allclose (
+584 result_angles [ 0 ][ i_strain_100p :],
+585 θ_fse [ i_strain_100p :],
+586 atol = 1 ,
+587 rtol = 0 ,
+588 )
+589 590 # Check that results match Fortran output past 40% strain.
+591 nt . assert_allclose (
+592 result_angles [ 0 ][ i_strain_40p :],
+593 M0_drexF90 [ i_strain_40p :],
+594 atol = 0 ,
+595 rtol = 0.1 , # At 40% strain the match is worse than at higher strain.
+596 )
+597 nt . assert_allclose (
+598 result_angles [ 2 ][ i_strain_40p :],
+599 M50_drexF90 [ i_strain_40p :],
+600 atol = 1 ,
+601 rtol = 0 ,
+602 )
+603 nt . assert_allclose (
+604 result_angles [ 4 ][ i_strain_40p :],
+605 M200_drexF90 [ i_strain_40p :],
+606 atol = 1.5 ,
+607 rtol = 0 ,
+608 )
609 610 if outdir is not None :
-611 schema = {
-612 "delimiter" : "," ,
-613 "missing" : "-" ,
-614 "fields" : [
-615 {
-616 "name" : "strain" ,
-617 "type" : "integer" ,
-618 "unit" : "percent" ,
-619 "fill" : 999999 ,
-620 }
-621 ],
-622 }
-623 _io . save_scsv (
-624 f " { out_basepath } _strains.scsv" ,
-625 schema ,
-626 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-627 )
-628 np . savez (
-629 _io . resolve_path ( f " { out_basepath } _ensemble_means.npz" ),
-630 angles = result_angles ,
-631 err = result_angles_err ,
-632 )
-633 fig = _vis . figure (
-634 figsize = ( _vis . DEFAULT_FIG_WIDTH * 3 , _vis . DEFAULT_FIG_HEIGHT )
-635 )
-636 fig , ax , colors = _vis . alignment (
-637 fig . add_subplot (),
-638 strains ,
-639 result_angles ,
-640 markers ,
-641 labels ,
-642 err = result_angles_err ,
-643 θ_max = 80 ,
-644 θ_fse = θ_fse ,
-645 )
-646 (
-647 _ ,
-648 _ ,
-649 _ ,
-650 data_Skemer2016 ,
-651 indices ,
-652 ) = _vis . show_Skemer2016_ShearStrainAngles (
-653 ax ,
-654 [
-655 "Z&K 1200 C" ,
-656 "Z&K 1300 C" ,
-657 "Skemer 2011" ,
-658 "Hansen 2014" ,
-659 "Warren 2008" ,
-660 "Webber 2010" ,
-661 "H&W 2015" ,
-662 ],
-663 [ "v" , "^" , "o" , "s" , "v" , "o" , "s" ],
-664 [ "k" , "k" , "k" , "k" , "k" , "k" , "k" ],
-665 [ "none" , "none" , "none" , "none" , None , None , None ],
-666 [
-667 "Zhang & Karato, 1995 (1473 K)" ,
-668 "Zhang & Karato, 1995 (1573 K)" ,
-669 "Skemer et al., 2011 (1500 K)" ,
-670 "Hansen et al., 2014 (1473 K)" ,
-671 "Warren et al., 2008" ,
-672 "Webber et al., 2010" ,
-673 "Hansen & Warren, 2015" ,
-674 ],
-675 fabric = _core . MineralFabric . olivine_A ,
-676 )
-677 _legend = _utils . redraw_legend ( ax , loc = "upper right" , ncols = 3 )
-678 fig . savefig (
-679 _io . resolve_path ( f " { out_basepath } .pdf" ),
-680 bbox_extra_artists = ( _legend ,),
-681 bbox_inches = "tight" ,
-682 )
-683 r2vals = []
-684 for angles in result_angles :
-685 _angles = PchipInterpolator ( strains , angles )
-686 r2 = np . sum (
-687 [
-688 ( a - b ) ** 2
-689 for a , b in zip (
-690 _angles (
-691 np . take ( data_Skemer2016 . shear_strain , indices ) / 200
-692 ),
-693 np . take ( data_Skemer2016 . angle , indices ),
-694 )
-695 ]
-696 )
-697 r2vals . append ( r2 )
-698 _log . info (
-699 "Sums of squared residuals (r-values) for each M∗: %s " , r2vals
-700 )
+610 @pytest . mark . slow
+611 def test_GBM_calibration ( self , outdir , seeds , ncpus ):
+612 r """Compare results for various values of $$M^∗$$ to A-type olivine data.
+613 614 Velocity gradient:
+615 $$
+616 \bm{L} = 10^{-4} ×
+617 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
+618 $$
+619 620 Unlike `test_dvdx_GBM`,
+621 grain boudary sliding is enabled here (see `_io.DEFAULT_PARAMS`).
+622 Data are provided by [Skemer & Hansen, 2016](http://dx.doi.org/10.1016/j.tecto.2015.12.003).
+623 624 """
+625 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+626 strain_rate = 1
+627 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+628 timestamps = np . linspace ( 0 , 3.2 , 65 ) # Solve until D₀t=3.2 ('shear' γ=6.4).
+629 params = _io . DEFAULT_PARAMS
+630 params [ "number_of_grains" ] = 5000
+631 gbm_mobilities = ( 0 , 10 , 50 , 125 ) # Must be in ascending order.
+632 markers = ( "x" , "*" , "1" , "." )
+633 # Uses 100 seeds by default; use all 1000 if you have more RAM and CPU time.
+634 _seeds = seeds [: 100 ]
+635 n_seeds = len ( _seeds )
+636 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
+637 θ_fse = np . zeros_like ( timestamps )
+638 strains = timestamps * strain_rate
+639 640 optional_logging = cl . nullcontext ()
+641 if outdir is not None :
+642 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _calibration"
+643 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+644 labels = []
+645 646 with optional_logging :
+647 clock_start = process_time ()
+648 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+649 return_fse = True if m == 0 else False
+650 params [ "gbm_mobility" ] = gbm_mobility
+651 _run = ft . partial (
+652 self . run ,
+653 params ,
+654 timestamps ,
+655 strain_rate ,
+656 get_velocity_gradient ,
+657 shear_direction ,
+658 return_fse = return_fse ,
+659 )
+660 with Pool ( processes = ncpus ) as pool :
+661 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+662 mineral , fse_angles = out
+663 angles [ m , s , :] = [
+664 _diagnostics . smallest_angle ( v , shear_direction )
+665 for v in _diagnostics . elasticity_components (
+666 _minerals . voigt_averages ([ mineral ], params )
+667 )[ "hexagonal_axis" ]
+668 ]
+669 # Save the whole mineral for the first seed only.
+670 if outdir is not None and s == 0 :
+671 mineral . save (
+672 f " { out_basepath } .npz" ,
+673 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
+674 )
+675 if return_fse :
+676 θ_fse += fse_angles
+677 678 if return_fse :
+679 θ_fse /= n_seeds
+680 681 if outdir is not None :
+682 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
+683 684 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+685 686 # Take ensemble means and optionally plot figure.
+687 _log . info ( "postprocessing results..." )
+688 result_angles = angles . mean ( axis = 1 )
+689 result_angles_err = angles . std ( axis = 1 )
+690 691 if outdir is not None :
+692 schema = {
+693 "delimiter" : "," ,
+694 "missing" : "-" ,
+695 "fields" : [
+696 {
+697 "name" : "strain" ,
+698 "type" : "integer" ,
+699 "unit" : "percent" ,
+700 "fill" : 999999 ,
+701 }
+702 ],
+703 }
+704 _io . save_scsv (
+705 f " { out_basepath } _strains.scsv" ,
+706 schema ,
+707 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+708 )
+709 np . savez (
+710 _io . resolve_path ( f " { out_basepath } _ensemble_means.npz" ),
+711 angles = result_angles ,
+712 err = result_angles_err ,
+713 )
+714 fig = _vis . figure (
+715 figsize = ( _vis . DEFAULT_FIG_WIDTH * 3 , _vis . DEFAULT_FIG_HEIGHT )
+716 )
+717 fig , ax , colors = _vis . alignment (
+718 fig . add_subplot (),
+719 strains ,
+720 result_angles ,
+721 markers ,
+722 labels ,
+723 err = result_angles_err ,
+724 θ_max = 80 ,
+725 θ_fse = θ_fse ,
+726 )
+727 (
+728 _ ,
+729 _ ,
+730 _ ,
+731 data_Skemer2016 ,
+732 indices ,
+733 ) = _vis . show_Skemer2016_ShearStrainAngles (
+734 ax ,
+735 [
+736 "Z&K 1200 C" ,
+737 "Z&K 1300 C" ,
+738 "Skemer 2011" ,
+739 "Hansen 2014" ,
+740 "Warren 2008" ,
+741 "Webber 2010" ,
+742 "H&W 2015" ,
+743 ],
+744 [ "v" , "^" , "o" , "s" , "v" , "o" , "s" ],
+745 [ "k" , "k" , "k" , "k" , "k" , "k" , "k" ],
+746 [ "none" , "none" , "none" , "none" , None , None , None ],
+747 [
+748 "Zhang & Karato, 1995 (1473 K)" ,
+749 "Zhang & Karato, 1995 (1573 K)" ,
+750 "Skemer et al., 2011 (1500 K)" ,
+751 "Hansen et al., 2014 (1473 K)" ,
+752 "Warren et al., 2008" ,
+753 "Webber et al., 2010" ,
+754 "Hansen & Warren, 2015" ,
+755 ],
+756 fabric = _core . MineralFabric . olivine_A ,
+757 )
+758 _legend = _utils . redraw_legend ( ax , loc = "upper right" , ncols = 3 )
+759 fig . savefig (
+760 _io . resolve_path ( f " { out_basepath } .pdf" ),
+761 bbox_extra_artists = ( _legend ,),
+762 bbox_inches = "tight" ,
+763 )
+764 r2vals = []
+765 for angles in result_angles :
+766 _angles = PchipInterpolator ( strains , angles )
+767 r2 = np . sum (
+768 [
+769 ( a - b ) ** 2
+770 for a , b in zip (
+771 _angles (
+772 np . take ( data_Skemer2016 . shear_strain , indices ) / 200
+773 ),
+774 np . take ( data_Skemer2016 . angle , indices ),
+775 )
+776 ]
+777 )
+778 r2vals . append ( r2 )
+779 _log . info (
+780 "Sums of squared residuals (r-values) for each M∗: %s " , r2vals
+781 )
+782 783 @pytest . mark . big
+784 def test_dudz_pathline ( self , outdir , seed ):
+785 """Test alignment of olivine a-axis for a polycrystal advected on a pathline."""
+786 test_id = "dudz_pathline"
+787 optional_logging = cl . nullcontext ()
+788 if outdir is not None :
+789 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _ { test_id } "
+790 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+791 792 with optional_logging :
+793 shear_direction = [ 1 , 0 , 0 ] # Used to calculate the angular diagnostics.
+794 strain_rate = 1e-15 # Moderate, realistic shear in the upper mantle.
+795 get_velocity , get_velocity_gradient = _velocity . simple_shear_2d (
+796 "X" , "Z" , strain_rate
+797 )
+798 n_timesteps = 10
+799 timestamps , get_position = _paths . get_pathline (
+800 Ŋ ([ 1e5 , 0e0 , 1e5 ]),
+801 get_velocity ,
+802 get_velocity_gradient ,
+803 Ŋ ([ - 2e5 , 0e0 , - 2e5 ]),
+804 Ŋ ([ 2e5 , 0e0 , 2e5 ]),
+805 2 ,
+806 regular_steps = n_timesteps ,
+807 )
+808 positions = [ get_position ( t ) for t in timestamps ]
+809 velocity_gradients = [ get_velocity_gradient ( Ŋ ( x )) for x in positions ]
+810 811 params = _io . DEFAULT_PARAMS
+812 params [ "number_of_grains" ] = 5000
+813 olA = _minerals . Mineral ( n_grains = params [ "number_of_grains" ], seed = seed )
+814 deformation_gradient = np . eye ( 3 )
+815 strains = np . zeros_like ( timestamps )
+816 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+817 strains [ t ] = strains [ t - 1 ] + (
+818 _utils . strain_increment ( timestamps [ t ] - time , velocity_gradients [ t ])
+819 )
+820 _log . info ( "step %d / %d (ε = %.2f )" , t , len ( timestamps ) - 1 , strains [ t ])
+821 deformation_gradient = olA . update_orientations (
+822 params ,
+823 deformation_gradient ,
+824 get_velocity_gradient ,
+825 pathline = ( time , timestamps [ t ], get_position ),
+826 )
+827 828 orient_resampled , fractions_resampled = _stats . resample_orientations (
+829 olA . orientations , olA . fractions , seed = seed
+830 )
+831 # About 36GB, 26 min needed with float64. GitHub macos runner has 14GB.
+832 misorient_indices = _diagnostics . misorientation_indices (
+833 orient_resampled ,
+834 _geo . LatticeSystem . orthorhombic ,
+835 ncpus = 3 ,
+836 )
+837 cpo_vectors = np . zeros (( n_timesteps + 1 , 3 ))
+838 cpo_angles = np . zeros ( n_timesteps + 1 )
+839 for i , matrices in enumerate ( orient_resampled ):
+840 cpo_vectors [ i ] = _diagnostics . bingham_average (
+841 matrices ,
+842 axis = _minerals . OLIVINE_PRIMARY_AXIS [ olA . fabric ],
+843 )
+844 cpo_angles [ i ] = _diagnostics . smallest_angle (
+845 cpo_vectors [ i ], Ŋ ( shear_direction , dtype = np . float64 )
+846 )
+847 848 # Check for mostly decreasing CPO angles (exclude initial condition).
+849 _log . debug ( "cpo angles: %s " , cpo_angles )
+850 nt . assert_array_less ( np . diff ( cpo_angles [ 1 :]), np . ones ( n_timesteps - 1 ))
+851 # Check for increasing CPO strength (M-index).
+852 _log . debug ( "cpo strengths: %s " , misorient_indices )
+853 nt . assert_array_less (
+854 np . full ( n_timesteps , - 0.01 ), np . diff ( misorient_indices )
+855 )
+856 # Check that last angle is <5° (M*=125) or <10° (M*=10).
+857 assert cpo_angles [ - 1 ] < 5
+858 859 if outdir is not None :
+860 fig , ax , _ , _ = _vis . pathline_box2d (
+861 None ,
+862 get_velocity ,
+863 "xz" ,
+864 strains ,
+865 positions ,
+866 "." ,
+867 Ŋ ([ - 2e5 , - 2e5 ]),
+868 Ŋ ([ 2e5 , 2e5 ]),
+869 [ 20 , 20 ],
+870 cpo_vectors = cpo_vectors ,
+871 cpo_strengths = misorient_indices ,
+872 )
+873 fig . savefig ( f " { out_basepath } .pdf" )
+
+
+
+
+ class
+ TestPreliminaries :
+
+ View Source
+
+ 31 class TestPreliminaries :
+ 32 """Preliminary tests to check that various auxiliary routines are working."""
+ 33 34 def test_strain_increment ( self ):
+ 35 """Test for accumulating strain via strain increment calculations."""
+ 36 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "X" , "Z" , 1 )
+ 37 timestamps = np . linspace ( 0 , 1 , 10 ) # Solve until D₀t=1 (tensorial strain).
+ 38 strains_inc = np . zeros_like ( timestamps )
+ 39 L = get_velocity_gradient ( Ŋ ([ 0e0 , 0e0 , 0e0 ]))
+ 40 for i , ε in enumerate ( strains_inc [ 1 :]):
+ 41 strains_inc [ i + 1 ] = strains_inc [ i ] + _utils . strain_increment (
+ 42 timestamps [ 1 ] - timestamps [ 0 ],
+ 43 L ,
+ 44 )
+ 45 # For constant timesteps, check strains == positive_timestamps * strain_rate.
+ 46 nt . assert_allclose ( strains_inc , timestamps , atol = 6e-16 , rtol = 0 )
+ 47 48 # Same thing, but for strain rate similar to experiments.
+ 49 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , 1e-5 )
+ 50 timestamps = np . linspace ( 0 , 1e6 , 10 ) # Solve until D₀t=10 (tensorial strain).
+ 51 strains_inc = np . zeros_like ( timestamps )
+ 52 L = get_velocity_gradient ( Ŋ ([ 0e0 , 0e0 , 0e0 ]))
+ 53 for i , ε in enumerate ( strains_inc [ 1 :]):
+ 54 strains_inc [ i + 1 ] = strains_inc [ i ] + _utils . strain_increment (
+ 55 timestamps [ 1 ] - timestamps [ 0 ],
+ 56 L ,
+ 57 )
+ 58 nt . assert_allclose ( strains_inc , timestamps * 1e-5 , atol = 5e-15 , rtol = 0 )
+ 59 60 # Again, but this time the particle will move (using get_pathline).
+ 61 # We use a 400km x 400km box and a strain rate of 1e-15 s⁻¹.
+ 62 get_velocity , get_velocity_gradient = _velocity . simple_shear_2d ( "X" , "Z" , 1e-15 )
+ 63 timestamps , get_position = _paths . get_pathline (
+ 64 Ŋ ([ 1e5 , 0e0 , 1e5 ]),
+ 65 get_velocity ,
+ 66 get_velocity_gradient ,
+ 67 Ŋ ([ - 2e5 , 0e0 , - 2e5 ]),
+ 68 Ŋ ([ 2e5 , 0e0 , 2e5 ]),
+ 69 2 ,
+ 70 regular_steps = 10 ,
+ 71 )
+ 72 positions = [ get_position ( t ) for t in timestamps ]
+ 73 velocity_gradients = [ get_velocity_gradient ( Ŋ ( x )) for x in positions ]
+ 74 75 # Check that polycrystal is experiencing steady velocity gradient.
+ 76 nt . assert_array_equal (
+ 77 velocity_gradients , np . full_like ( velocity_gradients , velocity_gradients [ 0 ])
+ 78 )
+ 79 # Check that positions are changing as expected.
+ 80 xdiff = np . diff ( Ŋ ([ x [ 0 ] for x in positions ]))
+ 81 zdiff = np . diff ( Ŋ ([ x [ 2 ] for x in positions ]))
+ 82 assert xdiff [ 0 ] > 0
+ 83 assert zdiff [ 0 ] == 0
+ 84 nt . assert_allclose ( xdiff , np . full_like ( xdiff , xdiff [ 0 ]), rtol = 0 , atol = 1e-10 )
+ 85 nt . assert_allclose ( zdiff , np . full_like ( zdiff , zdiff [ 0 ]), rtol = 0 , atol = 1e-10 )
+ 86 strains_inc = np . zeros_like ( timestamps )
+ 87 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+ 88 strains_inc [ t ] = strains_inc [ t - 1 ] + (
+ 89 _utils . strain_increment ( timestamps [ t ] - time , velocity_gradients [ t ])
+ 90 )
+ 91 # fig, ax, _, _ = _vis.pathline_box2d(
+ 92 # None,
+ 93 # get_velocity,
+ 94 # "xz",
+ 95 # strains_inc,
+ 96 # positions,
+ 97 # ".",
+ 98 # Ŋ([-2e5, -2e5]),
+ 99 # Ŋ([2e5, 2e5]),
+100 # [20, 20],
+101 # )
+102 # fig.savefig("/tmp/fig.png")
+103 nt . assert_allclose (
+104 strains_inc ,
+105 ( timestamps - timestamps [ 0 ]) * 1e-15 ,
+106 atol = 5e-15 ,
+107 rtol = 0 ,
+108 )
+Preliminary tests to check that various auxiliary routines are working.
+
+
+
+
+ def
+ test_strain_increment (self ):
+
+ View Source
+
+
34 def test_strain_increment ( self ):
+ 35 """Test for accumulating strain via strain increment calculations."""
+ 36 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "X" , "Z" , 1 )
+ 37 timestamps = np . linspace ( 0 , 1 , 10 ) # Solve until D₀t=1 (tensorial strain).
+ 38 strains_inc = np . zeros_like ( timestamps )
+ 39 L = get_velocity_gradient ( Ŋ ([ 0e0 , 0e0 , 0e0 ]))
+ 40 for i , ε in enumerate ( strains_inc [ 1 :]):
+ 41 strains_inc [ i + 1 ] = strains_inc [ i ] + _utils . strain_increment (
+ 42 timestamps [ 1 ] - timestamps [ 0 ],
+ 43 L ,
+ 44 )
+ 45 # For constant timesteps, check strains == positive_timestamps * strain_rate.
+ 46 nt . assert_allclose ( strains_inc , timestamps , atol = 6e-16 , rtol = 0 )
+ 47 48 # Same thing, but for strain rate similar to experiments.
+ 49 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , 1e-5 )
+ 50 timestamps = np . linspace ( 0 , 1e6 , 10 ) # Solve until D₀t=10 (tensorial strain).
+ 51 strains_inc = np . zeros_like ( timestamps )
+ 52 L = get_velocity_gradient ( Ŋ ([ 0e0 , 0e0 , 0e0 ]))
+ 53 for i , ε in enumerate ( strains_inc [ 1 :]):
+ 54 strains_inc [ i + 1 ] = strains_inc [ i ] + _utils . strain_increment (
+ 55 timestamps [ 1 ] - timestamps [ 0 ],
+ 56 L ,
+ 57 )
+ 58 nt . assert_allclose ( strains_inc , timestamps * 1e-5 , atol = 5e-15 , rtol = 0 )
+ 59 60 # Again, but this time the particle will move (using get_pathline).
+ 61 # We use a 400km x 400km box and a strain rate of 1e-15 s⁻¹.
+ 62 get_velocity , get_velocity_gradient = _velocity . simple_shear_2d ( "X" , "Z" , 1e-15 )
+ 63 timestamps , get_position = _paths . get_pathline (
+ 64 Ŋ ([ 1e5 , 0e0 , 1e5 ]),
+ 65 get_velocity ,
+ 66 get_velocity_gradient ,
+ 67 Ŋ ([ - 2e5 , 0e0 , - 2e5 ]),
+ 68 Ŋ ([ 2e5 , 0e0 , 2e5 ]),
+ 69 2 ,
+ 70 regular_steps = 10 ,
+ 71 )
+ 72 positions = [ get_position ( t ) for t in timestamps ]
+ 73 velocity_gradients = [ get_velocity_gradient ( Ŋ ( x )) for x in positions ]
+ 74 75 # Check that polycrystal is experiencing steady velocity gradient.
+ 76 nt . assert_array_equal (
+ 77 velocity_gradients , np . full_like ( velocity_gradients , velocity_gradients [ 0 ])
+ 78 )
+ 79 # Check that positions are changing as expected.
+ 80 xdiff = np . diff ( Ŋ ([ x [ 0 ] for x in positions ]))
+ 81 zdiff = np . diff ( Ŋ ([ x [ 2 ] for x in positions ]))
+ 82 assert xdiff [ 0 ] > 0
+ 83 assert zdiff [ 0 ] == 0
+ 84 nt . assert_allclose ( xdiff , np . full_like ( xdiff , xdiff [ 0 ]), rtol = 0 , atol = 1e-10 )
+ 85 nt . assert_allclose ( zdiff , np . full_like ( zdiff , zdiff [ 0 ]), rtol = 0 , atol = 1e-10 )
+ 86 strains_inc = np . zeros_like ( timestamps )
+ 87 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+ 88 strains_inc [ t ] = strains_inc [ t - 1 ] + (
+ 89 _utils . strain_increment ( timestamps [ t ] - time , velocity_gradients [ t ])
+ 90 )
+ 91 # fig, ax, _, _ = _vis.pathline_box2d(
+ 92 # None,
+ 93 # get_velocity,
+ 94 # "xz",
+ 95 # strains_inc,
+ 96 # positions,
+ 97 # ".",
+ 98 # Ŋ([-2e5, -2e5]),
+ 99 # Ŋ([2e5, 2e5]),
+100 # [20, 20],
+101 # )
+102 # fig.savefig("/tmp/fig.png")
+103 nt . assert_allclose (
+104 strains_inc ,
+105 ( timestamps - timestamps [ 0 ]) * 1e-15 ,
+106 atol = 5e-15 ,
+107 rtol = 0 ,
+108 )
+
+
+
+
Test for accumulating strain via strain increment calculations.
+
+
+
+
27 class TestOlivineA :
- 28 """Tests for stationary A-type olivine polycrystals in 2D simple shear."""
- 29 30 class_id = "olivineA"
- 31 32 @classmethod
- 33 def get_position ( cls , t ):
- 34 return np . zeros ( 3 ) # These crystals are stationary.
- 35 36 @classmethod
- 37 def run (
- 38 cls ,
- 39 params ,
- 40 timestamps ,
- 41 strain_rate ,
- 42 get_velocity_gradient ,
- 43 shear_direction ,
- 44 seed = None ,
- 45 return_fse = None ,
- 46 ):
- 47 """Reusable logic for 2D olivine (A-type) simple shear tests.
- 48 49 Returns a tuple with the mineral and the FSE angle (or `None` if `return_fse` is
- 50 `None`).
- 51 52 """
- 53 mineral = _minerals . Mineral (
- 54 phase = _core . MineralPhase . olivine ,
- 55 fabric = _core . MineralFabric . olivine_A ,
- 56 regime = _core . DeformationRegime . dislocation ,
- 57 n_grains = params [ "number_of_grains" ],
- 58 seed = seed ,
- 59 )
- 60 deformation_gradient = np . eye ( 3 ) # Undeformed initial state.
- 61 θ_fse = np . empty_like ( timestamps )
- 62 θ_fse [ 0 ] = 45
- 63 64 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
- 65 # Set up logging message depending on dynamic parameter and seeds.
- 66 msg_start = (
- 67 f "N = { params [ 'number_of_grains' ] } ; "
- 68 + f "λ∗ = { params [ 'nucleation_efficiency' ] } ; "
- 69 + f "X = { params [ 'gbs_threshold' ] } ; "
- 70 + f "M∗ = { params [ 'gbm_mobility' ] } ; "
- 71 )
- 72 if seed is not None :
- 73 msg_start += f "# { seed } ; "
- 74 75 _log . info ( msg_start + "step %s / %s (t = %s )" , t , len ( timestamps ) - 1 , time )
- 76 77 deformation_gradient = mineral . update_orientations (
- 78 params ,
- 79 deformation_gradient ,
- 80 get_velocity_gradient ,
- 81 pathline = ( time , timestamps [ t ], cls . get_position ),
- 82 )
- 83 _log . debug (
- 84 "› velocity gradient = %s " ,
- 85 get_velocity_gradient ( None ) . flatten (),
- 86 )
- 87 _log . debug ( "› strain D₀t = %.2f " , strain_rate * timestamps [ t ])
- 88 _log . debug (
- 89 "› grain fractions: median = %s , max = %s , min = %s " ,
- 90 np . median ( mineral . fractions [ - 1 ]),
- 91 np . max ( mineral . fractions [ - 1 ]),
- 92 np . min ( mineral . fractions [ - 1 ]),
- 93 )
- 94 if return_fse :
- 95 _ , fse_v = _diagnostics . finite_strain ( deformation_gradient )
- 96 θ_fse [ t ] = _diagnostics . smallest_angle ( fse_v , shear_direction )
- 97 else :
- 98 θ_fse = None
- 99 100 return mineral , θ_fse
-101 102 @classmethod
-103 def interp_GBM_Kaminski2001 ( cls , strains ):
-104 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
-105 _log . info ( "interpolating target CPO angles..." )
-106 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2001_GBMshear.scsv" )
-107 cs_M0 = PchipInterpolator (
-108 _utils . remove_nans ( data . equivalent_strain_M0 ) / 200 ,
-109 _utils . remove_nans ( data . angle_M0 ),
-110 )
-111 cs_M50 = PchipInterpolator (
-112 _utils . remove_nans ( data . equivalent_strain_M50 ) / 200 ,
-113 _utils . remove_nans ( data . angle_M50 ),
-114 )
-115 cs_M200 = PchipInterpolator (
-116 _utils . remove_nans ( data . equivalent_strain_M200 ) / 200 ,
-117 _utils . remove_nans ( data . angle_M200 ),
-118 )
-119 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
-120 121 @classmethod
-122 def interp_GBM_FortranDRex ( cls , strains ):
-123 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-124 _log . info ( "interpolating target CPO angles..." )
-125 data = _io . read_scsv ( _io . data ( "drexF90" ) / "olA_D1E4_dt50_X0_L5.scsv" )
-126 data_strains = np . linspace ( 0 , 1 , 200 )
-127 cs_M0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M0_angle ))
-128 cs_M50 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M50_angle ))
-129 cs_M200 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M200_angle ))
-130 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
-131 132 @classmethod
-133 def interp_GBS_FortranDRex ( cls , strains ):
-134 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-135 _log . info ( "interpolating target CPO angles..." )
-136 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_fortran.scsv" )
-137 data_strains = np . linspace ( 0 , 1 , 200 )
-138 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
-139 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
-140 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
-141 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
-142 143 @classmethod
-144 def interp_GBS_long_FortranDRex ( cls , strains ):
-145 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-146 _log . info ( "interpolating target CPO angles..." )
-147 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_long_fortran.scsv" )
-148 data_strains = np . linspace ( 0 , 2.5 , 500 )
-149 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
-150 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
-151 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
-152 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
-153 154 @classmethod
-155 def interp_GBS_Kaminski2004 ( cls , strains ):
-156 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
-157 _log . info ( "interpolating target CPO angles..." )
-158 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2004_GBSshear.scsv" )
-159 cs_X0 = PchipInterpolator (
-160 _utils . remove_nans ( data . dimensionless_time_X0 ),
-161 45 + _utils . remove_nans ( data . angle_X0 ),
-162 )
-163 cs_X0d2 = PchipInterpolator (
-164 _utils . remove_nans ( data . dimensionless_time_X0d2 ),
-165 45 + _utils . remove_nans ( data . angle_X0d2 ),
-166 )
-167 cs_X0d4 = PchipInterpolator (
-168 _utils . remove_nans ( data . dimensionless_time_X0d4 ),
-169 45 + _utils . remove_nans ( data . angle_X0d4 ),
-170 )
-171 return [ cs_X0 ( strains ), cs_X0d2 ( strains ), cs_X0d4 ( strains )]
-172 173 def test_zero_recrystallisation ( self , seed ):
-174 """Check that M*=0 is a reliable switch to turn off recrystallisation."""
-175 params = _io . DEFAULT_PARAMS
-176 params [ "gbm_mobility" ] = 0
-177 strain_rate = 1
-178 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
-179 shear_direction = [ 0 , 1 , 0 ]
-180 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-181 mineral , _ = self . run (
-182 params ,
-183 timestamps ,
-184 strain_rate ,
-185 get_velocity_gradient ,
-186 shear_direction ,
-187 seed = seed ,
-188 )
-189 for fractions in mineral . fractions [ 1 :]:
-190 nt . assert_allclose ( fractions , mineral . fractions [ 0 ], atol = 1e-15 , rtol = 0 )
-191 192 @pytest . mark . parametrize ( "gbm_mobility" , [ 50 , 100 , 150 ])
-193 def test_grainsize_median ( self , seed , gbm_mobility ):
-194 """Check that M*={50,100,150}, λ*=5 causes decreasing grain size median."""
-195 params = _io . DEFAULT_PARAMS
-196 params [ "gbm_mobility" ] = gbm_mobility
-197 params [ "nucleation_efficiency" ] = 5
-198 strain_rate = 1
-199 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
-200 n_timestamps = len ( timestamps )
-201 shear_direction = [ 0 , 1 , 0 ]
-202 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-203 mineral , _ = self . run (
-204 params ,
-205 timestamps ,
-206 strain_rate ,
-207 get_velocity_gradient ,
-208 shear_direction ,
-209 seed = seed ,
-210 )
-211 medians = np . empty ( n_timestamps )
-212 for i , fractions in enumerate ( mineral . fractions ):
-213 medians [ i ] = np . median ( fractions )
-214 215 # The first diff is positive (~1e-6) before nucleation sets in.
-216 nt . assert_array_less ( np . diff ( medians )[ 1 :], np . full ( n_timestamps - 2 , 0 ))
-217 218 @pytest . mark . slow
-219 @pytest . mark . parametrize ( "gbs_threshold" , [ 0 , 0.2 , 0.4 ])
-220 @pytest . mark . parametrize ( "nucleation_efficiency" , [ 3 , 5 , 10 ])
-221 def test_dvdx_ensemble (
-222 self , outdir , seeds_nearX45 , ncpus , gbs_threshold , nucleation_efficiency
-223 ):
-224 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
-225 226 Velocity gradient:
-227 $$\bm{L} = \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}$$
-228 229 """
-230 strain_rate = 1
-231 timestamps = np . linspace ( 0 , 1 , 201 ) # Solve until D₀t=1 ('shear' γ=2).
-232 n_timestamps = len ( timestamps )
-233 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
-234 _seeds = seeds_nearX45
-235 n_seeds = len ( _seeds )
-236 237 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-238 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-239 240 gbm_mobilities = [ 0 , 50 , 125 , 200 ]
-241 markers = ( "x" , "*" , "d" , "s" )
-242 243 _id = f "X { _io . stringify ( gbs_threshold ) } _L { _io . stringify ( nucleation_efficiency ) } "
-244 # Output setup with optional logging and data series labels.
-245 θ_fse = np . empty_like ( timestamps )
-246 angles = np . empty (( len ( gbm_mobilities ), n_seeds , n_timestamps ))
-247 optional_logging = cl . nullcontext ()
-248 if outdir is not None :
-249 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _dvdx_ensemble_ { _id } "
-250 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-251 labels = []
-252 253 with optional_logging :
-254 clock_start = process_time ()
-255 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-256 if m == 0 :
-257 return_fse = True
-258 else :
-259 return_fse = False
-260 261 params = {
-262 "olivine_fraction" : 1.0 ,
-263 "enstatite_fraction" : 0.0 ,
-264 "stress_exponent" : 1.5 ,
-265 "deformation_exponent" : 3.5 ,
-266 "gbm_mobility" : gbm_mobility ,
-267 "gbs_threshold" : gbs_threshold ,
-268 "nucleation_efficiency" : nucleation_efficiency ,
-269 "number_of_grains" : 5000 ,
-270 "initial_olivine_fabric" : "A" ,
-271 }
+ 111 class TestOlivineA :
+112 """Tests for stationary A-type olivine polycrystals in 2D simple shear."""
+113 114 class_id = "olivineA"
+115 116 @classmethod
+117 def run (
+118 cls ,
+119 params ,
+120 timestamps ,
+121 strain_rate ,
+122 get_velocity_gradient ,
+123 shear_direction ,
+124 seed = None ,
+125 return_fse = None ,
+126 get_position = lambda t : np . zeros ( 3 ), # Stationary particles by default.
+127 ):
+128 """Reusable logic for 2D olivine (A-type) simple shear tests.
+129 130 Returns a tuple with the mineral and the FSE angle (or `None` if `return_fse` is
+131 `None`).
+132 133 """
+134 mineral = _minerals . Mineral (
+135 phase = _core . MineralPhase . olivine ,
+136 fabric = _core . MineralFabric . olivine_A ,
+137 regime = _core . DeformationRegime . dislocation ,
+138 n_grains = params [ "number_of_grains" ],
+139 seed = seed ,
+140 )
+141 deformation_gradient = np . eye ( 3 ) # Undeformed initial state.
+142 θ_fse = np . empty_like ( timestamps )
+143 θ_fse [ 0 ] = 45
+144 145 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+146 # Set up logging message depending on dynamic parameter and seeds.
+147 msg_start = (
+148 f "N = { params [ 'number_of_grains' ] } ; "
+149 + f "λ∗ = { params [ 'nucleation_efficiency' ] } ; "
+150 + f "X = { params [ 'gbs_threshold' ] } ; "
+151 + f "M∗ = { params [ 'gbm_mobility' ] } ; "
+152 )
+153 if seed is not None :
+154 msg_start += f "# { seed } ; "
+155 156 _log . info ( msg_start + "step %s / %s (t = %s )" , t , len ( timestamps ) - 1 , time )
+157 158 deformation_gradient = mineral . update_orientations (
+159 params ,
+160 deformation_gradient ,
+161 get_velocity_gradient ,
+162 pathline = ( time , timestamps [ t ], get_position ),
+163 )
+164 _log . debug (
+165 "› velocity gradient = %s " ,
+166 get_velocity_gradient ( None ) . flatten (),
+167 )
+168 _log . debug ( "› strain D₀t = %.2f " , strain_rate * timestamps [ t ])
+169 _log . debug (
+170 "› grain fractions: median = %s , max = %s , min = %s " ,
+171 np . median ( mineral . fractions [ - 1 ]),
+172 np . max ( mineral . fractions [ - 1 ]),
+173 np . min ( mineral . fractions [ - 1 ]),
+174 )
+175 if return_fse :
+176 _ , fse_v = _diagnostics . finite_strain ( deformation_gradient )
+177 θ_fse [ t ] = _diagnostics . smallest_angle ( fse_v , shear_direction )
+178 else :
+179 θ_fse = None
+180 181 return mineral , θ_fse
+182 183 @classmethod
+184 def interp_GBM_Kaminski2001 ( cls , strains ):
+185 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
+186 _log . info ( "interpolating target CPO angles..." )
+187 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2001_GBMshear.scsv" )
+188 cs_M0 = PchipInterpolator (
+189 _utils . remove_nans ( data . equivalent_strain_M0 ) / 200 ,
+190 _utils . remove_nans ( data . angle_M0 ),
+191 )
+192 cs_M50 = PchipInterpolator (
+193 _utils . remove_nans ( data . equivalent_strain_M50 ) / 200 ,
+194 _utils . remove_nans ( data . angle_M50 ),
+195 )
+196 cs_M200 = PchipInterpolator (
+197 _utils . remove_nans ( data . equivalent_strain_M200 ) / 200 ,
+198 _utils . remove_nans ( data . angle_M200 ),
+199 )
+200 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
+201 202 @classmethod
+203 def interp_GBM_FortranDRex ( cls , strains ):
+204 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+205 _log . info ( "interpolating target CPO angles..." )
+206 data = _io . read_scsv ( _io . data ( "drexF90" ) / "olA_D1E4_dt50_X0_L5.scsv" )
+207 data_strains = np . linspace ( 0 , 1 , 200 )
+208 cs_M0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M0_angle ))
+209 cs_M50 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M50_angle ))
+210 cs_M200 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M200_angle ))
+211 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
+212 213 @classmethod
+214 def interp_GBS_FortranDRex ( cls , strains ):
+215 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+216 _log . info ( "interpolating target CPO angles..." )
+217 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_fortran.scsv" )
+218 data_strains = np . linspace ( 0 , 1 , 200 )
+219 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
+220 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
+221 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
+222 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
+223 224 @classmethod
+225 def interp_GBS_long_FortranDRex ( cls , strains ):
+226 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+227 _log . info ( "interpolating target CPO angles..." )
+228 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_long_fortran.scsv" )
+229 data_strains = np . linspace ( 0 , 2.5 , 500 )
+230 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
+231 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
+232 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
+233 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
+234 235 @classmethod
+236 def interp_GBS_Kaminski2004 ( cls , strains ):
+237 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
+238 _log . info ( "interpolating target CPO angles..." )
+239 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2004_GBSshear.scsv" )
+240 cs_X0 = PchipInterpolator (
+241 _utils . remove_nans ( data . dimensionless_time_X0 ),
+242 45 + _utils . remove_nans ( data . angle_X0 ),
+243 )
+244 cs_X0d2 = PchipInterpolator (
+245 _utils . remove_nans ( data . dimensionless_time_X0d2 ),
+246 45 + _utils . remove_nans ( data . angle_X0d2 ),
+247 )
+248 cs_X0d4 = PchipInterpolator (
+249 _utils . remove_nans ( data . dimensionless_time_X0d4 ),
+250 45 + _utils . remove_nans ( data . angle_X0d4 ),
+251 )
+252 return [ cs_X0 ( strains ), cs_X0d2 ( strains ), cs_X0d4 ( strains )]
+253 254 def test_zero_recrystallisation ( self , seed ):
+255 """Check that M*=0 is a reliable switch to turn off recrystallisation."""
+256 params = _io . DEFAULT_PARAMS
+257 params [ "gbm_mobility" ] = 0
+258 strain_rate = 1
+259 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
+260 shear_direction = [ 0 , 1 , 0 ]
+261 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+262 mineral , _ = self . run (
+263 params ,
+264 timestamps ,
+265 strain_rate ,
+266 get_velocity_gradient ,
+267 shear_direction ,
+268 seed = seed ,
+269 )
+270 for fractions in mineral . fractions [ 1 :]:
+271 nt . assert_allclose ( fractions , mineral . fractions [ 0 ], atol = 1e-15 , rtol = 0 )
272 273 _run = ft . partial (
-274 self . run ,
-275 params ,
-276 timestamps ,
-277 strain_rate ,
-278 get_velocity_gradient ,
-279 shear_direction ,
-280 return_fse = return_fse ,
-281 )
-282 with Pool ( processes = ncpus ) as pool :
-283 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-284 mineral , fse_angles = out
-285 angles [ m , s , :] = [
-286 _diagnostics . smallest_angle ( v , shear_direction )
-287 for v in _diagnostics . elasticity_components (
-288 _minerals . voigt_averages ([ mineral ], params )
-289 )[ "hexagonal_axis" ]
-290 ]
-291 # Save the whole mineral for the first seed only.
-292 if outdir is not None and s == 0 :
-293 postfix = (
-294 f "M { _io . stringify ( gbm_mobility ) } "
-295 + f "_X { _io . stringify ( gbs_threshold ) } "
-296 + f "_L { _io . stringify ( nucleation_efficiency ) } "
-297 )
-298 mineral . save ( f " { out_basepath } .npz" , postfix = postfix )
-299 if return_fse :
-300 θ_fse += fse_angles
-301 302 if return_fse :
-303 θ_fse /= n_seeds
-304 305 if outdir is not None :
-306 labels . append ( f "$M^∗$ = { gbm_mobility } " )
-307 308 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+273 @pytest . mark . parametrize ( "gbm_mobility" , [ 50 , 100 , 150 ])
+274 def test_grainsize_median ( self , seed , gbm_mobility ):
+275 """Check that M*={50,100,150}, λ*=5 causes decreasing grain size median."""
+276 params = _io . DEFAULT_PARAMS
+277 params [ "gbm_mobility" ] = gbm_mobility
+278 params [ "nucleation_efficiency" ] = 5
+279 strain_rate = 1
+280 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
+281 n_timestamps = len ( timestamps )
+282 shear_direction = [ 0 , 1 , 0 ]
+283 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+284 mineral , _ = self . run (
+285 params ,
+286 timestamps ,
+287 strain_rate ,
+288 get_velocity_gradient ,
+289 shear_direction ,
+290 seed = seed ,
+291 )
+292 medians = np . empty ( n_timestamps )
+293 for i , fractions in enumerate ( mineral . fractions ):
+294 medians [ i ] = np . median ( fractions )
+295 296 # The first diff is positive (~1e-6) before nucleation sets in.
+297 nt . assert_array_less ( np . diff ( medians )[ 1 :], np . full ( n_timestamps - 2 , 0 ))
+298 299 @pytest . mark . slow
+300 @pytest . mark . parametrize ( "gbs_threshold" , [ 0 , 0.2 , 0.4 ])
+301 @pytest . mark . parametrize ( "nucleation_efficiency" , [ 3 , 5 , 10 ])
+302 def test_dvdx_ensemble (
+303 self , outdir , seeds_nearX45 , ncpus , gbs_threshold , nucleation_efficiency
+304 ):
+305 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
+306 307 Velocity gradient:
+308 $$\bm{L} = \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}$$
309 310 # Take ensemble means and optionally plot figure.
-311 strains = timestamps * strain_rate
-312 _log . info ( "postprocessing results for %s " , _id )
-313 result_angles = angles . mean ( axis = 1 )
-314 result_angles_err = angles . std ( axis = 1 )
-315 316 if outdir is not None :
-317 schema = {
-318 "delimiter" : "," ,
-319 "missing" : "-" ,
-320 "fields" : [
-321 {
-322 "name" : "strain" ,
-323 "type" : "integer" ,
-324 "unit" : "percent" ,
-325 "fill" : 999999 ,
-326 }
-327 ],
-328 }
-329 np . savez (
-330 f " { out_basepath } .npz" ,
-331 angles = result_angles ,
-332 angles_err = result_angles_err ,
-333 )
-334 _io . save_scsv (
-335 f " { out_basepath } _strains.scsv" ,
-336 schema ,
-337 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-338 )
-339 fig , ax , colors = _vis . alignment (
-340 None ,
-341 strains ,
-342 result_angles ,
-343 markers ,
-344 labels ,
-345 err = result_angles_err ,
-346 θ_max = 60 ,
-347 θ_fse = θ_fse ,
-348 )
-349 fig . savefig ( _io . resolve_path ( f " { out_basepath } .pdf" ))
-350 351 @pytest . mark . slow
-352 def test_dvdx_GBM ( self , outdir , seeds_nearX45 , ncpus ):
-353 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
-354 355 Velocity gradient:
-356 $$
-357 \bm{L} = 10^{-4} ×
-358 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
-359 $$
-360 361 Results are compared to the Fortran 90 output.
-362 363 """
-364 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-365 strain_rate = 1e-4
-366 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-367 timestamps = np . linspace ( 0 , 1e4 , 51 ) # Solve until D₀t=1 ('shear' γ=2).
-368 i_strain_40p = 10 # Index of 40% strain, lower strains are not relevant here.
-369 i_strain_100p = 25 # Index of 100% strain, when M*=0 matches FSE.
-370 params = _io . DEFAULT_PARAMS
-371 params [ "gbs_threshold" ] = 0 # No GBS, to match the Fortran parameters.
-372 gbm_mobilities = ( 0 , 10 , 50 , 125 , 200 ) # Must be in ascending order.
-373 markers = ( "x" , "." , "*" , "d" , "s" )
-374 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
-375 _seeds = seeds_nearX45
-376 n_seeds = len ( _seeds )
-377 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
-378 θ_fse = np . zeros_like ( timestamps )
-379 strains = timestamps * strain_rate
-380 M0_drexF90 , M50_drexF90 , M200_drexF90 = self . interp_GBM_FortranDRex ( strains )
-381 382 optional_logging = cl . nullcontext ()
-383 if outdir is not None :
-384 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _mobility"
-385 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-386 labels = []
-387 388 with optional_logging :
-389 clock_start = process_time ()
-390 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-391 if m == 0 :
-392 return_fse = True
-393 else :
-394 return_fse = False
-395 params [ "gbm_mobility" ] = gbm_mobility
+310 """
+311 strain_rate = 1
+312 timestamps = np . linspace ( 0 , 1 , 201 ) # Solve until D₀t=1 ('shear' γ=2).
+313 n_timestamps = len ( timestamps )
+314 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
+315 _seeds = seeds_nearX45
+316 n_seeds = len ( _seeds )
+317 318 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+319 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+320 321 gbm_mobilities = [ 0 , 50 , 125 , 200 ]
+322 markers = ( "x" , "*" , "d" , "s" )
+323 324 _id = f "X { _io . stringify ( gbs_threshold ) } _L { _io . stringify ( nucleation_efficiency ) } "
+325 # Output setup with optional logging and data series labels.
+326 θ_fse = np . empty_like ( timestamps )
+327 angles = np . empty (( len ( gbm_mobilities ), n_seeds , n_timestamps ))
+328 optional_logging = cl . nullcontext ()
+329 if outdir is not None :
+330 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _dvdx_ensemble_ { _id } "
+331 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+332 labels = []
+333 334 with optional_logging :
+335 clock_start = process_time ()
+336 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+337 if m == 0 :
+338 return_fse = True
+339 else :
+340 return_fse = False
+341 342 params = {
+343 "olivine_fraction" : 1.0 ,
+344 "enstatite_fraction" : 0.0 ,
+345 "stress_exponent" : 1.5 ,
+346 "deformation_exponent" : 3.5 ,
+347 "gbm_mobility" : gbm_mobility ,
+348 "gbs_threshold" : gbs_threshold ,
+349 "nucleation_efficiency" : nucleation_efficiency ,
+350 "number_of_grains" : 5000 ,
+351 "initial_olivine_fabric" : "A" ,
+352 }
+353 354 _run = ft . partial (
+355 self . run ,
+356 params ,
+357 timestamps ,
+358 strain_rate ,
+359 get_velocity_gradient ,
+360 shear_direction ,
+361 return_fse = return_fse ,
+362 )
+363 with Pool ( processes = ncpus ) as pool :
+364 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+365 mineral , fse_angles = out
+366 angles [ m , s , :] = [
+367 _diagnostics . smallest_angle ( v , shear_direction )
+368 for v in _diagnostics . elasticity_components (
+369 _minerals . voigt_averages ([ mineral ], params )
+370 )[ "hexagonal_axis" ]
+371 ]
+372 # Save the whole mineral for the first seed only.
+373 if outdir is not None and s == 0 :
+374 postfix = (
+375 f "M { _io . stringify ( gbm_mobility ) } "
+376 + f "_X { _io . stringify ( gbs_threshold ) } "
+377 + f "_L { _io . stringify ( nucleation_efficiency ) } "
+378 )
+379 mineral . save ( f " { out_basepath } .npz" , postfix = postfix )
+380 if return_fse :
+381 θ_fse += fse_angles
+382 383 if return_fse :
+384 θ_fse /= n_seeds
+385 386 if outdir is not None :
+387 labels . append ( f "$M^∗$ = { gbm_mobility } " )
+388 389 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+390 391 # Take ensemble means and optionally plot figure.
+392 strains = timestamps * strain_rate
+393 _log . info ( "postprocessing results for %s " , _id )
+394 result_angles = angles . mean ( axis = 1 )
+395 result_angles_err = angles . std ( axis = 1 )
396 397 _run = ft . partial (
-398 self . run ,
-399 params ,
-400 timestamps ,
-401 strain_rate ,
-402 get_velocity_gradient ,
-403 shear_direction ,
-404 return_fse = True ,
-405 )
-406 with Pool ( processes = ncpus ) as pool :
-407 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-408 mineral , fse_angles = out
-409 angles [ m , s , :] = [
-410 _diagnostics . smallest_angle ( v , shear_direction )
-411 for v in _diagnostics . elasticity_components (
-412 _minerals . voigt_averages ([ mineral ], params )
-413 )[ "hexagonal_axis" ]
-414 ]
-415 # Save the whole mineral for the first seed only.
-416 if outdir is not None and s == 0 :
-417 mineral . save (
-418 f " { out_basepath } .npz" ,
-419 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
-420 )
-421 if return_fse :
-422 θ_fse += fse_angles
-423 424 if return_fse :
-425 θ_fse /= n_seeds
-426 427 if outdir is not None :
-428 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
-429 430 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+397 if outdir is not None :
+398 schema = {
+399 "delimiter" : "," ,
+400 "missing" : "-" ,
+401 "fields" : [
+402 {
+403 "name" : "strain" ,
+404 "type" : "integer" ,
+405 "unit" : "percent" ,
+406 "fill" : 999999 ,
+407 }
+408 ],
+409 }
+410 np . savez (
+411 f " { out_basepath } .npz" ,
+412 angles = result_angles ,
+413 angles_err = result_angles_err ,
+414 )
+415 _io . save_scsv (
+416 f " { out_basepath } _strains.scsv" ,
+417 schema ,
+418 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+419 )
+420 fig , ax , colors = _vis . alignment (
+421 None ,
+422 strains ,
+423 result_angles ,
+424 markers ,
+425 labels ,
+426 err = result_angles_err ,
+427 θ_max = 60 ,
+428 θ_fse = θ_fse ,
+429 )
+430 fig . savefig ( _io . resolve_path ( f " { out_basepath } .pdf" ))
431 432 # Take ensemble means and optionally plot figure.
-433 _log . info ( "postprocessing results..." )
-434 result_angles = angles . mean ( axis = 1 )
-435 result_angles_err = angles . std ( axis = 1 )
-436 437 if outdir is not None :
-438 schema = {
-439 "delimiter" : "," ,
-440 "missing" : "-" ,
-441 "fields" : [
-442 {
-443 "name" : "strain" ,
-444 "type" : "integer" ,
-445 "unit" : "percent" ,
-446 "fill" : 999999 ,
-447 }
-448 ],
-449 }
-450 _io . save_scsv (
-451 f " { out_basepath } _strains.scsv" ,
-452 schema ,
-453 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-454 )
-455 np . savez (
-456 f " { out_basepath } _angles.npz" ,
-457 angles = result_angles ,
-458 err = result_angles_err ,
-459 )
-460 fig , ax , colors = _vis . alignment (
-461 None ,
-462 strains ,
-463 result_angles ,
-464 markers ,
-465 labels ,
-466 err = result_angles_err ,
-467 θ_max = 60 ,
-468 θ_fse = θ_fse ,
-469 )
-470 ax . plot ( strains , M0_drexF90 , c = colors [ 0 ])
-471 ax . plot ( strains , M50_drexF90 , c = colors [ 2 ])
-472 ax . plot ( strains , M200_drexF90 , c = colors [ 4 ])
-473 _vis . show_Skemer2016_ShearStrainAngles (
-474 ax ,
-475 [ "Z&K 1200 C" , "Z&K 1300 C" ],
-476 [ "v" , "^" ],
-477 [ "k" , "k" ],
-478 [ "none" , None ],
-479 [
-480 "Zhang & Karato, 1995 \n (1473 K)" ,
-481 "Zhang & Karato, 1995 \n (1573 K)" ,
-482 ],
-483 _core . MineralFabric . olivine_A ,
-484 )
-485 # There is a lot of stuff on this legend, so put it outside the axes.
-486 # These values might need to be tweaked depending on the font size, etc.
-487 _legend = _utils . redraw_legend ( ax , fig = fig , bbox_to_anchor = ( 1.66 , 0.99 ))
-488 fig . savefig (
-489 _io . resolve_path ( f " { out_basepath } .pdf" ),
-490 bbox_extra_artists = ( _legend ,),
-491 bbox_inches = "tight" ,
-492 )
-493 494 # Check that GBM speeds up the alignment between 40% and 100% strain.
-495 _log . info ( "checking grain orientations..." )
-496 for i , θ in enumerate ( result_angles [: - 1 ], start = 1 ):
-497 nt . assert_array_less (
-498 result_angles [ i ][ i_strain_40p : i_strain_100p ],
-499 θ [ i_strain_40p : i_strain_100p ],
-500 )
-501 502 # Check that M*=0 matches FSE (±1°) past 100% strain.
-503 nt . assert_allclose (
-504 result_angles [ 0 ][ i_strain_100p :],
-505 θ_fse [ i_strain_100p :],
-506 atol = 1 ,
-507 rtol = 0 ,
-508 )
-509 510 # Check that results match Fortran output past 40% strain.
-511 nt . assert_allclose (
-512 result_angles [ 0 ][ i_strain_40p :],
-513 M0_drexF90 [ i_strain_40p :],
-514 atol = 0 ,
-515 rtol = 0.1 , # At 40% strain the match is worse than at higher strain.
-516 )
-517 nt . assert_allclose (
-518 result_angles [ 2 ][ i_strain_40p :],
-519 M50_drexF90 [ i_strain_40p :],
-520 atol = 1 ,
-521 rtol = 0 ,
-522 )
-523 nt . assert_allclose (
-524 result_angles [ 4 ][ i_strain_40p :],
-525 M200_drexF90 [ i_strain_40p :],
-526 atol = 1.5 ,
-527 rtol = 0 ,
-528 )
-529 530 @pytest . mark . slow
-531 def test_GBM_calibration ( self , outdir , seeds , ncpus ):
-532 r """Compare results for various values of $$M^∗$$ to A-type olivine data.
-533 534 Velocity gradient:
-535 $$
-536 \bm{L} = 10^{-4} ×
-537 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
-538 $$
-539 540 Unlike `test_dvdx_GBM`,
-541 grain boudary sliding is enabled here (see `_io.DEFAULT_PARAMS`).
-542 Data are provided by [Skemer & Hansen, 2016](http://dx.doi.org/10.1016/j.tecto.2015.12.003).
-543 544 """
-545 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-546 strain_rate = 1
-547 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-548 timestamps = np . linspace ( 0 , 3.2 , 65 ) # Solve until D₀t=3.2 ('shear' γ=6.4).
-549 params = _io . DEFAULT_PARAMS
-550 params [ "number_of_grains" ] = 5000
-551 gbm_mobilities = ( 0 , 10 , 50 , 125 ) # Must be in ascending order.
-552 markers = ( "x" , "*" , "1" , "." )
-553 # Uses 100 seeds by default; use all 1000 if you have more RAM and CPU time.
-554 _seeds = seeds [: 100 ]
-555 n_seeds = len ( _seeds )
-556 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
-557 θ_fse = np . zeros_like ( timestamps )
-558 strains = timestamps * strain_rate
-559 560 optional_logging = cl . nullcontext ()
-561 if outdir is not None :
-562 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _calibration"
-563 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-564 labels = []
-565 566 with optional_logging :
-567 clock_start = process_time ()
-568 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-569 return_fse = True if m == 0 else False
-570 params [ "gbm_mobility" ] = gbm_mobility
-571 _run = ft . partial (
-572 self . run ,
-573 params ,
-574 timestamps ,
-575 strain_rate ,
-576 get_velocity_gradient ,
-577 shear_direction ,
-578 return_fse = return_fse ,
-579 )
-580 with Pool ( processes = ncpus ) as pool :
-581 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-582 mineral , fse_angles = out
-583 angles [ m , s , :] = [
-584 _diagnostics . smallest_angle ( v , shear_direction )
-585 for v in _diagnostics . elasticity_components (
-586 _minerals . voigt_averages ([ mineral ], params )
-587 )[ "hexagonal_axis" ]
-588 ]
-589 # Save the whole mineral for the first seed only.
-590 if outdir is not None and s == 0 :
-591 mineral . save (
-592 f " { out_basepath } .npz" ,
-593 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
-594 )
-595 if return_fse :
-596 θ_fse += fse_angles
-597 598 if return_fse :
-599 θ_fse /= n_seeds
-600 601 if outdir is not None :
-602 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
-603 604 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
-605 606 # Take ensemble means and optionally plot figure.
-607 _log . info ( "postprocessing results..." )
-608 result_angles = angles . mean ( axis = 1 )
-609 result_angles_err = angles . std ( axis = 1 )
+432 @pytest . mark . slow
+433 def test_dvdx_GBM ( self , outdir , seeds_nearX45 , ncpus ):
+434 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
+435 436 Velocity gradient:
+437 $$
+438 \bm{L} = 10^{-4} ×
+439 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
+440 $$
+441 442 Results are compared to the Fortran 90 output.
+443 444 """
+445 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+446 strain_rate = 1e-4
+447 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+448 timestamps = np . linspace ( 0 , 1e4 , 51 ) # Solve until D₀t=1 ('shear' γ=2).
+449 i_strain_40p = 10 # Index of 40% strain, lower strains are not relevant here.
+450 i_strain_100p = 25 # Index of 100% strain, when M*=0 matches FSE.
+451 params = _io . DEFAULT_PARAMS
+452 params [ "gbs_threshold" ] = 0 # No GBS, to match the Fortran parameters.
+453 gbm_mobilities = ( 0 , 10 , 50 , 125 , 200 ) # Must be in ascending order.
+454 markers = ( "x" , "." , "*" , "d" , "s" )
+455 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
+456 _seeds = seeds_nearX45
+457 n_seeds = len ( _seeds )
+458 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
+459 θ_fse = np . zeros_like ( timestamps )
+460 strains = timestamps * strain_rate
+461 M0_drexF90 , M50_drexF90 , M200_drexF90 = self . interp_GBM_FortranDRex ( strains )
+462 463 optional_logging = cl . nullcontext ()
+464 if outdir is not None :
+465 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _mobility"
+466 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+467 labels = []
+468 469 with optional_logging :
+470 clock_start = process_time ()
+471 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+472 if m == 0 :
+473 return_fse = True
+474 else :
+475 return_fse = False
+476 params [ "gbm_mobility" ] = gbm_mobility
+477 478 _run = ft . partial (
+479 self . run ,
+480 params ,
+481 timestamps ,
+482 strain_rate ,
+483 get_velocity_gradient ,
+484 shear_direction ,
+485 return_fse = True ,
+486 )
+487 with Pool ( processes = ncpus ) as pool :
+488 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+489 mineral , fse_angles = out
+490 angles [ m , s , :] = [
+491 _diagnostics . smallest_angle ( v , shear_direction )
+492 for v in _diagnostics . elasticity_components (
+493 _minerals . voigt_averages ([ mineral ], params )
+494 )[ "hexagonal_axis" ]
+495 ]
+496 # Save the whole mineral for the first seed only.
+497 if outdir is not None and s == 0 :
+498 mineral . save (
+499 f " { out_basepath } .npz" ,
+500 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
+501 )
+502 if return_fse :
+503 θ_fse += fse_angles
+504 505 if return_fse :
+506 θ_fse /= n_seeds
+507 508 if outdir is not None :
+509 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
+510 511 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+512 513 # Take ensemble means and optionally plot figure.
+514 _log . info ( "postprocessing results..." )
+515 result_angles = angles . mean ( axis = 1 )
+516 result_angles_err = angles . std ( axis = 1 )
+517 518 if outdir is not None :
+519 schema = {
+520 "delimiter" : "," ,
+521 "missing" : "-" ,
+522 "fields" : [
+523 {
+524 "name" : "strain" ,
+525 "type" : "integer" ,
+526 "unit" : "percent" ,
+527 "fill" : 999999 ,
+528 }
+529 ],
+530 }
+531 _io . save_scsv (
+532 f " { out_basepath } _strains.scsv" ,
+533 schema ,
+534 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+535 )
+536 np . savez (
+537 f " { out_basepath } _angles.npz" ,
+538 angles = result_angles ,
+539 err = result_angles_err ,
+540 )
+541 fig , ax , colors = _vis . alignment (
+542 None ,
+543 strains ,
+544 result_angles ,
+545 markers ,
+546 labels ,
+547 err = result_angles_err ,
+548 θ_max = 60 ,
+549 θ_fse = θ_fse ,
+550 )
+551 ax . plot ( strains , M0_drexF90 , c = colors [ 0 ])
+552 ax . plot ( strains , M50_drexF90 , c = colors [ 2 ])
+553 ax . plot ( strains , M200_drexF90 , c = colors [ 4 ])
+554 _vis . show_Skemer2016_ShearStrainAngles (
+555 ax ,
+556 [ "Z&K 1200 C" , "Z&K 1300 C" ],
+557 [ "v" , "^" ],
+558 [ "k" , "k" ],
+559 [ "none" , None ],
+560 [
+561 "Zhang & Karato, 1995 \n (1473 K)" ,
+562 "Zhang & Karato, 1995 \n (1573 K)" ,
+563 ],
+564 _core . MineralFabric . olivine_A ,
+565 )
+566 # There is a lot of stuff on this legend, so put it outside the axes.
+567 # These values might need to be tweaked depending on the font size, etc.
+568 _legend = _utils . redraw_legend ( ax , fig = fig , bbox_to_anchor = ( 1.66 , 0.99 ))
+569 fig . savefig (
+570 _io . resolve_path ( f " { out_basepath } .pdf" ),
+571 bbox_extra_artists = ( _legend ,),
+572 bbox_inches = "tight" ,
+573 )
+574 575 # Check that GBM speeds up the alignment between 40% and 100% strain.
+576 _log . info ( "checking grain orientations..." )
+577 for i , θ in enumerate ( result_angles [: - 1 ], start = 1 ):
+578 nt . assert_array_less (
+579 result_angles [ i ][ i_strain_40p : i_strain_100p ],
+580 θ [ i_strain_40p : i_strain_100p ],
+581 )
+582 583 # Check that M*=0 matches FSE (±1°) past 100% strain.
+584 nt . assert_allclose (
+585 result_angles [ 0 ][ i_strain_100p :],
+586 θ_fse [ i_strain_100p :],
+587 atol = 1 ,
+588 rtol = 0 ,
+589 )
+590 591 # Check that results match Fortran output past 40% strain.
+592 nt . assert_allclose (
+593 result_angles [ 0 ][ i_strain_40p :],
+594 M0_drexF90 [ i_strain_40p :],
+595 atol = 0 ,
+596 rtol = 0.1 , # At 40% strain the match is worse than at higher strain.
+597 )
+598 nt . assert_allclose (
+599 result_angles [ 2 ][ i_strain_40p :],
+600 M50_drexF90 [ i_strain_40p :],
+601 atol = 1 ,
+602 rtol = 0 ,
+603 )
+604 nt . assert_allclose (
+605 result_angles [ 4 ][ i_strain_40p :],
+606 M200_drexF90 [ i_strain_40p :],
+607 atol = 1.5 ,
+608 rtol = 0 ,
+609 )
610 611 if outdir is not None :
-612 schema = {
-613 "delimiter" : "," ,
-614 "missing" : "-" ,
-615 "fields" : [
-616 {
-617 "name" : "strain" ,
-618 "type" : "integer" ,
-619 "unit" : "percent" ,
-620 "fill" : 999999 ,
-621 }
-622 ],
-623 }
-624 _io . save_scsv (
-625 f " { out_basepath } _strains.scsv" ,
-626 schema ,
-627 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-628 )
-629 np . savez (
-630 _io . resolve_path ( f " { out_basepath } _ensemble_means.npz" ),
-631 angles = result_angles ,
-632 err = result_angles_err ,
-633 )
-634 fig = _vis . figure (
-635 figsize = ( _vis . DEFAULT_FIG_WIDTH * 3 , _vis . DEFAULT_FIG_HEIGHT )
-636 )
-637 fig , ax , colors = _vis . alignment (
-638 fig . add_subplot (),
-639 strains ,
-640 result_angles ,
-641 markers ,
-642 labels ,
-643 err = result_angles_err ,
-644 θ_max = 80 ,
-645 θ_fse = θ_fse ,
-646 )
-647 (
-648 _ ,
-649 _ ,
-650 _ ,
-651 data_Skemer2016 ,
-652 indices ,
-653 ) = _vis . show_Skemer2016_ShearStrainAngles (
-654 ax ,
-655 [
-656 "Z&K 1200 C" ,
-657 "Z&K 1300 C" ,
-658 "Skemer 2011" ,
-659 "Hansen 2014" ,
-660 "Warren 2008" ,
-661 "Webber 2010" ,
-662 "H&W 2015" ,
-663 ],
-664 [ "v" , "^" , "o" , "s" , "v" , "o" , "s" ],
-665 [ "k" , "k" , "k" , "k" , "k" , "k" , "k" ],
-666 [ "none" , "none" , "none" , "none" , None , None , None ],
-667 [
-668 "Zhang & Karato, 1995 (1473 K)" ,
-669 "Zhang & Karato, 1995 (1573 K)" ,
-670 "Skemer et al., 2011 (1500 K)" ,
-671 "Hansen et al., 2014 (1473 K)" ,
-672 "Warren et al., 2008" ,
-673 "Webber et al., 2010" ,
-674 "Hansen & Warren, 2015" ,
-675 ],
-676 fabric = _core . MineralFabric . olivine_A ,
-677 )
-678 _legend = _utils . redraw_legend ( ax , loc = "upper right" , ncols = 3 )
-679 fig . savefig (
-680 _io . resolve_path ( f " { out_basepath } .pdf" ),
-681 bbox_extra_artists = ( _legend ,),
-682 bbox_inches = "tight" ,
-683 )
-684 r2vals = []
-685 for angles in result_angles :
-686 _angles = PchipInterpolator ( strains , angles )
-687 r2 = np . sum (
-688 [
-689 ( a - b ) ** 2
-690 for a , b in zip (
-691 _angles (
-692 np . take ( data_Skemer2016 . shear_strain , indices ) / 200
-693 ),
-694 np . take ( data_Skemer2016 . angle , indices ),
-695 )
-696 ]
-697 )
-698 r2vals . append ( r2 )
-699 _log . info (
-700 "Sums of squared residuals (r-values) for each M∗: %s " , r2vals
-701 )
+611 @pytest . mark . slow
+612 def test_GBM_calibration ( self , outdir , seeds , ncpus ):
+613 r """Compare results for various values of $$M^∗$$ to A-type olivine data.
+614 615 Velocity gradient:
+616 $$
+617 \bm{L} = 10^{-4} ×
+618 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
+619 $$
+620 621 Unlike `test_dvdx_GBM`,
+622 grain boudary sliding is enabled here (see `_io.DEFAULT_PARAMS`).
+623 Data are provided by [Skemer & Hansen, 2016](http://dx.doi.org/10.1016/j.tecto.2015.12.003).
+624 625 """
+626 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+627 strain_rate = 1
+628 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+629 timestamps = np . linspace ( 0 , 3.2 , 65 ) # Solve until D₀t=3.2 ('shear' γ=6.4).
+630 params = _io . DEFAULT_PARAMS
+631 params [ "number_of_grains" ] = 5000
+632 gbm_mobilities = ( 0 , 10 , 50 , 125 ) # Must be in ascending order.
+633 markers = ( "x" , "*" , "1" , "." )
+634 # Uses 100 seeds by default; use all 1000 if you have more RAM and CPU time.
+635 _seeds = seeds [: 100 ]
+636 n_seeds = len ( _seeds )
+637 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
+638 θ_fse = np . zeros_like ( timestamps )
+639 strains = timestamps * strain_rate
+640 641 optional_logging = cl . nullcontext ()
+642 if outdir is not None :
+643 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _calibration"
+644 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+645 labels = []
+646 647 with optional_logging :
+648 clock_start = process_time ()
+649 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+650 return_fse = True if m == 0 else False
+651 params [ "gbm_mobility" ] = gbm_mobility
+652 _run = ft . partial (
+653 self . run ,
+654 params ,
+655 timestamps ,
+656 strain_rate ,
+657 get_velocity_gradient ,
+658 shear_direction ,
+659 return_fse = return_fse ,
+660 )
+661 with Pool ( processes = ncpus ) as pool :
+662 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+663 mineral , fse_angles = out
+664 angles [ m , s , :] = [
+665 _diagnostics . smallest_angle ( v , shear_direction )
+666 for v in _diagnostics . elasticity_components (
+667 _minerals . voigt_averages ([ mineral ], params )
+668 )[ "hexagonal_axis" ]
+669 ]
+670 # Save the whole mineral for the first seed only.
+671 if outdir is not None and s == 0 :
+672 mineral . save (
+673 f " { out_basepath } .npz" ,
+674 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
+675 )
+676 if return_fse :
+677 θ_fse += fse_angles
+678 679 if return_fse :
+680 θ_fse /= n_seeds
+681 682 if outdir is not None :
+683 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
+684 685 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+686 687 # Take ensemble means and optionally plot figure.
+688 _log . info ( "postprocessing results..." )
+689 result_angles = angles . mean ( axis = 1 )
+690 result_angles_err = angles . std ( axis = 1 )
+691 692 if outdir is not None :
+693 schema = {
+694 "delimiter" : "," ,
+695 "missing" : "-" ,
+696 "fields" : [
+697 {
+698 "name" : "strain" ,
+699 "type" : "integer" ,
+700 "unit" : "percent" ,
+701 "fill" : 999999 ,
+702 }
+703 ],
+704 }
+705 _io . save_scsv (
+706 f " { out_basepath } _strains.scsv" ,
+707 schema ,
+708 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+709 )
+710 np . savez (
+711 _io . resolve_path ( f " { out_basepath } _ensemble_means.npz" ),
+712 angles = result_angles ,
+713 err = result_angles_err ,
+714 )
+715 fig = _vis . figure (
+716 figsize = ( _vis . DEFAULT_FIG_WIDTH * 3 , _vis . DEFAULT_FIG_HEIGHT )
+717 )
+718 fig , ax , colors = _vis . alignment (
+719 fig . add_subplot (),
+720 strains ,
+721 result_angles ,
+722 markers ,
+723 labels ,
+724 err = result_angles_err ,
+725 θ_max = 80 ,
+726 θ_fse = θ_fse ,
+727 )
+728 (
+729 _ ,
+730 _ ,
+731 _ ,
+732 data_Skemer2016 ,
+733 indices ,
+734 ) = _vis . show_Skemer2016_ShearStrainAngles (
+735 ax ,
+736 [
+737 "Z&K 1200 C" ,
+738 "Z&K 1300 C" ,
+739 "Skemer 2011" ,
+740 "Hansen 2014" ,
+741 "Warren 2008" ,
+742 "Webber 2010" ,
+743 "H&W 2015" ,
+744 ],
+745 [ "v" , "^" , "o" , "s" , "v" , "o" , "s" ],
+746 [ "k" , "k" , "k" , "k" , "k" , "k" , "k" ],
+747 [ "none" , "none" , "none" , "none" , None , None , None ],
+748 [
+749 "Zhang & Karato, 1995 (1473 K)" ,
+750 "Zhang & Karato, 1995 (1573 K)" ,
+751 "Skemer et al., 2011 (1500 K)" ,
+752 "Hansen et al., 2014 (1473 K)" ,
+753 "Warren et al., 2008" ,
+754 "Webber et al., 2010" ,
+755 "Hansen & Warren, 2015" ,
+756 ],
+757 fabric = _core . MineralFabric . olivine_A ,
+758 )
+759 _legend = _utils . redraw_legend ( ax , loc = "upper right" , ncols = 3 )
+760 fig . savefig (
+761 _io . resolve_path ( f " { out_basepath } .pdf" ),
+762 bbox_extra_artists = ( _legend ,),
+763 bbox_inches = "tight" ,
+764 )
+765 r2vals = []
+766 for angles in result_angles :
+767 _angles = PchipInterpolator ( strains , angles )
+768 r2 = np . sum (
+769 [
+770 ( a - b ) ** 2
+771 for a , b in zip (
+772 _angles (
+773 np . take ( data_Skemer2016 . shear_strain , indices ) / 200
+774 ),
+775 np . take ( data_Skemer2016 . angle , indices ),
+776 )
+777 ]
+778 )
+779 r2vals . append ( r2 )
+780 _log . info (
+781 "Sums of squared residuals (r-values) for each M∗: %s " , r2vals
+782 )
+783 784 @pytest . mark . big
+785 def test_dudz_pathline ( self , outdir , seed ):
+786 """Test alignment of olivine a-axis for a polycrystal advected on a pathline."""
+787 test_id = "dudz_pathline"
+788 optional_logging = cl . nullcontext ()
+789 if outdir is not None :
+790 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _ { test_id } "
+791 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+792 793 with optional_logging :
+794 shear_direction = [ 1 , 0 , 0 ] # Used to calculate the angular diagnostics.
+795 strain_rate = 1e-15 # Moderate, realistic shear in the upper mantle.
+796 get_velocity , get_velocity_gradient = _velocity . simple_shear_2d (
+797 "X" , "Z" , strain_rate
+798 )
+799 n_timesteps = 10
+800 timestamps , get_position = _paths . get_pathline (
+801 Ŋ ([ 1e5 , 0e0 , 1e5 ]),
+802 get_velocity ,
+803 get_velocity_gradient ,
+804 Ŋ ([ - 2e5 , 0e0 , - 2e5 ]),
+805 Ŋ ([ 2e5 , 0e0 , 2e5 ]),
+806 2 ,
+807 regular_steps = n_timesteps ,
+808 )
+809 positions = [ get_position ( t ) for t in timestamps ]
+810 velocity_gradients = [ get_velocity_gradient ( Ŋ ( x )) for x in positions ]
+811 812 params = _io . DEFAULT_PARAMS
+813 params [ "number_of_grains" ] = 5000
+814 olA = _minerals . Mineral ( n_grains = params [ "number_of_grains" ], seed = seed )
+815 deformation_gradient = np . eye ( 3 )
+816 strains = np . zeros_like ( timestamps )
+817 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+818 strains [ t ] = strains [ t - 1 ] + (
+819 _utils . strain_increment ( timestamps [ t ] - time , velocity_gradients [ t ])
+820 )
+821 _log . info ( "step %d / %d (ε = %.2f )" , t , len ( timestamps ) - 1 , strains [ t ])
+822 deformation_gradient = olA . update_orientations (
+823 params ,
+824 deformation_gradient ,
+825 get_velocity_gradient ,
+826 pathline = ( time , timestamps [ t ], get_position ),
+827 )
+828 829 orient_resampled , fractions_resampled = _stats . resample_orientations (
+830 olA . orientations , olA . fractions , seed = seed
+831 )
+832 # About 36GB, 26 min needed with float64. GitHub macos runner has 14GB.
+833 misorient_indices = _diagnostics . misorientation_indices (
+834 orient_resampled ,
+835 _geo . LatticeSystem . orthorhombic ,
+836 ncpus = 3 ,
+837 )
+838 cpo_vectors = np . zeros (( n_timesteps + 1 , 3 ))
+839 cpo_angles = np . zeros ( n_timesteps + 1 )
+840 for i , matrices in enumerate ( orient_resampled ):
+841 cpo_vectors [ i ] = _diagnostics . bingham_average (
+842 matrices ,
+843 axis = _minerals . OLIVINE_PRIMARY_AXIS [ olA . fabric ],
+844 )
+845 cpo_angles [ i ] = _diagnostics . smallest_angle (
+846 cpo_vectors [ i ], Ŋ ( shear_direction , dtype = np . float64 )
+847 )
+848 849 # Check for mostly decreasing CPO angles (exclude initial condition).
+850 _log . debug ( "cpo angles: %s " , cpo_angles )
+851 nt . assert_array_less ( np . diff ( cpo_angles [ 1 :]), np . ones ( n_timesteps - 1 ))
+852 # Check for increasing CPO strength (M-index).
+853 _log . debug ( "cpo strengths: %s " , misorient_indices )
+854 nt . assert_array_less (
+855 np . full ( n_timesteps , - 0.01 ), np . diff ( misorient_indices )
+856 )
+857 # Check that last angle is <5° (M*=125) or <10° (M*=10).
+858 assert cpo_angles [ - 1 ] < 5
+859 860 if outdir is not None :
+861 fig , ax , _ , _ = _vis . pathline_box2d (
+862 None ,
+863 get_velocity ,
+864 "xz" ,
+865 strains ,
+866 positions ,
+867 "." ,
+868 Ŋ ([ - 2e5 , - 2e5 ]),
+869 Ŋ ([ 2e5 , 2e5 ]),
+870 [ 20 , 20 ],
+871 cpo_vectors = cpo_vectors ,
+872 cpo_strengths = misorient_indices ,
+873 )
+874 fig . savefig ( f " { out_basepath } .pdf" )
-
-
-
-
@classmethod
-
-
def
-
get_position (cls , t ):
-
-
View Source
-
-
-
-
32 @classmethod
-33 def get_position ( cls , t ):
-34 return np . zeros ( 3 ) # These crystals are stationary.
-
-
-
-
-
@@ -1571,77 +2012,78 @@
@classmethod
def
- run ( cls , params , timestamps , strain_rate , get_velocity_gradient , shear_direction , seed = None , return_fse = None ):
+ run ( cls , params , timestamps , strain_rate , get_velocity_gradient , shear_direction , seed = None , return_fse = None , get_position =< function TestOlivineA .< lambda >> ):
View Source
- 36 @classmethod
- 37 def run (
- 38 cls ,
- 39 params ,
- 40 timestamps ,
- 41 strain_rate ,
- 42 get_velocity_gradient ,
- 43 shear_direction ,
- 44 seed = None ,
- 45 return_fse = None ,
- 46 ):
- 47 """Reusable logic for 2D olivine (A-type) simple shear tests.
- 48 49 Returns a tuple with the mineral and the FSE angle (or `None` if `return_fse` is
- 50 `None`).
- 51 52 """
- 53 mineral = _minerals . Mineral (
- 54 phase = _core . MineralPhase . olivine ,
- 55 fabric = _core . MineralFabric . olivine_A ,
- 56 regime = _core . DeformationRegime . dislocation ,
- 57 n_grains = params [ "number_of_grains" ],
- 58 seed = seed ,
- 59 )
- 60 deformation_gradient = np . eye ( 3 ) # Undeformed initial state.
- 61 θ_fse = np . empty_like ( timestamps )
- 62 θ_fse [ 0 ] = 45
- 63 64 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
- 65 # Set up logging message depending on dynamic parameter and seeds.
- 66 msg_start = (
- 67 f "N = { params [ 'number_of_grains' ] } ; "
- 68 + f "λ∗ = { params [ 'nucleation_efficiency' ] } ; "
- 69 + f "X = { params [ 'gbs_threshold' ] } ; "
- 70 + f "M∗ = { params [ 'gbm_mobility' ] } ; "
- 71 )
- 72 if seed is not None :
- 73 msg_start += f "# { seed } ; "
- 74 75 _log . info ( msg_start + "step %s / %s (t = %s )" , t , len ( timestamps ) - 1 , time )
- 76 77 deformation_gradient = mineral . update_orientations (
- 78 params ,
- 79 deformation_gradient ,
- 80 get_velocity_gradient ,
- 81 pathline = ( time , timestamps [ t ], cls . get_position ),
- 82 )
- 83 _log . debug (
- 84 "› velocity gradient = %s " ,
- 85 get_velocity_gradient ( None ) . flatten (),
- 86 )
- 87 _log . debug ( "› strain D₀t = %.2f " , strain_rate * timestamps [ t ])
- 88 _log . debug (
- 89 "› grain fractions: median = %s , max = %s , min = %s " ,
- 90 np . median ( mineral . fractions [ - 1 ]),
- 91 np . max ( mineral . fractions [ - 1 ]),
- 92 np . min ( mineral . fractions [ - 1 ]),
- 93 )
- 94 if return_fse :
- 95 _ , fse_v = _diagnostics . finite_strain ( deformation_gradient )
- 96 θ_fse [ t ] = _diagnostics . smallest_angle ( fse_v , shear_direction )
- 97 else :
- 98 θ_fse = None
- 99 100 return mineral , θ_fse
+ 116 @classmethod
+117 def run (
+118 cls ,
+119 params ,
+120 timestamps ,
+121 strain_rate ,
+122 get_velocity_gradient ,
+123 shear_direction ,
+124 seed = None ,
+125 return_fse = None ,
+126 get_position = lambda t : np . zeros ( 3 ), # Stationary particles by default.
+127 ):
+128 """Reusable logic for 2D olivine (A-type) simple shear tests.
+129 130 Returns a tuple with the mineral and the FSE angle (or `None` if `return_fse` is
+131 `None`).
+132 133 """
+134 mineral = _minerals . Mineral (
+135 phase = _core . MineralPhase . olivine ,
+136 fabric = _core . MineralFabric . olivine_A ,
+137 regime = _core . DeformationRegime . dislocation ,
+138 n_grains = params [ "number_of_grains" ],
+139 seed = seed ,
+140 )
+141 deformation_gradient = np . eye ( 3 ) # Undeformed initial state.
+142 θ_fse = np . empty_like ( timestamps )
+143 θ_fse [ 0 ] = 45
+144 145 for t , time in enumerate ( timestamps [: - 1 ], start = 1 ):
+146 # Set up logging message depending on dynamic parameter and seeds.
+147 msg_start = (
+148 f "N = { params [ 'number_of_grains' ] } ; "
+149 + f "λ∗ = { params [ 'nucleation_efficiency' ] } ; "
+150 + f "X = { params [ 'gbs_threshold' ] } ; "
+151 + f "M∗ = { params [ 'gbm_mobility' ] } ; "
+152 )
+153 if seed is not None :
+154 msg_start += f "# { seed } ; "
+155 156 _log . info ( msg_start + "step %s / %s (t = %s )" , t , len ( timestamps ) - 1 , time )
+157 158 deformation_gradient = mineral . update_orientations (
+159 params ,
+160 deformation_gradient ,
+161 get_velocity_gradient ,
+162 pathline = ( time , timestamps [ t ], get_position ),
+163 )
+164 _log . debug (
+165 "› velocity gradient = %s " ,
+166 get_velocity_gradient ( None ) . flatten (),
+167 )
+168 _log . debug ( "› strain D₀t = %.2f " , strain_rate * timestamps [ t ])
+169 _log . debug (
+170 "› grain fractions: median = %s , max = %s , min = %s " ,
+171 np . median ( mineral . fractions [ - 1 ]),
+172 np . max ( mineral . fractions [ - 1 ]),
+173 np . min ( mineral . fractions [ - 1 ]),
+174 )
+175 if return_fse :
+176 _ , fse_v = _diagnostics . finite_strain ( deformation_gradient )
+177 θ_fse [ t ] = _diagnostics . smallest_angle ( fse_v , shear_direction )
+178 else :
+179 θ_fse = None
+180 181 return mineral , θ_fse
102 @classmethod
-103 def interp_GBM_Kaminski2001 ( cls , strains ):
-104 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
-105 _log . info ( "interpolating target CPO angles..." )
-106 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2001_GBMshear.scsv" )
-107 cs_M0 = PchipInterpolator (
-108 _utils . remove_nans ( data . equivalent_strain_M0 ) / 200 ,
-109 _utils . remove_nans ( data . angle_M0 ),
-110 )
-111 cs_M50 = PchipInterpolator (
-112 _utils . remove_nans ( data . equivalent_strain_M50 ) / 200 ,
-113 _utils . remove_nans ( data . angle_M50 ),
-114 )
-115 cs_M200 = PchipInterpolator (
-116 _utils . remove_nans ( data . equivalent_strain_M200 ) / 200 ,
-117 _utils . remove_nans ( data . angle_M200 ),
-118 )
-119 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
+ 183 @classmethod
+184 def interp_GBM_Kaminski2001 ( cls , strains ):
+185 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
+186 _log . info ( "interpolating target CPO angles..." )
+187 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2001_GBMshear.scsv" )
+188 cs_M0 = PchipInterpolator (
+189 _utils . remove_nans ( data . equivalent_strain_M0 ) / 200 ,
+190 _utils . remove_nans ( data . angle_M0 ),
+191 )
+192 cs_M50 = PchipInterpolator (
+193 _utils . remove_nans ( data . equivalent_strain_M50 ) / 200 ,
+194 _utils . remove_nans ( data . angle_M50 ),
+195 )
+196 cs_M200 = PchipInterpolator (
+197 _utils . remove_nans ( data . equivalent_strain_M200 ) / 200 ,
+198 _utils . remove_nans ( data . angle_M200 ),
+199 )
+200 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
121 @classmethod
-122 def interp_GBM_FortranDRex ( cls , strains ):
-123 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-124 _log . info ( "interpolating target CPO angles..." )
-125 data = _io . read_scsv ( _io . data ( "drexF90" ) / "olA_D1E4_dt50_X0_L5.scsv" )
-126 data_strains = np . linspace ( 0 , 1 , 200 )
-127 cs_M0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M0_angle ))
-128 cs_M50 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M50_angle ))
-129 cs_M200 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M200_angle ))
-130 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
+ 202 @classmethod
+203 def interp_GBM_FortranDRex ( cls , strains ):
+204 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+205 _log . info ( "interpolating target CPO angles..." )
+206 data = _io . read_scsv ( _io . data ( "drexF90" ) / "olA_D1E4_dt50_X0_L5.scsv" )
+207 data_strains = np . linspace ( 0 , 1 , 200 )
+208 cs_M0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M0_angle ))
+209 cs_M50 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M50_angle ))
+210 cs_M200 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . M200_angle ))
+211 return [ cs_M0 ( strains ), cs_M50 ( strains ), cs_M200 ( strains )]
132 @classmethod
-133 def interp_GBS_FortranDRex ( cls , strains ):
-134 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-135 _log . info ( "interpolating target CPO angles..." )
-136 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_fortran.scsv" )
-137 data_strains = np . linspace ( 0 , 1 , 200 )
-138 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
-139 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
-140 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
-141 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
+ 213 @classmethod
+214 def interp_GBS_FortranDRex ( cls , strains ):
+215 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+216 _log . info ( "interpolating target CPO angles..." )
+217 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_fortran.scsv" )
+218 data_strains = np . linspace ( 0 , 1 , 200 )
+219 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
+220 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
+221 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
+222 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
143 @classmethod
-144 def interp_GBS_long_FortranDRex ( cls , strains ):
-145 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
-146 _log . info ( "interpolating target CPO angles..." )
-147 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_long_fortran.scsv" )
-148 data_strains = np . linspace ( 0 , 2.5 , 500 )
-149 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
-150 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
-151 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
-152 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
+ 224 @classmethod
+225 def interp_GBS_long_FortranDRex ( cls , strains ):
+226 """Interpolate angles produced using 'tools/drex_forward_simpleshear.f90'."""
+227 _log . info ( "interpolating target CPO angles..." )
+228 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "a_axis_GBS_long_fortran.scsv" )
+229 data_strains = np . linspace ( 0 , 2.5 , 500 )
+230 cs_X0 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X0 ))
+231 cs_X20 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X20 ))
+232 cs_X40 = PchipInterpolator ( data_strains , _utils . remove_nans ( data . a_mean_X40 ))
+233 return [ cs_X0 ( strains ), cs_X20 ( strains ), cs_X40 ( strains )]
154 @classmethod
-155 def interp_GBS_Kaminski2004 ( cls , strains ):
-156 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
-157 _log . info ( "interpolating target CPO angles..." )
-158 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2004_GBSshear.scsv" )
-159 cs_X0 = PchipInterpolator (
-160 _utils . remove_nans ( data . dimensionless_time_X0 ),
-161 45 + _utils . remove_nans ( data . angle_X0 ),
-162 )
-163 cs_X0d2 = PchipInterpolator (
-164 _utils . remove_nans ( data . dimensionless_time_X0d2 ),
-165 45 + _utils . remove_nans ( data . angle_X0d2 ),
-166 )
-167 cs_X0d4 = PchipInterpolator (
-168 _utils . remove_nans ( data . dimensionless_time_X0d4 ),
-169 45 + _utils . remove_nans ( data . angle_X0d4 ),
-170 )
-171 return [ cs_X0 ( strains ), cs_X0d2 ( strains ), cs_X0d4 ( strains )]
+ 235 @classmethod
+236 def interp_GBS_Kaminski2004 ( cls , strains ):
+237 """Interpolate Kaminski & Ribe, 2001 data to get target angles at `strains`."""
+238 _log . info ( "interpolating target CPO angles..." )
+239 data = _io . read_scsv ( _io . data ( "thirdparty" ) / "Kaminski2004_GBSshear.scsv" )
+240 cs_X0 = PchipInterpolator (
+241 _utils . remove_nans ( data . dimensionless_time_X0 ),
+242 45 + _utils . remove_nans ( data . angle_X0 ),
+243 )
+244 cs_X0d2 = PchipInterpolator (
+245 _utils . remove_nans ( data . dimensionless_time_X0d2 ),
+246 45 + _utils . remove_nans ( data . angle_X0d2 ),
+247 )
+248 cs_X0d4 = PchipInterpolator (
+249 _utils . remove_nans ( data . dimensionless_time_X0d4 ),
+250 45 + _utils . remove_nans ( data . angle_X0d4 ),
+251 )
+252 return [ cs_X0 ( strains ), cs_X0d2 ( strains ), cs_X0d4 ( strains )]
173 def test_zero_recrystallisation ( self , seed ):
-174 """Check that M*=0 is a reliable switch to turn off recrystallisation."""
-175 params = _io . DEFAULT_PARAMS
-176 params [ "gbm_mobility" ] = 0
-177 strain_rate = 1
-178 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
-179 shear_direction = [ 0 , 1 , 0 ]
-180 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-181 mineral , _ = self . run (
-182 params ,
-183 timestamps ,
-184 strain_rate ,
-185 get_velocity_gradient ,
-186 shear_direction ,
-187 seed = seed ,
-188 )
-189 for fractions in mineral . fractions [ 1 :]:
-190 nt . assert_allclose ( fractions , mineral . fractions [ 0 ], atol = 1e-15 , rtol = 0 )
+ 254 def test_zero_recrystallisation ( self , seed ):
+255 """Check that M*=0 is a reliable switch to turn off recrystallisation."""
+256 params = _io . DEFAULT_PARAMS
+257 params [ "gbm_mobility" ] = 0
+258 strain_rate = 1
+259 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
+260 shear_direction = [ 0 , 1 , 0 ]
+261 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+262 mineral , _ = self . run (
+263 params ,
+264 timestamps ,
+265 strain_rate ,
+266 get_velocity_gradient ,
+267 shear_direction ,
+268 seed = seed ,
+269 )
+270 for fractions in mineral . fractions [ 1 :]:
+271 nt . assert_allclose ( fractions , mineral . fractions [ 0 ], atol = 1e-15 , rtol = 0 )
192 @pytest . mark . parametrize ( "gbm_mobility" , [ 50 , 100 , 150 ])
-193 def test_grainsize_median ( self , seed , gbm_mobility ):
-194 """Check that M*={50,100,150}, λ*=5 causes decreasing grain size median."""
-195 params = _io . DEFAULT_PARAMS
-196 params [ "gbm_mobility" ] = gbm_mobility
-197 params [ "nucleation_efficiency" ] = 5
-198 strain_rate = 1
-199 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
-200 n_timestamps = len ( timestamps )
-201 shear_direction = [ 0 , 1 , 0 ]
-202 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-203 mineral , _ = self . run (
-204 params ,
-205 timestamps ,
-206 strain_rate ,
-207 get_velocity_gradient ,
-208 shear_direction ,
-209 seed = seed ,
-210 )
-211 medians = np . empty ( n_timestamps )
-212 for i , fractions in enumerate ( mineral . fractions ):
-213 medians [ i ] = np . median ( fractions )
-214 215 # The first diff is positive (~1e-6) before nucleation sets in.
-216 nt . assert_array_less ( np . diff ( medians )[ 1 :], np . full ( n_timestamps - 2 , 0 ))
+ 273 @pytest . mark . parametrize ( "gbm_mobility" , [ 50 , 100 , 150 ])
+274 def test_grainsize_median ( self , seed , gbm_mobility ):
+275 """Check that M*={50,100,150}, λ*=5 causes decreasing grain size median."""
+276 params = _io . DEFAULT_PARAMS
+277 params [ "gbm_mobility" ] = gbm_mobility
+278 params [ "nucleation_efficiency" ] = 5
+279 strain_rate = 1
+280 timestamps = np . linspace ( 0 , 1 , 25 ) # Solve until D₀t=1 (tensorial strain).
+281 n_timestamps = len ( timestamps )
+282 shear_direction = [ 0 , 1 , 0 ]
+283 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+284 mineral , _ = self . run (
+285 params ,
+286 timestamps ,
+287 strain_rate ,
+288 get_velocity_gradient ,
+289 shear_direction ,
+290 seed = seed ,
+291 )
+292 medians = np . empty ( n_timestamps )
+293 for i , fractions in enumerate ( mineral . fractions ):
+294 medians [ i ] = np . median ( fractions )
+295 296 # The first diff is positive (~1e-6) before nucleation sets in.
+297 nt . assert_array_less ( np . diff ( medians )[ 1 :], np . full ( n_timestamps - 2 , 0 ))
218 @pytest . mark . slow
-219 @pytest . mark . parametrize ( "gbs_threshold" , [ 0 , 0.2 , 0.4 ])
-220 @pytest . mark . parametrize ( "nucleation_efficiency" , [ 3 , 5 , 10 ])
-221 def test_dvdx_ensemble (
-222 self , outdir , seeds_nearX45 , ncpus , gbs_threshold , nucleation_efficiency
-223 ):
-224 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
-225 226 Velocity gradient:
-227 $$\bm{L} = \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}$$
-228 229 """
-230 strain_rate = 1
-231 timestamps = np . linspace ( 0 , 1 , 201 ) # Solve until D₀t=1 ('shear' γ=2).
-232 n_timestamps = len ( timestamps )
-233 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
-234 _seeds = seeds_nearX45
-235 n_seeds = len ( _seeds )
-236 237 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-238 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-239 240 gbm_mobilities = [ 0 , 50 , 125 , 200 ]
-241 markers = ( "x" , "*" , "d" , "s" )
-242 243 _id = f "X { _io . stringify ( gbs_threshold ) } _L { _io . stringify ( nucleation_efficiency ) } "
-244 # Output setup with optional logging and data series labels.
-245 θ_fse = np . empty_like ( timestamps )
-246 angles = np . empty (( len ( gbm_mobilities ), n_seeds , n_timestamps ))
-247 optional_logging = cl . nullcontext ()
-248 if outdir is not None :
-249 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _dvdx_ensemble_ { _id } "
-250 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-251 labels = []
-252 253 with optional_logging :
-254 clock_start = process_time ()
-255 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-256 if m == 0 :
-257 return_fse = True
-258 else :
-259 return_fse = False
-260 261 params = {
-262 "olivine_fraction" : 1.0 ,
-263 "enstatite_fraction" : 0.0 ,
-264 "stress_exponent" : 1.5 ,
-265 "deformation_exponent" : 3.5 ,
-266 "gbm_mobility" : gbm_mobility ,
-267 "gbs_threshold" : gbs_threshold ,
-268 "nucleation_efficiency" : nucleation_efficiency ,
-269 "number_of_grains" : 5000 ,
-270 "initial_olivine_fabric" : "A" ,
-271 }
-272 273 _run = ft . partial (
-274 self . run ,
-275 params ,
-276 timestamps ,
-277 strain_rate ,
-278 get_velocity_gradient ,
-279 shear_direction ,
-280 return_fse = return_fse ,
-281 )
-282 with Pool ( processes = ncpus ) as pool :
-283 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-284 mineral , fse_angles = out
-285 angles [ m , s , :] = [
-286 _diagnostics . smallest_angle ( v , shear_direction )
-287 for v in _diagnostics . elasticity_components (
-288 _minerals . voigt_averages ([ mineral ], params )
-289 )[ "hexagonal_axis" ]
-290 ]
-291 # Save the whole mineral for the first seed only.
-292 if outdir is not None and s == 0 :
-293 postfix = (
-294 f "M { _io . stringify ( gbm_mobility ) } "
-295 + f "_X { _io . stringify ( gbs_threshold ) } "
-296 + f "_L { _io . stringify ( nucleation_efficiency ) } "
-297 )
-298 mineral . save ( f " { out_basepath } .npz" , postfix = postfix )
-299 if return_fse :
-300 θ_fse += fse_angles
-301 302 if return_fse :
-303 θ_fse /= n_seeds
-304 305 if outdir is not None :
-306 labels . append ( f "$M^∗$ = { gbm_mobility } " )
-307 308 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+ 299 @pytest . mark . slow
+300 @pytest . mark . parametrize ( "gbs_threshold" , [ 0 , 0.2 , 0.4 ])
+301 @pytest . mark . parametrize ( "nucleation_efficiency" , [ 3 , 5 , 10 ])
+302 def test_dvdx_ensemble (
+303 self , outdir , seeds_nearX45 , ncpus , gbs_threshold , nucleation_efficiency
+304 ):
+305 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
+306 307 Velocity gradient:
+308 $$\bm{L} = \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}$$
309 310 # Take ensemble means and optionally plot figure.
-311 strains = timestamps * strain_rate
-312 _log . info ( "postprocessing results for %s " , _id )
-313 result_angles = angles . mean ( axis = 1 )
-314 result_angles_err = angles . std ( axis = 1 )
-315 316 if outdir is not None :
-317 schema = {
-318 "delimiter" : "," ,
-319 "missing" : "-" ,
-320 "fields" : [
-321 {
-322 "name" : "strain" ,
-323 "type" : "integer" ,
-324 "unit" : "percent" ,
-325 "fill" : 999999 ,
-326 }
-327 ],
-328 }
-329 np . savez (
-330 f " { out_basepath } .npz" ,
-331 angles = result_angles ,
-332 angles_err = result_angles_err ,
-333 )
-334 _io . save_scsv (
-335 f " { out_basepath } _strains.scsv" ,
-336 schema ,
-337 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-338 )
-339 fig , ax , colors = _vis . alignment (
-340 None ,
-341 strains ,
-342 result_angles ,
-343 markers ,
-344 labels ,
-345 err = result_angles_err ,
-346 θ_max = 60 ,
-347 θ_fse = θ_fse ,
-348 )
-349 fig . savefig ( _io . resolve_path ( f " { out_basepath } .pdf" ))
+310 """
+311 strain_rate = 1
+312 timestamps = np . linspace ( 0 , 1 , 201 ) # Solve until D₀t=1 ('shear' γ=2).
+313 n_timestamps = len ( timestamps )
+314 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
+315 _seeds = seeds_nearX45
+316 n_seeds = len ( _seeds )
+317 318 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+319 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+320 321 gbm_mobilities = [ 0 , 50 , 125 , 200 ]
+322 markers = ( "x" , "*" , "d" , "s" )
+323 324 _id = f "X { _io . stringify ( gbs_threshold ) } _L { _io . stringify ( nucleation_efficiency ) } "
+325 # Output setup with optional logging and data series labels.
+326 θ_fse = np . empty_like ( timestamps )
+327 angles = np . empty (( len ( gbm_mobilities ), n_seeds , n_timestamps ))
+328 optional_logging = cl . nullcontext ()
+329 if outdir is not None :
+330 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _dvdx_ensemble_ { _id } "
+331 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+332 labels = []
+333 334 with optional_logging :
+335 clock_start = process_time ()
+336 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+337 if m == 0 :
+338 return_fse = True
+339 else :
+340 return_fse = False
+341 342 params = {
+343 "olivine_fraction" : 1.0 ,
+344 "enstatite_fraction" : 0.0 ,
+345 "stress_exponent" : 1.5 ,
+346 "deformation_exponent" : 3.5 ,
+347 "gbm_mobility" : gbm_mobility ,
+348 "gbs_threshold" : gbs_threshold ,
+349 "nucleation_efficiency" : nucleation_efficiency ,
+350 "number_of_grains" : 5000 ,
+351 "initial_olivine_fabric" : "A" ,
+352 }
+353 354 _run = ft . partial (
+355 self . run ,
+356 params ,
+357 timestamps ,
+358 strain_rate ,
+359 get_velocity_gradient ,
+360 shear_direction ,
+361 return_fse = return_fse ,
+362 )
+363 with Pool ( processes = ncpus ) as pool :
+364 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+365 mineral , fse_angles = out
+366 angles [ m , s , :] = [
+367 _diagnostics . smallest_angle ( v , shear_direction )
+368 for v in _diagnostics . elasticity_components (
+369 _minerals . voigt_averages ([ mineral ], params )
+370 )[ "hexagonal_axis" ]
+371 ]
+372 # Save the whole mineral for the first seed only.
+373 if outdir is not None and s == 0 :
+374 postfix = (
+375 f "M { _io . stringify ( gbm_mobility ) } "
+376 + f "_X { _io . stringify ( gbs_threshold ) } "
+377 + f "_L { _io . stringify ( nucleation_efficiency ) } "
+378 )
+379 mineral . save ( f " { out_basepath } .npz" , postfix = postfix )
+380 if return_fse :
+381 θ_fse += fse_angles
+382 383 if return_fse :
+384 θ_fse /= n_seeds
+385 386 if outdir is not None :
+387 labels . append ( f "$M^∗$ = { gbm_mobility } " )
+388 389 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+390 391 # Take ensemble means and optionally plot figure.
+392 strains = timestamps * strain_rate
+393 _log . info ( "postprocessing results for %s " , _id )
+394 result_angles = angles . mean ( axis = 1 )
+395 result_angles_err = angles . std ( axis = 1 )
+396 397 if outdir is not None :
+398 schema = {
+399 "delimiter" : "," ,
+400 "missing" : "-" ,
+401 "fields" : [
+402 {
+403 "name" : "strain" ,
+404 "type" : "integer" ,
+405 "unit" : "percent" ,
+406 "fill" : 999999 ,
+407 }
+408 ],
+409 }
+410 np . savez (
+411 f " { out_basepath } .npz" ,
+412 angles = result_angles ,
+413 angles_err = result_angles_err ,
+414 )
+415 _io . save_scsv (
+416 f " { out_basepath } _strains.scsv" ,
+417 schema ,
+418 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+419 )
+420 fig , ax , colors = _vis . alignment (
+421 None ,
+422 strains ,
+423 result_angles ,
+424 markers ,
+425 labels ,
+426 err = result_angles_err ,
+427 θ_max = 60 ,
+428 θ_fse = θ_fse ,
+429 )
+430 fig . savefig ( _io . resolve_path ( f " { out_basepath } .pdf" ))
351 @pytest . mark . slow
-352 def test_dvdx_GBM ( self , outdir , seeds_nearX45 , ncpus ):
-353 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
-354 355 Velocity gradient:
-356 $$
-357 \bm{L} = 10^{-4} ×
-358 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
-359 $$
-360 361 Results are compared to the Fortran 90 output.
-362 363 """
-364 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-365 strain_rate = 1e-4
-366 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-367 timestamps = np . linspace ( 0 , 1e4 , 51 ) # Solve until D₀t=1 ('shear' γ=2).
-368 i_strain_40p = 10 # Index of 40% strain, lower strains are not relevant here.
-369 i_strain_100p = 25 # Index of 100% strain, when M*=0 matches FSE.
-370 params = _io . DEFAULT_PARAMS
-371 params [ "gbs_threshold" ] = 0 # No GBS, to match the Fortran parameters.
-372 gbm_mobilities = ( 0 , 10 , 50 , 125 , 200 ) # Must be in ascending order.
-373 markers = ( "x" , "." , "*" , "d" , "s" )
-374 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
-375 _seeds = seeds_nearX45
-376 n_seeds = len ( _seeds )
-377 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
-378 θ_fse = np . zeros_like ( timestamps )
-379 strains = timestamps * strain_rate
-380 M0_drexF90 , M50_drexF90 , M200_drexF90 = self . interp_GBM_FortranDRex ( strains )
-381 382 optional_logging = cl . nullcontext ()
-383 if outdir is not None :
-384 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _mobility"
-385 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-386 labels = []
-387 388 with optional_logging :
-389 clock_start = process_time ()
-390 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-391 if m == 0 :
-392 return_fse = True
-393 else :
-394 return_fse = False
-395 params [ "gbm_mobility" ] = gbm_mobility
-396 397 _run = ft . partial (
-398 self . run ,
-399 params ,
-400 timestamps ,
-401 strain_rate ,
-402 get_velocity_gradient ,
-403 shear_direction ,
-404 return_fse = True ,
-405 )
-406 with Pool ( processes = ncpus ) as pool :
-407 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-408 mineral , fse_angles = out
-409 angles [ m , s , :] = [
-410 _diagnostics . smallest_angle ( v , shear_direction )
-411 for v in _diagnostics . elasticity_components (
-412 _minerals . voigt_averages ([ mineral ], params )
-413 )[ "hexagonal_axis" ]
-414 ]
-415 # Save the whole mineral for the first seed only.
-416 if outdir is not None and s == 0 :
-417 mineral . save (
-418 f " { out_basepath } .npz" ,
-419 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
-420 )
-421 if return_fse :
-422 θ_fse += fse_angles
-423 424 if return_fse :
-425 θ_fse /= n_seeds
-426 427 if outdir is not None :
-428 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
-429 430 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
-431 432 # Take ensemble means and optionally plot figure.
-433 _log . info ( "postprocessing results..." )
-434 result_angles = angles . mean ( axis = 1 )
-435 result_angles_err = angles . std ( axis = 1 )
-436 437 if outdir is not None :
-438 schema = {
-439 "delimiter" : "," ,
-440 "missing" : "-" ,
-441 "fields" : [
-442 {
-443 "name" : "strain" ,
-444 "type" : "integer" ,
-445 "unit" : "percent" ,
-446 "fill" : 999999 ,
-447 }
-448 ],
-449 }
-450 _io . save_scsv (
-451 f " { out_basepath } _strains.scsv" ,
-452 schema ,
-453 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-454 )
-455 np . savez (
-456 f " { out_basepath } _angles.npz" ,
-457 angles = result_angles ,
-458 err = result_angles_err ,
-459 )
-460 fig , ax , colors = _vis . alignment (
-461 None ,
-462 strains ,
-463 result_angles ,
-464 markers ,
-465 labels ,
-466 err = result_angles_err ,
-467 θ_max = 60 ,
-468 θ_fse = θ_fse ,
-469 )
-470 ax . plot ( strains , M0_drexF90 , c = colors [ 0 ])
-471 ax . plot ( strains , M50_drexF90 , c = colors [ 2 ])
-472 ax . plot ( strains , M200_drexF90 , c = colors [ 4 ])
-473 _vis . show_Skemer2016_ShearStrainAngles (
-474 ax ,
-475 [ "Z&K 1200 C" , "Z&K 1300 C" ],
-476 [ "v" , "^" ],
-477 [ "k" , "k" ],
-478 [ "none" , None ],
-479 [
-480 "Zhang & Karato, 1995 \n (1473 K)" ,
-481 "Zhang & Karato, 1995 \n (1573 K)" ,
-482 ],
-483 _core . MineralFabric . olivine_A ,
-484 )
-485 # There is a lot of stuff on this legend, so put it outside the axes.
-486 # These values might need to be tweaked depending on the font size, etc.
-487 _legend = _utils . redraw_legend ( ax , fig = fig , bbox_to_anchor = ( 1.66 , 0.99 ))
-488 fig . savefig (
-489 _io . resolve_path ( f " { out_basepath } .pdf" ),
-490 bbox_extra_artists = ( _legend ,),
-491 bbox_inches = "tight" ,
-492 )
-493 494 # Check that GBM speeds up the alignment between 40% and 100% strain.
-495 _log . info ( "checking grain orientations..." )
-496 for i , θ in enumerate ( result_angles [: - 1 ], start = 1 ):
-497 nt . assert_array_less (
-498 result_angles [ i ][ i_strain_40p : i_strain_100p ],
-499 θ [ i_strain_40p : i_strain_100p ],
-500 )
-501 502 # Check that M*=0 matches FSE (±1°) past 100% strain.
-503 nt . assert_allclose (
-504 result_angles [ 0 ][ i_strain_100p :],
-505 θ_fse [ i_strain_100p :],
-506 atol = 1 ,
-507 rtol = 0 ,
-508 )
-509 510 # Check that results match Fortran output past 40% strain.
-511 nt . assert_allclose (
-512 result_angles [ 0 ][ i_strain_40p :],
-513 M0_drexF90 [ i_strain_40p :],
-514 atol = 0 ,
-515 rtol = 0.1 , # At 40% strain the match is worse than at higher strain.
-516 )
-517 nt . assert_allclose (
-518 result_angles [ 2 ][ i_strain_40p :],
-519 M50_drexF90 [ i_strain_40p :],
-520 atol = 1 ,
-521 rtol = 0 ,
-522 )
-523 nt . assert_allclose (
-524 result_angles [ 4 ][ i_strain_40p :],
-525 M200_drexF90 [ i_strain_40p :],
-526 atol = 1.5 ,
-527 rtol = 0 ,
-528 )
+ 432 @pytest . mark . slow
+433 def test_dvdx_GBM ( self , outdir , seeds_nearX45 , ncpus ):
+434 r """Test a-axis alignment to shear in Y direction (init. SCCS near 45° from X).
+435 436 Velocity gradient:
+437 $$
+438 \bm{L} = 10^{-4} ×
+439 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
+440 $$
+441 442 Results are compared to the Fortran 90 output.
+443 444 """
+445 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+446 strain_rate = 1e-4
+447 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+448 timestamps = np . linspace ( 0 , 1e4 , 51 ) # Solve until D₀t=1 ('shear' γ=2).
+449 i_strain_40p = 10 # Index of 40% strain, lower strains are not relevant here.
+450 i_strain_100p = 25 # Index of 100% strain, when M*=0 matches FSE.
+451 params = _io . DEFAULT_PARAMS
+452 params [ "gbs_threshold" ] = 0 # No GBS, to match the Fortran parameters.
+453 gbm_mobilities = ( 0 , 10 , 50 , 125 , 200 ) # Must be in ascending order.
+454 markers = ( "x" , "." , "*" , "d" , "s" )
+455 # Use `seeds` instead of `seeds_nearX45` if you have even more RAM and CPU time.
+456 _seeds = seeds_nearX45
+457 n_seeds = len ( _seeds )
+458 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
+459 θ_fse = np . zeros_like ( timestamps )
+460 strains = timestamps * strain_rate
+461 M0_drexF90 , M50_drexF90 , M200_drexF90 = self . interp_GBM_FortranDRex ( strains )
+462 463 optional_logging = cl . nullcontext ()
+464 if outdir is not None :
+465 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _mobility"
+466 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+467 labels = []
+468 469 with optional_logging :
+470 clock_start = process_time ()
+471 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+472 if m == 0 :
+473 return_fse = True
+474 else :
+475 return_fse = False
+476 params [ "gbm_mobility" ] = gbm_mobility
+477 478 _run = ft . partial (
+479 self . run ,
+480 params ,
+481 timestamps ,
+482 strain_rate ,
+483 get_velocity_gradient ,
+484 shear_direction ,
+485 return_fse = True ,
+486 )
+487 with Pool ( processes = ncpus ) as pool :
+488 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+489 mineral , fse_angles = out
+490 angles [ m , s , :] = [
+491 _diagnostics . smallest_angle ( v , shear_direction )
+492 for v in _diagnostics . elasticity_components (
+493 _minerals . voigt_averages ([ mineral ], params )
+494 )[ "hexagonal_axis" ]
+495 ]
+496 # Save the whole mineral for the first seed only.
+497 if outdir is not None and s == 0 :
+498 mineral . save (
+499 f " { out_basepath } .npz" ,
+500 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
+501 )
+502 if return_fse :
+503 θ_fse += fse_angles
+504 505 if return_fse :
+506 θ_fse /= n_seeds
+507 508 if outdir is not None :
+509 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
+510 511 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+512 513 # Take ensemble means and optionally plot figure.
+514 _log . info ( "postprocessing results..." )
+515 result_angles = angles . mean ( axis = 1 )
+516 result_angles_err = angles . std ( axis = 1 )
+517 518 if outdir is not None :
+519 schema = {
+520 "delimiter" : "," ,
+521 "missing" : "-" ,
+522 "fields" : [
+523 {
+524 "name" : "strain" ,
+525 "type" : "integer" ,
+526 "unit" : "percent" ,
+527 "fill" : 999999 ,
+528 }
+529 ],
+530 }
+531 _io . save_scsv (
+532 f " { out_basepath } _strains.scsv" ,
+533 schema ,
+534 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+535 )
+536 np . savez (
+537 f " { out_basepath } _angles.npz" ,
+538 angles = result_angles ,
+539 err = result_angles_err ,
+540 )
+541 fig , ax , colors = _vis . alignment (
+542 None ,
+543 strains ,
+544 result_angles ,
+545 markers ,
+546 labels ,
+547 err = result_angles_err ,
+548 θ_max = 60 ,
+549 θ_fse = θ_fse ,
+550 )
+551 ax . plot ( strains , M0_drexF90 , c = colors [ 0 ])
+552 ax . plot ( strains , M50_drexF90 , c = colors [ 2 ])
+553 ax . plot ( strains , M200_drexF90 , c = colors [ 4 ])
+554 _vis . show_Skemer2016_ShearStrainAngles (
+555 ax ,
+556 [ "Z&K 1200 C" , "Z&K 1300 C" ],
+557 [ "v" , "^" ],
+558 [ "k" , "k" ],
+559 [ "none" , None ],
+560 [
+561 "Zhang & Karato, 1995 \n (1473 K)" ,
+562 "Zhang & Karato, 1995 \n (1573 K)" ,
+563 ],
+564 _core . MineralFabric . olivine_A ,
+565 )
+566 # There is a lot of stuff on this legend, so put it outside the axes.
+567 # These values might need to be tweaked depending on the font size, etc.
+568 _legend = _utils . redraw_legend ( ax , fig = fig , bbox_to_anchor = ( 1.66 , 0.99 ))
+569 fig . savefig (
+570 _io . resolve_path ( f " { out_basepath } .pdf" ),
+571 bbox_extra_artists = ( _legend ,),
+572 bbox_inches = "tight" ,
+573 )
+574 575 # Check that GBM speeds up the alignment between 40% and 100% strain.
+576 _log . info ( "checking grain orientations..." )
+577 for i , θ in enumerate ( result_angles [: - 1 ], start = 1 ):
+578 nt . assert_array_less (
+579 result_angles [ i ][ i_strain_40p : i_strain_100p ],
+580 θ [ i_strain_40p : i_strain_100p ],
+581 )
+582 583 # Check that M*=0 matches FSE (±1°) past 100% strain.
+584 nt . assert_allclose (
+585 result_angles [ 0 ][ i_strain_100p :],
+586 θ_fse [ i_strain_100p :],
+587 atol = 1 ,
+588 rtol = 0 ,
+589 )
+590 591 # Check that results match Fortran output past 40% strain.
+592 nt . assert_allclose (
+593 result_angles [ 0 ][ i_strain_40p :],
+594 M0_drexF90 [ i_strain_40p :],
+595 atol = 0 ,
+596 rtol = 0.1 , # At 40% strain the match is worse than at higher strain.
+597 )
+598 nt . assert_allclose (
+599 result_angles [ 2 ][ i_strain_40p :],
+600 M50_drexF90 [ i_strain_40p :],
+601 atol = 1 ,
+602 rtol = 0 ,
+603 )
+604 nt . assert_allclose (
+605 result_angles [ 4 ][ i_strain_40p :],
+606 M200_drexF90 [ i_strain_40p :],
+607 atol = 1.5 ,
+608 rtol = 0 ,
+609 )
530 @pytest . mark . slow
-531 def test_GBM_calibration ( self , outdir , seeds , ncpus ):
-532 r """Compare results for various values of $$M^∗$$ to A-type olivine data.
-533 534 Velocity gradient:
-535 $$
-536 \bm{L} = 10^{-4} ×
-537 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
-538 $$
-539 540 Unlike `test_dvdx_GBM`,
-541 grain boudary sliding is enabled here (see `_io.DEFAULT_PARAMS`).
-542 Data are provided by [Skemer & Hansen, 2016](http://dx.doi.org/10.1016/j.tecto.2015.12.003).
-543 544 """
-545 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
-546 strain_rate = 1
-547 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
-548 timestamps = np . linspace ( 0 , 3.2 , 65 ) # Solve until D₀t=3.2 ('shear' γ=6.4).
-549 params = _io . DEFAULT_PARAMS
-550 params [ "number_of_grains" ] = 5000
-551 gbm_mobilities = ( 0 , 10 , 50 , 125 ) # Must be in ascending order.
-552 markers = ( "x" , "*" , "1" , "." )
-553 # Uses 100 seeds by default; use all 1000 if you have more RAM and CPU time.
-554 _seeds = seeds [: 100 ]
-555 n_seeds = len ( _seeds )
-556 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
-557 θ_fse = np . zeros_like ( timestamps )
-558 strains = timestamps * strain_rate
-559 560 optional_logging = cl . nullcontext ()
-561 if outdir is not None :
-562 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _calibration"
-563 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
-564 labels = []
-565 566 with optional_logging :
-567 clock_start = process_time ()
-568 for m , gbm_mobility in enumerate ( gbm_mobilities ):
-569 return_fse = True if m == 0 else False
-570 params [ "gbm_mobility" ] = gbm_mobility
-571 _run = ft . partial (
-572 self . run ,
-573 params ,
-574 timestamps ,
-575 strain_rate ,
-576 get_velocity_gradient ,
-577 shear_direction ,
-578 return_fse = return_fse ,
-579 )
-580 with Pool ( processes = ncpus ) as pool :
-581 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
-582 mineral , fse_angles = out
-583 angles [ m , s , :] = [
-584 _diagnostics . smallest_angle ( v , shear_direction )
-585 for v in _diagnostics . elasticity_components (
-586 _minerals . voigt_averages ([ mineral ], params )
-587 )[ "hexagonal_axis" ]
-588 ]
-589 # Save the whole mineral for the first seed only.
-590 if outdir is not None and s == 0 :
-591 mineral . save (
-592 f " { out_basepath } .npz" ,
-593 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
-594 )
-595 if return_fse :
-596 θ_fse += fse_angles
-597 598 if return_fse :
-599 θ_fse /= n_seeds
-600 601 if outdir is not None :
-602 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
-603 604 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
-605 606 # Take ensemble means and optionally plot figure.
-607 _log . info ( "postprocessing results..." )
-608 result_angles = angles . mean ( axis = 1 )
-609 result_angles_err = angles . std ( axis = 1 )
-610 611 if outdir is not None :
-612 schema = {
-613 "delimiter" : "," ,
-614 "missing" : "-" ,
-615 "fields" : [
-616 {
-617 "name" : "strain" ,
-618 "type" : "integer" ,
-619 "unit" : "percent" ,
-620 "fill" : 999999 ,
-621 }
-622 ],
-623 }
-624 _io . save_scsv (
-625 f " { out_basepath } _strains.scsv" ,
-626 schema ,
-627 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
-628 )
-629 np . savez (
-630 _io . resolve_path ( f " { out_basepath } _ensemble_means.npz" ),
-631 angles = result_angles ,
-632 err = result_angles_err ,
-633 )
-634 fig = _vis . figure (
-635 figsize = ( _vis . DEFAULT_FIG_WIDTH * 3 , _vis . DEFAULT_FIG_HEIGHT )
-636 )
-637 fig , ax , colors = _vis . alignment (
-638 fig . add_subplot (),
-639 strains ,
-640 result_angles ,
-641 markers ,
-642 labels ,
-643 err = result_angles_err ,
-644 θ_max = 80 ,
-645 θ_fse = θ_fse ,
-646 )
-647 (
-648 _ ,
-649 _ ,
-650 _ ,
-651 data_Skemer2016 ,
-652 indices ,
-653 ) = _vis . show_Skemer2016_ShearStrainAngles (
-654 ax ,
-655 [
-656 "Z&K 1200 C" ,
-657 "Z&K 1300 C" ,
-658 "Skemer 2011" ,
-659 "Hansen 2014" ,
-660 "Warren 2008" ,
-661 "Webber 2010" ,
-662 "H&W 2015" ,
-663 ],
-664 [ "v" , "^" , "o" , "s" , "v" , "o" , "s" ],
-665 [ "k" , "k" , "k" , "k" , "k" , "k" , "k" ],
-666 [ "none" , "none" , "none" , "none" , None , None , None ],
-667 [
-668 "Zhang & Karato, 1995 (1473 K)" ,
-669 "Zhang & Karato, 1995 (1573 K)" ,
-670 "Skemer et al., 2011 (1500 K)" ,
-671 "Hansen et al., 2014 (1473 K)" ,
-672 "Warren et al., 2008" ,
-673 "Webber et al., 2010" ,
-674 "Hansen & Warren, 2015" ,
-675 ],
-676 fabric = _core . MineralFabric . olivine_A ,
-677 )
-678 _legend = _utils . redraw_legend ( ax , loc = "upper right" , ncols = 3 )
-679 fig . savefig (
-680 _io . resolve_path ( f " { out_basepath } .pdf" ),
-681 bbox_extra_artists = ( _legend ,),
-682 bbox_inches = "tight" ,
-683 )
-684 r2vals = []
-685 for angles in result_angles :
-686 _angles = PchipInterpolator ( strains , angles )
-687 r2 = np . sum (
-688 [
-689 ( a - b ) ** 2
-690 for a , b in zip (
-691 _angles (
-692 np . take ( data_Skemer2016 . shear_strain , indices ) / 200
-693 ),
-694 np . take ( data_Skemer2016 . angle , indices ),
-695 )
-696 ]
-697 )
-698 r2vals . append ( r2 )
-699 _log . info (
-700 "Sums of squared residuals (r-values) for each M∗: %s " , r2vals
-701 )
+ 611 @pytest . mark . slow
+612 def test_GBM_calibration ( self , outdir , seeds , ncpus ):
+613 r """Compare results for various values of $$M^∗$$ to A-type olivine data.
+614 615 Velocity gradient:
+616 $$
+617 \bm{L} = 10^{-4} ×
+618 \begin{bmatrix} 0 & 0 & 0 \cr 2 & 0 & 0 \cr 0 & 0 & 0 \end{bmatrix}
+619 $$
+620 621 Unlike `test_dvdx_GBM`,
+622 grain boudary sliding is enabled here (see `_io.DEFAULT_PARAMS`).
+623 Data are provided by [Skemer & Hansen, 2016](http://dx.doi.org/10.1016/j.tecto.2015.12.003).
+624 625 """
+626 shear_direction = [ 0 , 1 , 0 ] # Used to calculate the angular diagnostics.
+627 strain_rate = 1
+628 _ , get_velocity_gradient = _velocity . simple_shear_2d ( "Y" , "X" , strain_rate )
+629 timestamps = np . linspace ( 0 , 3.2 , 65 ) # Solve until D₀t=3.2 ('shear' γ=6.4).
+630 params = _io . DEFAULT_PARAMS
+631 params [ "number_of_grains" ] = 5000
+632 gbm_mobilities = ( 0 , 10 , 50 , 125 ) # Must be in ascending order.
+633 markers = ( "x" , "*" , "1" , "." )
+634 # Uses 100 seeds by default; use all 1000 if you have more RAM and CPU time.
+635 _seeds = seeds [: 100 ]
+636 n_seeds = len ( _seeds )
+637 angles = np . empty (( len ( gbm_mobilities ), n_seeds , len ( timestamps )))
+638 θ_fse = np . zeros_like ( timestamps )
+639 strains = timestamps * strain_rate
+640 641 optional_logging = cl . nullcontext ()
+642 if outdir is not None :
+643 out_basepath = f " { outdir } / { SUBDIR } / { self . class_id } _calibration"
+644 optional_logging = _log . logfile_enable ( f " { out_basepath } .log" )
+645 labels = []
+646 647 with optional_logging :
+648 clock_start = process_time ()
+649 for m , gbm_mobility in enumerate ( gbm_mobilities ):
+650 return_fse = True if m == 0 else False
+651 params [ "gbm_mobility" ] = gbm_mobility
+652 _run = ft . partial (
+653 self . run ,
+654 params ,
+655 timestamps ,
+656 strain_rate ,
+657 get_velocity_gradient ,
+658 shear_direction ,
+659 return_fse = return_fse ,
+660 )
+661 with Pool ( processes = ncpus ) as pool :
+662 for s , out in enumerate ( pool . imap_unordered ( _run , _seeds )):
+663 mineral , fse_angles = out
+664 angles [ m , s , :] = [
+665 _diagnostics . smallest_angle ( v , shear_direction )
+666 for v in _diagnostics . elasticity_components (
+667 _minerals . voigt_averages ([ mineral ], params )
+668 )[ "hexagonal_axis" ]
+669 ]
+670 # Save the whole mineral for the first seed only.
+671 if outdir is not None and s == 0 :
+672 mineral . save (
+673 f " { out_basepath } .npz" ,
+674 postfix = f "M { _io . stringify ( gbm_mobility ) } " ,
+675 )
+676 if return_fse :
+677 θ_fse += fse_angles
+678 679 if return_fse :
+680 θ_fse /= n_seeds
+681 682 if outdir is not None :
+683 labels . append ( f "$M^∗$ = { params [ 'gbm_mobility' ] } " )
+684 685 _log . info ( "elapsed CPU time: %s " , np . abs ( process_time () - clock_start ))
+686 687 # Take ensemble means and optionally plot figure.
+688 _log . info ( "postprocessing results..." )
+689 result_angles = angles . mean ( axis = 1 )
+690 result_angles_err = angles . std ( axis = 1 )
+691 692 if outdir is not None :
+693 schema = {
+694 "delimiter" : "," ,
+695 "missing" : "-" ,
+696 "fields" : [
+697 {
+698 "name" : "strain" ,
+699 "type" : "integer" ,
+700 "unit" : "percent" ,
+701 "fill" : 999999 ,
+702 }
+703 ],
+704 }
+705 _io . save_scsv (
+706 f " { out_basepath } _strains.scsv" ,
+707 schema ,
+708 [[ int ( D * 200 ) for D in strains ]], # Shear strain % is 200 * D₀.
+709 )
+710 np . savez (
+711 _io . resolve_path ( f " { out_basepath } _ensemble_means.npz" ),
+712 angles = result_angles ,
+713 err = result_angles_err ,
+714 )
+715 fig = _vis . figure (
+716 figsize = ( _vis . DEFAULT_FIG_WIDTH * 3 , _vis . DEFAULT_FIG_HEIGHT )
+717 )
+718 fig , ax , colors = _vis . alignment (
+719 fig . add_subplot (),
+720 strains ,
+721 result_angles ,
+722 markers ,
+723 labels ,
+724 err = result_angles_err ,
+725 θ_max = 80 ,
+726 θ_fse = θ_fse ,
+727 )
+728 (
+729 _ ,
+730 _ ,
+731 _ ,
+732 data_Skemer2016 ,
+733 indices ,
+734 ) = _vis . show_Skemer2016_ShearStrainAngles (
+735 ax ,
+736 [
+737 "Z&K 1200 C" ,
+738 "Z&K 1300 C" ,
+739 "Skemer 2011" ,
+740 "Hansen 2014" ,
+741 "Warren 2008" ,
+742 "Webber 2010" ,
+743 "H&W 2015" ,
+744 ],
+745 [ "v" , "^" , "o" , "s" , "v" , "o" , "s" ],
+746 [ "k" , "k" , "k" , "k" , "k" , "k" , "k" ],
+747 [ "none" , "none" , "none" , "none" , None , None , None ],
+748 [
+749 "Zhang & Karato, 1995 (1473 K)" ,
+750 "Zhang & Karato, 1995 (1573 K)" ,
+751 "Skemer et al., 2011 (1500 K)" ,
+752 "Hansen et al., 2014 (1473 K)" ,
+753 "Warren et al., 2008" ,
+754 "Webber et al., 2010" ,
+755 "Hansen & Warren, 2015" ,
+756 ],
+757 fabric = _core . MineralFabric . olivine_A ,
+758 )
+759 _legend = _utils . redraw_legend ( ax , loc = "upper right" , ncols = 3 )
+760 fig . savefig (
+761 _io . resolve_path ( f " { out_basepath } .pdf" ),
+762 bbox_extra_artists = ( _legend ,),
+763 bbox_inches = "tight" ,
+764 )
+765 r2vals = []
+766 for angles in result_angles :
+767 _angles = PchipInterpolator ( strains , angles )
+768 r2 = np . sum (
+769 [
+770 ( a - b ) ** 2
+771 for a , b in zip (
+772 _angles (
+773 np . take ( data_Skemer2016 . shear_strain , indices ) / 200
+774 ),
+775 np . take ( data_Skemer2016 . angle , indices ),
+776 )
+777 ]
+778 )
+779 r2vals . append ( r2 )
+780 _log . info (
+781 "Sums of squared residuals (r-values) for each M∗: %s " , r2vals
+782 )