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\n\n
\n\n

This software is currently in early development (pre-alpha)\nand therefore subject to breaking changes without notice.

\n\n
\n\n

About

\n\n

Viscoplastic 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
    \n
  • JIT-compiled CPO solver, based on the D-Rex model, which updates the\npolycrystal orientation distribution depending on the macroscopic velocity\ngradients
    • \n
  • Mineral class which stores attributes of a distinct mineral phase in the\npolycrystal and its texture snapshots
    • \n
  • Voigt averaging to calculate the average elastic tensor of a textured,\nmultiphase polycrystal
    • \n
  • Decomposition of average elastic tensors into components attributed to\nminerals with distinct lattice symmetries
    • \n
  • Crystallographic 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\n

The 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\n

Installation

\n\n

The minimum required Python version is set using requires-python in the\npyproject.toml file.\nFor installation instructions,\nsee the README file.

\n\n

Documentation

\n\n

The 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\n

The D-Rex kinematic CPO model

\n\n

The 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\n

The 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\n

where $b$ 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\n

The 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\n

Parameter reference

\n\n

Model 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.axes": {"fullname": "pydrex.axes", "modulename": "pydrex.axes", "kind": "module", "doc": "
\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\n

Thin 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", "bases": "matplotlib.axes._axes.Axes"}, "pydrex.axes.PoleFigureAxes.name": {"fullname": "pydrex.axes.PoleFigureAxes.name", "modulename": "pydrex.axes", "qualname": "PoleFigureAxes.name", "kind": "variable", "doc": "

\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\n

Args:

\n\n
    \n
  • data (array) \u2014 Nx3x3 array of orientation matrices
    • \n
  • density (bool, optional) \u2014 plot contoured pole figures, False by default
    • \n
  • ref_axes (string, optional) \u2014 letters specifying the horizontal and vertical\naxes of the pole figure, and respective labels
    • \n
  • hkl (array, optional) \u2014 crystallographic axis (one of the slip\ndirections of olivine, i.e. [1, 0, 0], [0, 1, 0] or [0, 0, 1])
    • \n
  • density_kwargs (dict, optional) \u2014 keyword arguments to pass to\npydrex.stats.point_density if density=True
    • \n
\n\n

Any 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\n

Supported properties are

\n\n

Properties:\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\n

All 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\n

Lists 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\n

Produces [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(npz_file_inspector=NPZFileInspector(), pole_figure_visualiser=PoleFigureVisualiser())"}, "pydrex.core": {"fullname": "pydrex.core", "modulename": "pydrex.core", "kind": "module", "doc": "
\n

PyDRex: Core D-Rex functions and enums.

\n
\n\n

The function derivatives implements the core D-Rex solver, which computes the\ncrystallographic rotation rate and changes in fractional grain volumes.

\n\n

Acronyms:

\n\n
    \n
  • CRSS = 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.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 1.e+00],\n [0.e+00, -1.e+00, 0.e+00]],\n\n [[0.e+00, 0.e+00, -1.e+00],\n [0.e+00, 0.e+00, 0.e+00],\n [1.e+00, 0.e+00, 0.e+00]],\n\n [[0.e+00, 1.e+00, 0.e+00],\n [-1.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00]]])"}, "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\n

The 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\n

Returns 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\n

Args:

\n\n
    \n
  • phase (MineralPhase) \u2014 ordinal number of the mineral phase
    • \n
  • fabric (MineralFabric) \u2014 ordinal number of the fabric type
    • \n
  • n_grains (int) \u2014 number of \"grains\" i.e. discrete volume segments
    • \n
  • orientations (array) \u2014 n_grainsx3x3 orientations (direction cosines)
    • \n
  • fractions (array) \u2014 volume fractions of the grains relative to aggregate volume
    • \n
  • strain_rate (array) \u2014 3x3 dimensionless macroscopic strain-rate tensor
    • \n
  • velocity_gradient (array) \u2014 3x3 dimensionless macroscopic velocity gradient
    • \n
  • stress_exponent (float) \u2014 p in dislocation_density \u221d shear_stress^p
    • \n
  • deformation_exponent (float) \u2014 n in shear_stress \u221d |deformation_rate|^(1/n)
    • \n
  • nucleation_efficiency (float) \u2014 parameter controlling grain nucleation
    • \n
  • gmb_mobility (float) \u2014 grain boundary mobility parameter
    • \n
  • volume_fraction (float) \u2014 volume fraction of the mineral phase relative to\nother phases (multiphase simulations)
    • \n
\n\n

Returns 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
\n"}, "pydrex.diagnostics.elasticity_components": {"fullname": "pydrex.diagnostics.elasticity_components", "modulename": "pydrex.diagnostics", "qualname": "elasticity_components", "kind": "function", "doc": "

Calculate elasticity decompositions for the given elasticity tensors.

\n\n

Args:

\n\n
    \n
  • voigt_matrices (array) \u2014 the Nx6x6 Voigt matrix representations of the averaged\nelasticity tensors for a series of polycrystal textures
    • \n
\n\n

Returns a dictionary with the following data series:

\n\n
    \n
  • 'bulk_modulus' \u2014 the computed bulk modulus for each Voigt matrix C
    • \n
  • 'shear_modulus' \u2014 the computed shear modulus for each Voigt matrix C
    • \n
  • '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
    • \n
  • 'percent_hexagonal' \u2014 for each C, the percentage of ||C|| attributed to\nhexagonally symmetric minerals
    • \n
  • 'percent_tetragonal' \u2014 for each C, the percentage of ||C|| attributed to\ntetragonally symmetric minerals
    • \n
  • 'percent_orthorhombic' \u2014 for each C, the percentage of ||C|| attributed to\northorhombically symmetric minerals
    • \n
  • 'percent_monoclinic' \u2014 for each C, the percentage of ||C|| attributed to\nmonoclinically symmetric minerals
    • \n
  • 'percent_triclinic' \u2014 for each C, the percentage of ||C|| attributed to\ntriclinically \"symmetric\" minerals (no mirror planes)
    • \n
  • '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\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
\n", "signature": "(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\n

Returns 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\n

See 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\n

Extracts 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\n

Compute 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\n

See 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\n

Calculate 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\n

Uses 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\n

See 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\n

The 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
\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\n

The 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\n

The 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\n

Attributes:\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\n

Attributes:\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\n

Attributes:\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\n

Attributes:

\n\n
    \n
  • message \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\n

The 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\n
\n\n

This 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\n

Spherical 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\n

By 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\n

Spherical 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\n

Returns 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\n

Calculate 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\n
q1_array.shape      q2_array.shape      len(output)\n---------------------------------------------------\nNxAx4               NxBx4               N\n
\n\n
\n\n

This method must be able to allocate a floating point array of shape Nx(A*B)

\n\n
\n\n

Uses ~25% less memory than the same operation with rotation matrices.

\n\n

See 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\n

Returned 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\n

Expects 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\n

Project 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\n

This 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\n

The 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\n

This 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\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
\n", "signature": "(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\n

PyDRex can read/write three kinds of plain text files:

\n\n
    \n
  • PyDRex configuration files, which specify simulation parameters and initial conditions
    • \n
  • 'SCSV' files, CSV files with YAML frontmatter for (small) scientific datasets
    • \n
  • Mesh files via meshio, to set up final mineral positions in steady flows.
    • \n
\n\n

SCSV 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\n

Prints 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\n

Args:

\n\n
    \n
  • stream \u2014 open output stream (e.g. file handle) where data should be written
    • \n
  • schema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keys
    • \n
  • comments (optional) \u2014 array of comments to be written above the schema, each on\na new line with an '#' prefix
    • \n
\n\n

See 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\n

Args:

\n\n
    \n
  • file \u2014 path to the file where the data should be written
    • \n
  • schema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keys
    • \n
  • data \u2014 data arrays (columns) of equal length
    • \n
\n\n

Optional 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\n

Relative 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\n

Python'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\n

By 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
\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
\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
\n"}, "pydrex.logger.ConsoleFormatter": {"fullname": "pydrex.logger.ConsoleFormatter", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter", "kind": "class", "doc": "

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\n

The 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\n

Args:

\n\n
    \n
  • level (string) \u2014 logging level name e.g. \"DEBUG\", \"ERROR\", etc.\nSee Python's logging module for details.
    • \n
  • handler (optional, logging.Handler) \u2014 alternative handler to control instead\nof the default, CONSOLE_LOGGER.
    • \n
\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\n

This 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\n

Acronyms:

\n\n
    \n
  • CPO = 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\n

The 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([[3.2071e+02, 6.984e+01, 7.122e+01, 0.e+00, 0.e+00, 0.e+00],\n [6.984e+01, 1.9725e+02, 7.48e+01, 0.e+00, 0.e+00, 0.e+00],\n [7.122e+01, 7.48e+01, 2.3432e+02, 0.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 6.377e+01, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 7.767e+01, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 0.e+00, 7.836e+01]])"}, "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\n

The 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([[2.369e+02, 7.96e+01, 6.32e+01, 0.e+00, 0.e+00, 0.e+00],\n [7.96e+01, 1.805e+02, 5.68e+01, 0.e+00, 0.e+00, 0.e+00],\n [6.32e+01, 5.68e+01, 2.304e+02, 0.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 8.43e+01, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 7.94e+01, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 0.e+00, 8.01e+01]])"}, "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\n

Tuples 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\n

Args:

\n\n
    \n
  • minerals \u2014 list of pydrex.minerals.Mineral instances storing orientations and\nfractional volumes of the grains within each distinct mineral phase
    • \n
  • weights (dict) \u2014 dictionary containing weights of each mineral\nphase, as a fraction of 1, in keys named \"_fraction\",\ne.g. \"olivine_fraction\"
    • \n
\n\n

Raises 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\n

A 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\n

The 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\n

Examples:

\n\n

Mineral with isotropic initial texture:

\n\n
\n
>>> import pydrex\n>>> pydrex.Mineral(\n>>>     phase=pydrex.MineralPhase.olivine,\n>>>     fabric=pydrex.MineralFabric.olivine_A,\n>>>     regime=pydrex.DeformationRegime.dislocation,\n>>>     n_grains=2000,\n>>> )\nMineral(phase=0, fabric=0, regime=1, n_grains=2000, ...)\n
\n
\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>>> 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>>> )\nMineral(phase=0, fabric=0, regime=1, n_grains=2000, ...)\n
\n
\n\n

Note that minerals can also be constructed from serialized data,\nsee Mineral.load and Mineral.from_file.

\n\n

Attributes:

\n\n
    \n
  • phase (pydrex.core.MineralPhase) \u2014 ordinal number of the mineral phase
    • \n
  • fabric (pydrex.core.MineralFabric) \u2014 ordinal number of the fabric type
    • \n
  • regime (pydrex.core.DeformationRegime) \u2014 ordinal number of the deformation\nregime
    • \n
  • n_grains (int) \u2014 number of grains in the aggregate
    • \n
  • fractions (list of arrays) \u2014 grain volume fractions for each texture snapshot
    • \n
  • orientations (list of arrays) \u2014 grain orientation matrices for each texture\nsnapshot
    • \n
  • seed (int) \u2014 seed used by the random number generator to set up the isotropic\ninitial condition when fractions_init or orientations_init are not provided
    • \n
  • lband (int) \u2014 passed to the scipy.integrate.LSODA solver
    • \n
  • uband (int) \u2014 passed to the scipy.integrate.LSODA solver
    • \n
\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\n

Update crystalline orientations and grain volume distribution\nfor minerals undergoing plastic deformation. Return the updated deformation\ngradient measuring the corresponding macroscopic deformation.

\n\n

Args:

\n\n
    \n
  • config (dict) \u2014 PyDRex configuration dictionary
    • \n
  • deformation_gradient (array) \u2014 3x3 initial deformation gradient tensor
    • \n
  • get_velocity_gradient (function) \u2014 callable with signature f(x) that returns\na 3x3 velocity gradient matrix at position x (vector)
    • \n
  • pathline (tuple) \u2014 tuple consisting of:\n
      \n
    1. the time at which to start the CPO integration (t_start)
      2. \n
    2. the time at which to stop the CPO integration (t_end)
      3. \n
    3. callable with signature f(t) that returns the position of the mineral at\ntime t \u2208 [t_start, t_end]
      4. \n
    • \n
\n\n

Any additional (optional) keyword arguments are passed to\nscipy.integrate.LSODA.

\n\n

Array 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\n

If postfix is not None, the data is appended to the NPZ file\nin fields ending with \"_postfix\".

\n\n

Raises a ValueError if the data shapes are not compatible.

\n\n

See 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\n

If postfix is not None, data is read from fields ending with \"_postfix\".

\n\n

See 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\n

If postfix is not None, data is read from fields ending with \u201c_postfix\u201d.

\n\n

See 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\n

The 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
\n\n

Args:

\n\n
    \n
  • final_location (array) \u2014 coordinates of the final location
    • \n
  • get_velocity (callable) \u2014 returns velocity vector at a point
    • \n
  • get_velocity_gradient (callable) \u2014 returns velocity gradient matrix at a point
    • \n
  • min_coords (array) \u2014 lower bound coordinates of the box
    • \n
  • max_coords (array) \u2014 upper bound coordinates of the box
    • \n
  • max_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
\n\n

Optional 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\n

Returns 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\n

Args:

\n\n
    \n
  • orientations (array) \u2014 NxMx3x3 array of orientations
    • \n
  • fractions (array) \u2014 NxM array of grain volume fractions
    • \n
  • n_samples (int) \u2014 optional number of samples to return, default is M
    • \n
  • seed (int) \u2014 optional seed for the random number generator, which is used to\npick random grain volume samples from the discrete distribution
    • \n
\n\n

Returns 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\n

The 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
\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\n

Estimate 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\n

Estimates 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
    \n
  • gridsteps (int) \u2014 the number of steps, i.e. number of points along a diameter of\nthe spherical counting grid
    • \n
  • weights (array) \u2014 auxiliary weights for each data point
    • \n
  • kernel (string) \u2014 the name of the kernel function to use, see\nSPHERICAL_COUNTING_KERNELS
    • \n
  • axial (bool) \u2014 toggle axial versions of the kernel functions\n(for crystallographic data this should normally be kept as True)
    • \n
\n\n

Any 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\n

Supported 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\n

For 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.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 1.e+00],\n [0.e+00, -1.e+00, 0.e+00]],\n\n [[0.e+00, 0.e+00, -1.e+00],\n [0.e+00, 0.e+00, 0.e+00],\n [1.e+00, 0.e+00, 0.e+00]],\n\n [[0.e+00, 1.e+00, 0.e+00],\n [-1.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00]]])"}, "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\n

Return 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\n

Any vector which is an eigenvector of both $d_{ij}$ and $v_{ij}$ is always normal to\na symmetry plane of the elastic medium.

\n\n

See 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\n

Monoclinic symmetry is characterised by 13 independent elasticity components.

\n\n

See 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\n

Orthorhombic symmetry is characterised by 9 independent elasticity components.

\n\n

See 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\n

Tetragonal symmetry is characterised by 6 independent elasticity components.

\n\n

See 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\n

Hexagonal symmetry (a.k.a. transverse isotropy) is characterised by 5 independent\nelasticity components.

\n\n

See 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
\n", "signature": "(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\n

See 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\n

See 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\n

Returns \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\n

On 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\n

The repeated last elements ensure that output and input arrays have equal shape.

\n\n

Examples:

\n\n
\n
>>> _get_steps(np.array([1, 2, 3, 4, 5]))\narray([[1, 1, 1, 1, 1]])\n
\n
\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\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
\n", "signature": "(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\n

See 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\n

Transparency 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\n

If 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
\n", "signature": "(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\n

Use 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\n

If 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\n

Any 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\n

For 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\n

The returned callables have signature f(x) where x is a 3D position vector.

\n\n

Args:

\n\n
    \n
  • direction (one of {\"X\", \"Y\", \"Z\"}) \u2014 velocity vector direction
    • \n
  • deformation_plane (one of {\"X\", \"Y\", \"Z\"}) \u2014 direction of velocity gradient
    • \n
  • strain_rate (float) \u2014 1/2 \u00d7 strength of velocity gradient
    • \n
\n", "signature": "(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\n

The velocity field is defined by:\n$$\n\\bm{u} = \\cos(\u03c0 x/2)\\sin(\u03c0 x/2) \\bm{\\hat{h}} - \\sin(\u03c0 x/2)\\cos(\u03c0 x/2) \\bm{\\hat{v}}\n$$\nwhere $\\bm{\\hat{h}}$ and $\\bm{\\hat{v}}$ are unit vectors in the chosen horizontal\nand vertical directions, respectively.

\n\n

The returned callables have signature f(x) where x is a 3D position vector.

\n\n

Args:

\n\n
    \n
  • horizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal direction
    • \n
  • vertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical direction
    • \n
  • velocity_edge (float) \u2014 velocity magnitude at the center of the cell edge
    • \n
\n", "signature": "(horizontal, vertical, velocity_edge):", "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\n

The 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\n

The returned callables have signature f(x) where x is a 3D position vector.

\n\n

Args:

\n\n
    \n
  • horizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal direction
    • \n
  • vertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical direction
    • \n
  • plate_speed (float) \u2014 speed of the \u201cplate\u201d i.e. upper boundary
    • \n
\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\n

Produces [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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n
    \n
  • get_velocity (callable) \u2014 object with call signature f(x) that returns\nthe 3D velocity vector at a given 3D position vector
    • \n
  • ref_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)
    • \n
  • colors (array) \u2014 monotonic values along a representative pathline in the flow
    • \n
  • positions (Nx3 array) \u2014 3D position vectors along the same pathline
    • \n
  • min_coords (array) \u2014 2D coordinates of the lower left corner of the domain
    • \n
  • max_coords (array) \u2014 2D coordinates of the upper right corner of the domain
    • \n
  • resolution (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 vectors
    • \n
  • aspect (str|float, optional) \u2014 see matplotlib.axes.Axes.set_aspect
    • \n
  • cmap (Matplotlib color map, optional) \u2014 color map for colors
    • \n
  • cpo_vectors (array, optional) \u2014 vectors to plot as bars at pathline locations
    • \n
  • cpo_strengths (array, optional) \u2014 strengths used to scale the cpo bars
    • \n
  • tick_formatter (callable, optional) \u2014 function used to format tick labels
    • \n
\n\n

Additional keyword arguments are passed to the matplotlib.axes.Axes.quiver call\nused to plot the velocity vectors.

\n\n

Returns 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\n

Alignment 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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n
    \n
  • strains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain series
    • \n
  • angles (array) \u2014 Y-values, may be a 2D array of multiple angle series
    • \n
  • markers (sequence) \u2014 MatPlotLib markers to use for the data series
    • \n
  • labels (sequence) \u2014 labels to use for the data series
    • \n
  • err (array, optional) \u2014 standard errors for the angles, shapes must match
    • \n
  • \u03b8_max (int) \u2014 maximum angle (\u00b0) to show on the plot, should be less than 90
    • \n
  • \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)
    • \n
  • colors (array, optional) \u2014 color coordinates for series of angles
    • \n
  • cmaps (Matplotlib color maps, optional) \u2014 color maps for colors
    • \n
\n\n

If colors and cmaps are used, then angle values are colored individually within\neach angle series.

\n\n

Returns 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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n
    \n
  • strains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain series
    • \n
  • strengths (array) \u2014 Y-values, may be a 2D array of multiple strength series
    • \n
  • markers (sequence) \u2014 MatPlotLib markers to use for the data series
    • \n
  • labels (sequence) \u2014 labels to use for the data series
    • \n
  • err (array, optional) \u2014 standard errors for the strengths, shapes must match
    • \n
  • colors (array, optional) \u2014 color coordinates for series of strengths
    • \n
  • cpo_threshold (float, optional) \u2014 plot a dashed line at this threshold
    • \n
  • cmaps (Matplotlib color maps, optional) \u2014 color maps for colors
    • \n
\n\n

If colors and cmaps are used, then strength values are colored individually\nwithin each strength series.

\n\n

Returns 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\n

If 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\n

Plot 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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Returns a tuple containing:

\n\n
    \n
  • the figure handle
    • \n
  • the axes handle
    • \n
  • the set of colors used for the data series plots
    • \n
  • the Skemer 2016 dataset
    • \n
  • the 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\n

If 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\n

Returns 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\n

If 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\n

Returns 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\n

If ax is None, a new figure is created for the axes with a few opinionated default\nsettings (grid, constrained layout, high DPI).

\n\n

Returns 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\n

The 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\n

Running 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\n

Tests 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.\nTo mark a test as \u201cbig\u201d, add the @pytest.mark.big decorator above its method definition.

\n\n

Long 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, >46 cores).\nTo mark a test as slow, add the @pytest.mark.slow decorator above its method definition.

\n\n

Tests 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
    \n
  • logs 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),
    • \n
  • figures can be saved by (implementing and) calling a helper from pydrex.visualisation, and
    • \n
  • data 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\n

The 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\n

Velocity 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\n

Velocity 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\n

Velocity 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\n

Velocity 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\n

Grain growth rates are compared to analytical calculations.\nThe a-axes are distributed in the YX plane (i.e.\\ rotated around Z).

\n\n

Velocity 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\n

Unlike 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\n

Velocity 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\n

Initial condition: random orientations and uniform volumes in all Minerals.

\n\n

Plate 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
\n", "signature": "(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 applicable modules.

\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 as well.

\n", "signature": "():", "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\n

Returns 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\n

Velocity 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\n

Velocity 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\n

Results 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\n

Velocity 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\n

Unlike 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\n

The 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\n

Returns 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\n

The simulation runs for 5 Ma with a strain rate of 1.58e-14/s, resulting in an\naccumulated strain invariant of 2.5.

\n\n

The 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.

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Run 2D cell test with 10000 grains (~14GiB RAM requirement).

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Test to check that 5000 grains is \"enough\" to resolve transient features.

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Test to demonstrate stability of the dip at \u03b5 \u2248 3.75 for 5000+ grains.

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Simulate crystallographic preferred orientation evolution in polycrystals

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This software is currently in early development (pre-alpha)\nand therefore subject to breaking changes without notice.

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About

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Viscoplastic 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:

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  • JIT-compiled CPO solver, based on the D-Rex model, which updates the\npolycrystal orientation distribution depending on the macroscopic velocity\ngradients
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  • Mineral class which stores attributes of a distinct mineral phase in the\npolycrystal and its texture snapshots
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  • Voigt averaging to calculate the average elastic tensor of a textured,\nmultiphase polycrystal
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  • Decomposition of average elastic tensors into components attributed to\nminerals with distinct lattice symmetries
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  • Crystallographic pole figure visualisation (contouring is a work in progress)
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  • [work in progress] Texture diagnostics: M-index, bingham average,\nPoint-Girdle-Random symmetry, coaxial a.k.a \"BA\" index, etc.
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  • [work in progress] Seismic anisotropy diagnostics: % tensorial anisotropy,\nhexagonal symmetry a.k.a transverse isotropy direction, etc.
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The 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).

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Installation

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The minimum required Python version is set using requires-python in the\npyproject.toml file.\nFor installation instructions,\nsee the README file.

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Documentation

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The 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.

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The D-Rex kinematic CPO model

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The 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.

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The 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

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$$\n\u03c1 \u221d b^{-2} \\left(\\frac{\u03c3}{\u03bc}\\right)^{p}\n$$

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where $b$ 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...]

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The 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.

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Parameter reference

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Model 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:

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# 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
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\n

PyDRex: Custom Matplotlib Axes subclasses.

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Axes class designed for crystallographic pole figures.

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Thin matplotlib Axes wrapper for crystallographic pole figures.

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Projections are not performed automatically using default methods like\nscatter or plot. To actually plot the pole figures, use polefigure.

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Plot pole figure of crystallographic texture.

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Args:

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  • data (array) \u2014 Nx3x3 array of orientation matrices
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  • density (bool, optional) \u2014 plot contoured pole figures, False by default
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  • ref_axes (string, optional) \u2014 letters specifying the horizontal and vertical\naxes of the pole figure, and respective labels
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  • hkl (array, optional) \u2014 crystallographic axis (one of the slip\ndirections of olivine, i.e. [1, 0, 0], [0, 1, 0] or [0, 0, 1])
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  • density_kwargs (dict, optional) \u2014 keyword arguments to pass to\npydrex.stats.point_density if density=True
    • \n
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Any 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.

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Supported properties are

\n\n

Properties:\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\n

All 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\n

Lists 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\n

Produces [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(npz_file_inspector=NPZFileInspector(), pole_figure_visualiser=PoleFigureVisualiser())"}, "pydrex.core": {"fullname": "pydrex.core", "modulename": "pydrex.core", "kind": "module", "doc": "
\n

PyDRex: Core D-Rex functions and enums.

\n
\n\n

The function derivatives implements the core D-Rex solver, which computes the\ncrystallographic rotation rate and changes in fractional grain volumes.

\n\n

Acronyms:

\n\n
    \n
  • CRSS = 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.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 1.e+00],\n [0.e+00, -1.e+00, 0.e+00]],\n\n [[0.e+00, 0.e+00, -1.e+00],\n [0.e+00, 0.e+00, 0.e+00],\n [1.e+00, 0.e+00, 0.e+00]],\n\n [[0.e+00, 1.e+00, 0.e+00],\n [-1.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00]]])"}, "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\n

The 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\n

Returns 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\n

Args:

\n\n
    \n
  • phase (MineralPhase) \u2014 ordinal number of the mineral phase
    • \n
  • fabric (MineralFabric) \u2014 ordinal number of the fabric type
    • \n
  • n_grains (int) \u2014 number of \"grains\" i.e. discrete volume segments
    • \n
  • orientations (array) \u2014 n_grainsx3x3 orientations (direction cosines)
    • \n
  • fractions (array) \u2014 volume fractions of the grains relative to aggregate volume
    • \n
  • strain_rate (array) \u2014 3x3 dimensionless macroscopic strain-rate tensor
    • \n
  • velocity_gradient (array) \u2014 3x3 dimensionless macroscopic velocity gradient
    • \n
  • stress_exponent (float) \u2014 p in dislocation_density \u221d shear_stress^p
    • \n
  • deformation_exponent (float) \u2014 n in shear_stress \u221d |deformation_rate|^(1/n)
    • \n
  • nucleation_efficiency (float) \u2014 parameter controlling grain nucleation
    • \n
  • gmb_mobility (float) \u2014 grain boundary mobility parameter
    • \n
  • volume_fraction (float) \u2014 volume fraction of the mineral phase relative to\nother phases (multiphase simulations)
    • \n
\n\n

Returns 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
\n"}, "pydrex.diagnostics.elasticity_components": {"fullname": "pydrex.diagnostics.elasticity_components", "modulename": "pydrex.diagnostics", "qualname": "elasticity_components", "kind": "function", "doc": "

Calculate elasticity decompositions for the given elasticity tensors.

\n\n

Args:

\n\n
    \n
  • voigt_matrices (array) \u2014 the Nx6x6 Voigt matrix representations of the averaged\nelasticity tensors for a series of polycrystal textures
    • \n
\n\n

Returns a dictionary with the following data series:

\n\n
    \n
  • 'bulk_modulus' \u2014 the computed bulk modulus for each Voigt matrix C
    • \n
  • 'shear_modulus' \u2014 the computed shear modulus for each Voigt matrix C
    • \n
  • '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
    • \n
  • 'percent_hexagonal' \u2014 for each C, the percentage of ||C|| attributed to\nhexagonally symmetric minerals
    • \n
  • 'percent_tetragonal' \u2014 for each C, the percentage of ||C|| attributed to\ntetragonally symmetric minerals
    • \n
  • 'percent_orthorhombic' \u2014 for each C, the percentage of ||C|| attributed to\northorhombically symmetric minerals
    • \n
  • 'percent_monoclinic' \u2014 for each C, the percentage of ||C|| attributed to\nmonoclinically symmetric minerals
    • \n
  • 'percent_triclinic' \u2014 for each C, the percentage of ||C|| attributed to\ntriclinically \"symmetric\" minerals (no mirror planes)
    • \n
  • '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\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
\n", "signature": "(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\n

Returns 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\n

See 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\n

Extracts 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\n

Compute 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\n

See 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\n

Calculate 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\n

Uses 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\n

See 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\n

The 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
\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\n

The 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\n

The 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\n

Attributes:\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\n

Attributes:\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\n

Attributes:\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\n

Attributes:

\n\n
    \n
  • message \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\n

The 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\n
\n\n

This 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\n

Spherical 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\n

By 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\n

Spherical 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\n

Returns 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\n

Calculate 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\n
q1_array.shape      q2_array.shape      len(output)\n---------------------------------------------------\nNxAx4               NxBx4               N\n
\n\n
\n\n

This method must be able to allocate a floating point array of shape Nx(A*B)

\n\n
\n\n

Uses ~25% less memory than the same operation with rotation matrices.

\n\n

See 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\n

Returned 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\n

Expects 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\n

Project 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\n

This 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\n

The 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\n

This 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\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
\n", "signature": "(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\n

PyDRex can read/write three kinds of plain text files:

\n\n
    \n
  • PyDRex configuration files, which specify simulation parameters and initial conditions
    • \n
  • 'SCSV' files, CSV files with YAML frontmatter for (small) scientific datasets
    • \n
  • Mesh files via meshio, to set up final mineral positions in steady flows.
    • \n
\n\n

SCSV 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\n

Prints 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\n

Args:

\n\n
    \n
  • stream \u2014 open output stream (e.g. file handle) where data should be written
    • \n
  • schema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keys
    • \n
  • comments (optional) \u2014 array of comments to be written above the schema, each on\na new line with an '#' prefix
    • \n
\n\n

See 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\n

Args:

\n\n
    \n
  • file \u2014 path to the file where the data should be written
    • \n
  • schema \u2014 SCSV schema dictionary, with 'delimiter', 'missing' and 'fields' keys
    • \n
  • data \u2014 data arrays (columns) of equal length
    • \n
\n\n

Optional 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\n

Relative 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\n

Python'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\n

By 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
\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
\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
\n"}, "pydrex.logger.ConsoleFormatter": {"fullname": "pydrex.logger.ConsoleFormatter", "modulename": "pydrex.logger", "qualname": "ConsoleFormatter", "kind": "class", "doc": "

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\n

The 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\n

Args:

\n\n
    \n
  • level (string) \u2014 logging level name e.g. \"DEBUG\", \"ERROR\", etc.\nSee Python's logging module for details.
    • \n
  • handler (optional, logging.Handler) \u2014 alternative handler to control instead\nof the default, CONSOLE_LOGGER.
    • \n
\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\n

This 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\n

Acronyms:

\n\n
    \n
  • CPO = 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\n

The 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([[3.2071e+02, 6.984e+01, 7.122e+01, 0.e+00, 0.e+00, 0.e+00],\n [6.984e+01, 1.9725e+02, 7.48e+01, 0.e+00, 0.e+00, 0.e+00],\n [7.122e+01, 7.48e+01, 2.3432e+02, 0.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 6.377e+01, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 7.767e+01, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 0.e+00, 7.836e+01]])"}, "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\n

The 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([[2.369e+02, 7.96e+01, 6.32e+01, 0.e+00, 0.e+00, 0.e+00],\n [7.96e+01, 1.805e+02, 5.68e+01, 0.e+00, 0.e+00, 0.e+00],\n [6.32e+01, 5.68e+01, 2.304e+02, 0.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 8.43e+01, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 7.94e+01, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00, 0.e+00, 0.e+00, 8.01e+01]])"}, "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\n

Tuples 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\n

Args:

\n\n
    \n
  • minerals \u2014 list of pydrex.minerals.Mineral instances storing orientations and\nfractional volumes of the grains within each distinct mineral phase
    • \n
  • weights (dict) \u2014 dictionary containing weights of each mineral\nphase, as a fraction of 1, in keys named \"_fraction\",\ne.g. \"olivine_fraction\"
    • \n
\n\n

Raises 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\n

A 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\n

The 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\n

Examples:

\n\n

Mineral with isotropic initial texture:

\n\n
\n
>>> import pydrex\n>>> pydrex.Mineral(\n>>>     phase=pydrex.MineralPhase.olivine,\n>>>     fabric=pydrex.MineralFabric.olivine_A,\n>>>     regime=pydrex.DeformationRegime.dislocation,\n>>>     n_grains=2000,\n>>> )\nMineral(phase=0, fabric=0, regime=1, n_grains=2000, ...)\n
\n
\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>>> 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>>> )\nMineral(phase=0, fabric=0, regime=1, n_grains=2000, ...)\n
\n
\n\n

Note that minerals can also be constructed from serialized data,\nsee Mineral.load and Mineral.from_file.

\n\n

Attributes:

\n\n
    \n
  • phase (pydrex.core.MineralPhase) \u2014 ordinal number of the mineral phase
    • \n
  • fabric (pydrex.core.MineralFabric) \u2014 ordinal number of the fabric type
    • \n
  • regime (pydrex.core.DeformationRegime) \u2014 ordinal number of the deformation\nregime
    • \n
  • n_grains (int) \u2014 number of grains in the aggregate
    • \n
  • fractions (list of arrays) \u2014 grain volume fractions for each texture snapshot
    • \n
  • orientations (list of arrays) \u2014 grain orientation matrices for each texture\nsnapshot
    • \n
  • seed (int) \u2014 seed used by the random number generator to set up the isotropic\ninitial condition when fractions_init or orientations_init are not provided
    • \n
  • lband (int) \u2014 passed to the scipy.integrate.LSODA solver
    • \n
  • uband (int) \u2014 passed to the scipy.integrate.LSODA solver
    • \n
\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\n

Update crystalline orientations and grain volume distribution\nfor minerals undergoing plastic deformation. Return the updated deformation\ngradient measuring the corresponding macroscopic deformation.

\n\n

Args:

\n\n
    \n
  • config (dict) \u2014 PyDRex configuration dictionary
    • \n
  • deformation_gradient (array) \u2014 3x3 initial deformation gradient tensor
    • \n
  • get_velocity_gradient (function) \u2014 callable with signature f(x) that returns\na 3x3 velocity gradient matrix at position x (vector)
    • \n
  • pathline (tuple) \u2014 tuple consisting of:\n
      \n
    1. the time at which to start the CPO integration (t_start)
      2. \n
    2. the time at which to stop the CPO integration (t_end)
      3. \n
    3. callable with signature f(t) that returns the position of the mineral at\ntime t \u2208 [t_start, t_end]
      4. \n
    • \n
\n\n

Any additional (optional) keyword arguments are passed to\nscipy.integrate.LSODA.

\n\n

Array 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\n

If postfix is not None, the data is appended to the NPZ file\nin fields ending with \"_postfix\".

\n\n

Raises a ValueError if the data shapes are not compatible.

\n\n

See 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\n

If postfix is not None, data is read from fields ending with \"_postfix\".

\n\n

See 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\n

If postfix is not None, data is read from fields ending with \u201c_postfix\u201d.

\n\n

See 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\n

The 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
\n\n

Args:

\n\n
    \n
  • final_location (array) \u2014 coordinates of the final location
    • \n
  • get_velocity (callable) \u2014 returns velocity vector at a point
    • \n
  • get_velocity_gradient (callable) \u2014 returns velocity gradient matrix at a point
    • \n
  • min_coords (array) \u2014 lower bound coordinates of the box
    • \n
  • max_coords (array) \u2014 upper bound coordinates of the box
    • \n
  • max_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
\n\n

Optional 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\n

Returns 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\n

Args:

\n\n
    \n
  • orientations (array) \u2014 NxMx3x3 array of orientations
    • \n
  • fractions (array) \u2014 NxM array of grain volume fractions
    • \n
  • n_samples (int) \u2014 optional number of samples to return, default is M
    • \n
  • seed (int) \u2014 optional seed for the random number generator, which is used to\npick random grain volume samples from the discrete distribution
    • \n
\n\n

Returns 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\n

The 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
\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\n

Estimate 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\n

Estimates 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
    \n
  • gridsteps (int) \u2014 the number of steps, i.e. number of points along a diameter of\nthe spherical counting grid
    • \n
  • weights (array) \u2014 auxiliary weights for each data point
    • \n
  • kernel (string) \u2014 the name of the kernel function to use, see\nSPHERICAL_COUNTING_KERNELS
    • \n
  • axial (bool) \u2014 toggle axial versions of the kernel functions\n(for crystallographic data this should normally be kept as True)
    • \n
\n\n

Any 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\n

Supported 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\n

For 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.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 1.e+00],\n [0.e+00, -1.e+00, 0.e+00]],\n\n [[0.e+00, 0.e+00, -1.e+00],\n [0.e+00, 0.e+00, 0.e+00],\n [1.e+00, 0.e+00, 0.e+00]],\n\n [[0.e+00, 1.e+00, 0.e+00],\n [-1.e+00, 0.e+00, 0.e+00],\n [0.e+00, 0.e+00, 0.e+00]]])"}, "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\n

Return 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\n

Any vector which is an eigenvector of both $d_{ij}$ and $v_{ij}$ is always normal to\na symmetry plane of the elastic medium.

\n\n

See 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\n

Monoclinic symmetry is characterised by 13 independent elasticity components.

\n\n

See 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\n

Orthorhombic symmetry is characterised by 9 independent elasticity components.

\n\n

See 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\n

Tetragonal symmetry is characterised by 6 independent elasticity components.

\n\n

See 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\n

Hexagonal symmetry (a.k.a. transverse isotropy) is characterised by 5 independent\nelasticity components.

\n\n

See 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
\n", "signature": "(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\n

See 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\n

See 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\n

Returns \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\n

On 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\n

The repeated last elements ensure that output and input arrays have equal shape.

\n\n

Examples:

\n\n
\n
>>> _get_steps(np.array([1, 2, 3, 4, 5]))\narray([[1, 1, 1, 1, 1]])\n
\n
\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\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
\n", "signature": "(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\n

See 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\n

Transparency 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\n

If 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
\n", "signature": "(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\n

Use 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\n

If 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\n

Any 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\n

For 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\n

The returned callables have signature f(x) where x is a 3D position vector.

\n\n

Args:

\n\n
    \n
  • direction (one of {\"X\", \"Y\", \"Z\"}) \u2014 velocity vector direction
    • \n
  • deformation_plane (one of {\"X\", \"Y\", \"Z\"}) \u2014 direction of velocity gradient
    • \n
  • strain_rate (float) \u2014 1/2 \u00d7 strength of velocity gradient
    • \n
\n", "signature": "(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\n

The velocity field is defined by:\n$$\n\\bm{u} = \\cos(\u03c0 x/2)\\sin(\u03c0 x/2) \\bm{\\hat{h}} - \\sin(\u03c0 x/2)\\cos(\u03c0 x/2) \\bm{\\hat{v}}\n$$\nwhere $\\bm{\\hat{h}}$ and $\\bm{\\hat{v}}$ are unit vectors in the chosen horizontal\nand vertical directions, respectively.

\n\n

The returned callables have signature f(x) where x is a 3D position vector.

\n\n

Args:

\n\n
    \n
  • horizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal direction
    • \n
  • vertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical direction
    • \n
  • velocity_edge (float) \u2014 velocity magnitude at the center of the cell edge
    • \n
\n", "signature": "(horizontal, vertical, velocity_edge):", "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\n

The 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\n

The returned callables have signature f(x) where x is a 3D position vector.

\n\n

Args:

\n\n
    \n
  • horizontal (one of {\"X\", \"Y\", \"Z\"}) \u2014 horizontal direction
    • \n
  • vertical (one of {\"X\", \"Y\", \"Z\"}) \u2014 vertical direction
    • \n
  • plate_speed (float) \u2014 speed of the \u201cplate\u201d i.e. upper boundary
    • \n
\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\n

Produces [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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n
    \n
  • get_velocity (callable) \u2014 object with call signature f(x) that returns\nthe 3D velocity vector at a given 3D position vector
    • \n
  • ref_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)
    • \n
  • colors (array) \u2014 monotonic values along a representative pathline in the flow
    • \n
  • positions (Nx3 array) \u2014 3D position vectors along the same pathline
    • \n
  • min_coords (array) \u2014 2D coordinates of the lower left corner of the domain
    • \n
  • max_coords (array) \u2014 2D coordinates of the upper right corner of the domain
    • \n
  • resolution (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 vectors
    • \n
  • aspect (str|float, optional) \u2014 see matplotlib.axes.Axes.set_aspect
    • \n
  • cmap (Matplotlib color map, optional) \u2014 color map for colors
    • \n
  • cpo_vectors (array, optional) \u2014 vectors to plot as bars at pathline locations
    • \n
  • cpo_strengths (array, optional) \u2014 strengths used to scale the cpo bars
    • \n
  • tick_formatter (callable, optional) \u2014 function used to format tick labels
    • \n
\n\n

Additional keyword arguments are passed to the matplotlib.axes.Axes.quiver call\nused to plot the velocity vectors.

\n\n

Returns 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\n

Alignment 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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n
    \n
  • strains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain series
    • \n
  • angles (array) \u2014 Y-values, may be a 2D array of multiple angle series
    • \n
  • markers (sequence) \u2014 MatPlotLib markers to use for the data series
    • \n
  • labels (sequence) \u2014 labels to use for the data series
    • \n
  • err (array, optional) \u2014 standard errors for the angles, shapes must match
    • \n
  • \u03b8_max (int) \u2014 maximum angle (\u00b0) to show on the plot, should be less than 90
    • \n
  • \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)
    • \n
  • colors (array, optional) \u2014 color coordinates for series of angles
    • \n
  • cmaps (Matplotlib color maps, optional) \u2014 color maps for colors
    • \n
\n\n

If colors and cmaps are used, then angle values are colored individually within\neach angle series.

\n\n

Returns 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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Args:

\n\n
    \n
  • strains (array) \u2014 X-values, accumulated strain (tensorial) during CPO evolution,\nmay be a 2D array of multiple strain series
    • \n
  • strengths (array) \u2014 Y-values, may be a 2D array of multiple strength series
    • \n
  • markers (sequence) \u2014 MatPlotLib markers to use for the data series
    • \n
  • labels (sequence) \u2014 labels to use for the data series
    • \n
  • err (array, optional) \u2014 standard errors for the strengths, shapes must match
    • \n
  • colors (array, optional) \u2014 color coordinates for series of strengths
    • \n
  • cpo_threshold (float, optional) \u2014 plot a dashed line at this threshold
    • \n
  • cmaps (Matplotlib color maps, optional) \u2014 color maps for colors
    • \n
\n\n

If colors and cmaps are used, then strength values are colored individually\nwithin each strength series.

\n\n

Returns 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\n

If 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\n

Plot 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\n

If ax is None, a new figure and axes are created with figure_unless.

\n\n

Returns a tuple containing:

\n\n
    \n
  • the figure handle
    • \n
  • the axes handle
    • \n
  • the set of colors used for the data series plots
    • \n
  • the Skemer 2016 dataset
    • \n
  • the 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\n

If 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\n

Returns 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\n

If 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\n

Returns 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\n

If ax is None, a new figure is created for the axes with a few opinionated default\nsettings (grid, constrained layout, high DPI).

\n\n

Returns 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\n

The 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\n

Running 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\n

In total, the following custom pytest command line flags are defined by PyDRex:

\n\n
    \n
  • --outdir (described above)
    • \n
  • --runbig (enable tests which require a large amount of RAM)
    • \n
  • --runslow (enable slow tests which require HPC resources, implies --runbig)
    • \n
  • --ncpus (number of CPU cores to use for shared memory multiprocessing, set to one less than the available maximum by default)
    • \n
  • --fontsize (Matplotlib rcParams[\"font.size\"])
    • \n
  • --markersize (Matplotlib rcParams[\"lines.markersize\"])
    • \n
  • --linewidth (Matplotlib rcParams[\"lines.linewidth\"])
    • \n
\n\n

Tests 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\n

Long 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\n

Writing tests

\n\n
    \n

  • To 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.

    • \n

  • 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
\n\n

Tests 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
    \n
  • logs 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),
    • \n
  • figures can be saved by (implementing and) calling a helper from pydrex.visualisation, and
    • \n
  • data 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\n

The 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\n

Velocity 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\n

Velocity 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\n

Velocity 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\n

Velocity 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\n

Grain growth rates are compared to analytical calculations.\nThe a-axes are distributed in the YX plane (i.e.\\ rotated around Z).

\n\n

Velocity 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\n

Unlike 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\n

Velocity 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\n

Initial condition: random orientations and uniform volumes in all Minerals.

\n\n

Plate 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
\n", "signature": "(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 applicable modules.

\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 as well.

\n", "signature": "():", "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\n

Returns 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\n

Velocity 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\n

Velocity 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\n

Results 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\n

Velocity 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\n

Unlike 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\n

The 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\n

Returns 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\n

The simulation runs for 5 Ma with a strain rate of 1.58e-14/s, resulting in an\naccumulated strain invariant of 2.5.

\n\n

The 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.

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\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.

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Run 2D cell test with 10000 grains (~14GiB RAM requirement).

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Test to check that 5000 grains is \"enough\" to resolve transient features.

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Test to demonstrate stability of the dip at \u03b5 \u2248 3.75 for 5000+ grains.

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Contents

@@ -94,14 +97,34 @@

to produce output figures, data dumps and logs and save them in the directory "OUT". The value "." can be used to save these in the current directory.

-

Tests which require a “significant” amount of memory (<16GB RAM) are disabled by default. +

In total, the following custom pytest command line flags are defined by PyDRex:

+ +
    +
  • --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"])
    • +
+ +

Tests which require a “significant” amount of memory (> ~16GB RAM) are disabled by default. To fully check the functionality of the code, it is recommended to run these locally -by using the --runbig flag before moving to larger simulations. -To mark a test as “big”, add the @pytest.mark.big decorator above its method definition.

+by using the --runbig flag before moving to larger simulations.

Long tests/examples are also disabled by default and can be enabled with --runslow. -It is recommended to run these on a HPC cluster infrastructure (>100GB RAM, >46 cores). -To mark a test as slow, add the @pytest.mark.slow decorator above its method definition.

+It is recommended to run these on a HPC cluster infrastructure (>100GB RAM, >32 cores). +The number of cores to use for shared memory multiprocessing can be specified with --ncpus.

+ +

Writing tests

+ +
    +

  • To mark a test as “big” (i.e. requiring more than ~16GB RAM), apply the +@pytest.mark.big decorator to the corresponding method definition.

    • +

  • To mark a test as “slow” (i.e. requiring more than ~32 cores), apply the +@pytest.mark.slow decorator to the corresponding method definition.

    • +

Tests should not produce persistent output by default. If a test method can produce such output for debugging or visualisation,