Fix regressions in oncvpsp_gui.py

abipy/dfpt/phonons.py

@@ -1553,7 +1553,14 @@ def _get_non_anal_freqs(self, frac_direction):
             if np.allclose(cart_direction, d):
                 return self.non_anal_phfreqs[i]
 
-        raise ValueError("Non analytical contribution has not been calculated for reduced direction {0} ".format(frac_direction))
+        err_lines = [
+            f"Non analytical contribution has not been calculated for reduced direction: {frac_direction}",
+            "Available non_anal_directions:"
+        ]
+        for i, d in enumerate(self.non_anal_directions):
+            err_lines.append(f"{i} {d}")
+
+        raise ValueError("\n".join(err_lines))
 
     def _get_non_anal_phdispl(self, frac_direction):
         # directions for the qph2l in anaddb are given in cartesian coordinates

abipy/dfpt/phtk.py

@@ -116,28 +116,36 @@ def __init__(self, structure, directions, phfreqs, phdispl_cart, amu=None):
     @classmethod
     def from_file(cls, filepath: str) -> NonAnalyticalPh:
         """
-        Reads the non analytical directions, frequencies and displacements from the anaddb.nc file specified.
+        Reads the non analytical directions, frequencies and displacements from the nc file specified (usually anaddb.nc)
         Non existence of displacements is accepted for compatibility with abinit 8.0.6
-        Raises an error if the other values are not present in anaddb.nc.
+        Raises an error if the other values are not present in the netcdf file.
         """
         with ETSF_Reader(filepath) as r:
-            directions = r.read_value("non_analytical_directions")
-            phfreq = r.read_value("non_analytical_phonon_modes")
+            return cls.from_ncreader(r)
 
-            # need a default as the first abinit version including IFCs in the netcdf doesn't have this attribute
-            phdispl_cart = r.read_value("non_analytical_phdispl_cart", cmode="c", default=None)
+    @classmethod
+    def from_ncreader(cls, nc_reader) -> NonAnalyticalPh:
+        """
+        Build the object from a NetcdfReader.
+        """
+        r = nc_reader
+        directions = r.read_value("non_analytical_directions")
+        phfreq = r.read_value("non_analytical_phonon_modes")
 
-            structure = r.read_structure()
+        # need a default as the first abinit version including IFCs in the netcdf doesn't have this attribute
+        phdispl_cart = r.read_value("non_analytical_phdispl_cart", cmode="c", default=None)
+        structure = r.read_structure()
 
-            amu_list = r.read_value("atomic_mass_units", default=None)
-            if amu_list is not None:
-                # ntypat arrays
-                atomic_numbers = r.read_value("atomic_numbers")
-                amu = {at: a for at, a in zip(atomic_numbers, amu_list)}
-            else:
-                amu = None
+        amu_list = r.read_value("atomic_mass_units", default=None)
+
+        if amu_list is not None:
+            # ntypat arrays
+            atomic_numbers = r.read_value("atomic_numbers")
+            amu = {at: a for at, a in zip(atomic_numbers, amu_list)}
+        else:
+            amu = None
 
-            return cls(structure=structure, directions=directions, phfreqs=phfreq, phdispl_cart=phdispl_cart, amu=amu)
+        return cls(structure=structure, directions=directions, phfreqs=phfreq, phdispl_cart=phdispl_cart, amu=amu)
 
     @lazy_property
     def dyn_mat_eigenvect(self) -> np.ndarray:

abipy/eph/gpath.py

@@ -14,21 +14,21 @@
 from monty.termcolor import cprint
 from abipy.core.structure import Structure
 from abipy.core.kpoints import Kpath
-from abipy.core.mixins import AbinitNcFile, Has_Structure, Has_ElectronBands, Has_Header #, NotebookWriter
+from abipy.core.mixins import AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter
 from abipy.tools.typing import PathLike
 #from abipy.tools.numtools import BzRegularGridInterpolator, nparr_to_df
 from abipy.tools.plotting import (add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt, set_axlims, set_visible,
     rotate_ticklabels, ax_append_title, set_ax_xylabels, linestyles, Marker, set_grid_legend)
 #from abipy.tools import duck
 from abipy.electrons.ebands import ElectronBands, RobotWithEbands
 from abipy.dfpt.phonons import PhononBands
+from abipy.dfpt.phtk import NonAnalyticalPh
 from abipy.tools.typing import Figure
 from abipy.abio.robots import Robot
 from abipy.eph.common import BaseEphReader
 
 
-class GpathFile(AbinitNcFile, Has_Structure): # , NotebookWriter):
-#class GpathFile(AbinitNcFile, Has_Structure, Has_ElectronBands): # , NotebookWriter):
+class GpathFile(AbinitNcFile, Has_Structure, NotebookWriter):
     """
     This file stores the e-ph matrix elements along a k/q path
     and provides methods to analyze and plot results.
@@ -37,12 +37,13 @@ class GpathFile(AbinitNcFile, Has_Structure): # , NotebookWriter):
 
     .. code-block:: python
 
-        with GpathFile("out_GWAN.nc") as gpath:
-            print(gwan)
+        with GpathFile("out_GPATH.nc") as gpath:
+            print(gpath)
 
     .. rubric:: Inheritance Diagram
     .. inheritance-diagram:: GpathFile
     """
+
     @classmethod
     def from_file(cls, filepath: PathLike) -> GpathFile:
         """Initialize the object from a netcdf file."""
@@ -107,12 +108,13 @@ def to_string(self, verbose: int=0) -> str:
         return "\n".join(lines)
 
     @add_fig_kwargs
-    def plot_g_qpath(self, band_range, average_mode="all", ax_mat=None, fontsize=8, **kwargs) -> Figure:
+    def plot_g_qpath(self, band_range=None, with_q=False, average_mode="all", ax_mat=None, fontsize=8, **kwargs) -> Figure:
         """
         Plot ...
 
         Args:
             band_range:
+            with_q
             average_mode:
             ax_mat: List of |matplotlib-Axes| or None if a new figure should be created.
             fontsize: fontsize for legends and titles
@@ -122,24 +124,26 @@ def plot_g_qpath(self, band_range, average_mode="all", ax_mat=None, fontsize=8,
         ax_mat, fig, plt = get_axarray_fig_plt(ax_mat, nrows=nrows, ncols=ncols,
                                                sharex=False, sharey=False, squeeze=False)
 
+        qnorms = np.array([qpt.norm for qpt in self.phbands.qpoints]) if with_q else \
+                 np.ones(len(self.phbands.qpoints))
+        #band_range = (self.r.bstart, self.r.bstop) if band_range is None else band_range
+
         for spin in range(self.r.nsppol):
             g2_nuq, g2_nuq_unsym = self.r.get_g2nuq_average_spin(spin, band_range, average_mode)
 
             ax = ax_mat[0, spin]
-            #print(f"{g2_nuq_unsym.shape=}")
-            for nu in range(self.r.natom3):
-                ax.plot(g2_nuq[nu], label=f"sym {nu=}")
+            for mode in range(self.r.natom3):
+                ax.plot(g2_nuq[mode] * qnorms, label=f"sym {mode=}")
 
-            set_grid_legend(ax, fontsize, xlabel=r"$\mathbf{q}$ Wavevector", ylabel=r"$|g|$")
             self.phbands.decorate_ax(ax, units="meV")
-            #ax.set_ylabel(abu.wlabel_from_units(units))
-            #ax.set_xlabel("Wave Vector")
+            set_grid_legend(ax, fontsize, xlabel=r"Wavevector $\mathbf{q}$", ylabel=r"$|g|$")
 
             ax = ax_mat[1, spin]
-            for nu in range(self.r.natom3):
-                ax.plot(g2_nuq_unsym[nu], label=f"unsym {nu=}")
+            for mode in range(self.r.natom3):
+                ax.plot(g2_nuq_unsym[mode] * qnorms, label=f"unsym {mode=}")
+
             self.phbands.decorate_ax(ax, units="meV")
-            set_grid_legend(ax, fontsize, xlabel=r"$\mathbf{q}$ Wavevector", ylabel=r"$|g|$")
+            set_grid_legend(ax, fontsize, xlabel=r"Wavevector $\mathbf{q}$", ylabel=r"$|g|$")
 
             #ax.plot(self.r.phfreqs_ha * abu.Ha_meV) # , label=f"e_kq")
             #set_grid_legend(ax, fontsize, xlabel=r"$\mathbf{q}$ wavevector", ylabel=r"$\omega_{\mathbf{q}\nu}$ (meV)")
@@ -152,6 +156,36 @@ def plot_g_qpath(self, band_range, average_mode="all", ax_mat=None, fontsize=8,
 
         return fig
 
+    #@add_fig_kwargs
+    #def plot_g_kpath(self, band_range=None, with_q=False, average_mode="all", ax_mat=None, fontsize=8, **kwargs) -> Figure:
+
+    def yield_figs(self, **kwargs):  # pragma: no cover
+        """
+        This function *generates* a predefined list of matplotlib figures with minimal input from the user.
+        """
+        yield self.ebands.plot(show=False)
+        if self.r.eph_fix_korq == "k":
+            yield self.phbands.plot(show=False)
+            yield self.plot_g_qpath()
+        #if self.r.eph_fix_korq == "q":
+        #    yield self.plot_g_kpath()
+
+    def write_notebook(self, nbpath=None) -> str:
+        """
+        Write a jupyter_ notebook to ``nbpath``. If nbpath is None, a temporay file in the current
+        working directory is created. Return path to the notebook.
+        """
+        nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)
+
+        nb.cells.extend([
+            nbv.new_code_cell("gpath = abilab.abiopen('%s')" % self.filepath),
+            nbv.new_code_cell("print(gpath)"),
+            nbv.new_code_cell("gpath.ebands.plot();"),
+            nbv.new_code_cell("gpath.phbands.plot();"),
+        ])
+
+        return self._write_nb_nbpath(nb, nbpath)
+
 
 class GpathReader(BaseEphReader):
     """
@@ -181,10 +215,11 @@ def __init__(self, filepath: PathLike):
         self.eph_fix_wavec = self.read_value("eph_fix_wavevec")
         #self.completed = self.read_value("gstore_completed")
 
-        # Note conversion Fortran --> C for the isym index.
+        # Note conversion Fortran --> C for the bstart index.
         nband = self.read_dimvalue("nband")
         self.bstart = self.read_value("bstart") - 1
-        self.band_range = [self.bstart, nband]
+        self.bstop = self.read_value("bstop")
+        self.band_range = [self.bstart, self.bstop]
 
     def read_ebands(self):
         """
@@ -231,9 +266,11 @@ def read_phbands(self) -> PhononBands:
 
         path_qq = Kpath(structure.lattice.reciprocal_lattice, qpath_frac_coords, weights=None, names=None, ksampling=None)
 
+        non_anal_ph = NonAnalyticalPh.from_ncreader(self) if "non_analytical_directions" in self.rootgrp.variables else None
+
         return PhononBands(structure=structure, qpoints=path_qq, phfreqs=phfreqs, phdispl_cart=phdispl_cart, amu=amu,
-                           # TODO
-                           #non_anal_ph=non_anal_ph,
+                           non_anal_ph=non_anal_ph,
+                           # TODO ?
                            #epsinf=epsinf,
                            #zcart=zcart,
                            )
@@ -246,7 +283,7 @@ def get_g2nuq_average_spin(self, spin: int, band_range: list|tuple, average_mode
             spin: Spin index
             band_range:
             average_mode:
-            eps_mev: Tolerance in mev used to detect degeneracies
+            eps_mev: Tolerance in meV used to detect degeneracies.
         """
         # Consistency check
         if self.nk_path != 1:

abipy/panels/oncvpsp_gui.py

@@ -522,7 +522,7 @@ class OncvGui(AbipyParameterized):
     rcfact_dir = param.Selector(["centered", ">", "<"])
 
     ace_theme = param.ObjectSelector(default="chrome",
-                                    objects=pnw.Ace.param.theme.objects,
+                                    objects=pnw.CodeEditor.param.theme.objects,
                                     doc="Theme of the editor")
 
     history_idx = param.Integer(default=-1, label="History index")
@@ -543,7 +543,7 @@ def __init__(self, oncv_input, plotlyFlag, in_filepath="", **params):
                             #max_length=150,
                             )
 
-        self.input_ace = pnw.Ace(value=str(oncv_input), **self.ace_kwargs)
+        self.input_ace = pnw.CodeEditor(value=str(oncv_input), **self.ace_kwargs)
 
         # Add annotated example for documentation purposes.
         self.annotated_example = pn.pane.HTML(f"<pre><code> {GE_ANNOTATED} </code></pre>")
@@ -566,7 +566,7 @@ def __init__(self, oncv_input, plotlyFlag, in_filepath="", **params):
         #self.history_btn.on_click(self.on_history_btn)
 
         self.rc_qcut_btn = pnw.Button(name="Execute", button_type='primary')
-        
+
         self.plotlyFlag = plotlyFlag
 
     @param.depends("ace_theme")
@@ -661,7 +661,7 @@ def on_history_btn(self) -> pn.Column:
         if hist_len == 0 or idx >= hist_len:
             return pn.Column(f"hist_len == {hist_len}")
 
-        ace_hist = pnw.Ace(value=self.input_history[idx], **self.ace_kwargs)
+        ace_hist = pnw.CodeEditor(value=self.input_history[idx], **self.ace_kwargs)
 
         fromlines = self.input_history[idx].splitlines()
         tolines = self.input_ace.value.splitlines()
@@ -801,7 +801,7 @@ def on_change_qcut(self, event) -> None:
             try:
                 for qcut in qcut_values:
                     oncv_input.lparams[i0].qcut = qcut
-                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
             finally:
                 # Restore the initial value.
                 oncv_input.lparams[i0].qcut = qcut0
@@ -869,7 +869,7 @@ def on_change_debl(self, event) -> None:
             try:
                 for debl in debl_values:
                     oncv_input.lparams[i0].debl = debl
-                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
             finally:
                 # Restore the initial value.
                 oncv_input.lparams[i0].debl = debl0
@@ -910,7 +910,7 @@ def on_change_rc5(self, event) -> None:
             try:
                 for new_rc in rc5_values:
                     oncv_input.rc5 = new_rc
-                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
             finally:
                 # Restore the initial value.
                 oncv_input.rc5 = rc5
@@ -951,7 +951,7 @@ def on_change_dvloc0(self, event) -> None:
             try:
                 for new_dvloc in dvloc_values:
                     oncv_input.dvloc0 = new_dvloc
-                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
             finally:
                 # Restore the initial value.
                 oncv_input.dvloc0 = dvloc0
@@ -994,7 +994,7 @@ def on_change_rc(self, event) -> None:
             try:
                 for rc in rc_values:
                     oncv_input.lparams[i0].rc = rc
-                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
             finally:
                 # Restore the initial value.
                 oncv_input.lparams[i0].rc = rc0
@@ -1046,7 +1046,7 @@ def on_change_rhomodel(self, event) -> None:
                     try:
                         oncv_input.fcfact = fc
                         oncv_input.rcfact = rc
-                        psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                        psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
                         tasks.append((psgens[-1], {"fcfact": fc, "rcfact": rc}))
                         titles.append(f"fcfact: {fc}, rcfact: {rc}")
                     finally:
@@ -1059,7 +1059,7 @@ def on_change_rhomodel(self, event) -> None:
                 for fc in fcfact_values:
                     try:
                         oncv_input.fcfact = fc
-                        psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                        psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
                         tasks.append((psgens[-1], {"fcfact": fc}))
                         titles.append(f"fcfact: {fc}")
                     finally:
@@ -1137,7 +1137,7 @@ def rq_prod():
                 for rc, qcut in rq_prod():
                     oncv_input.lparams[i0].rc = rc
                     oncv_input.lparams[i0].qcut = qcut
-                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type))
+                    psgens.append(OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False))
             finally:
                 # Restore the initial value.
                 oncv_input.lparams[i0].rc = rc0
@@ -1171,7 +1171,7 @@ def on_execute_btn(self, event) -> None:
         """
         with ButtonContext(event.obj), Loading(self.out_area):
             oncv_input = self.get_oncv_input()
-            psgen = OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type)
+            psgen = OncvGenerator(input_str=str(oncv_input), calc_type=self.calc_type, use_mgga=False)
             print("Running in workdir:", psgen.workdir)
             psgen.start()
             retcode = psgen.wait()