Add test_qha_general_stress.py

Author: gmatteo

.github/workflows/gh-pages.yml

@@ -66,15 +66,16 @@ jobs:
             mkdir -p $HOME/.abinit/abipy/
             cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
             cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
-            # FIXME TEMPORARY HACK
-            #pip install git+https://github.com/gmatteo/pymatgen.git@master -U
+
+            # TEMPORARY HACK THAT MIGHT BE NEEDED IF THE PYMATGEN GUYS BREAK STUFF
+            pip install git+https://github.com/gmatteo/pymatgen.git@master -U
 
       - name: Build docs with Sphinx
         run: |
             conda activate abipy
             cd docs
             source install.sh
-            make
+            make -j
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2

.github/workflows/test.yml

@@ -63,6 +63,8 @@ jobs:
             mkdir -p $HOME/.abinit/abipy/
             cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
             cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
+            # TEMPORARY HACK THAT MIGHT BE NEEDED IF THE PYMATGEN GUYS BREAK STUFF
+            pip install git+https://github.com/gmatteo/pymatgen.git@master -U
 
       - name: pytest
         run: |

abipy/dfpt/qha_2D.py

@@ -1,12 +1,20 @@
+"""
+Added to compute ZSISA-QHA for systems with two degrees of freedom (2DOF).
+Capable of calculating anisotropic thermal expansion and lattice constants for uniaxial configurations.
+Requires PHDOS.nc and DDB files for GSR calculations or _GSR.nc files.
+If PHDOS.nc is available for all structures, normal interpolation for QHA will be applied.
+Supports the use of six PHDOS.nc files for specific structures to employ the E_infVib2 approximation.
+"""
+
 import os
 import abc
 import numpy as np
 import abipy.core.abinit_units as abu
 
-#from scipy.interpolate import UnivariateSpline
 #from monty.collections import dict2namedtuple
 #from monty.functools import lazy_property
 from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, get_axarray_fig_plt
+from abipy.tools.typing import Figure
 from abipy.electrons.gsr import GsrFile
 from abipy.dfpt.ddb import DdbFile
 from abipy.dfpt.phonons import PhdosFile # PhononBandsPlotter, PhononDos,
@@ -52,7 +60,7 @@ def __init__(self, structures, doses, energies, structures_from_phdos, eos_name=
         self.min_energy_idx = np.unravel_index(np.nanargmin(self.energies), self.energies.shape)
 
     @add_fig_kwargs
-    def plot_energies(self, ax=None, **kwargs):
+    def plot_energies(self, ax=None, **kwargs) -> Figure:
         """
         Plot energy surface and visualize minima in a 3D plot.
 
@@ -127,14 +135,13 @@ def find_minimum(self, f_interp, xy_init, tol=1e-6, max_iter=1000, step_size=0.0
         return xy[0], xy[1], min_energy
 
     @add_fig_kwargs
-    def plot_free_energies(self, tstart=800 , tstop=0 ,num=5, ax=None, **kwargs):
+    def plot_free_energies(self, tstart=800 , tstop=0 ,num=5, ax=None, **kwargs) -> Figure:
         """
         Plot free energy as a function of temperature in a 3D plot.
 
         Args:
             ax: Matplotlib axis for the plot.
         """
-
         ax, fig, plt = get_ax_fig_plt(ax, figsize=(10, 8))
         ax = fig.add_subplot(111, projection='3d')  # Create a 3D subplot
 
@@ -222,7 +229,7 @@ def plot_free_energies(self, tstart=800 , tstop=0 ,num=5, ax=None, **kwargs):
         return fig
 
     @add_fig_kwargs
-    def plot_thermal_expansion(self, tstart=800, tstop=0, num=81, ax=None, **kwargs):
+    def plot_thermal_expansion(self, tstart=800, tstop=0, num=81, ax=None, **kwargs) -> Figure:
         """
         Plots thermal expansion coefficients along the a-axis, c-axis, and volumetric alpha.
         Uses both QHA and a 9-point stencil for comparison.
@@ -234,7 +241,6 @@ def plot_thermal_expansion(self, tstart=800, tstop=0, num=81, ax=None, **kwargs)
             ax: Matplotlib axis object for plotting.
             **kwargs: Additional arguments for customization.
         """
-
         tmesh = np.linspace(tstart, tstop, num)
         ph_energies = self.get_vib_free_energies(tstart, tstop, num)
         ax, fig, plt = get_ax_fig_plt(ax, figsize=(10, 8))  # Ensure a valid plot axis
@@ -321,15 +327,15 @@ def plot_thermal_expansion(self, tstart=800, tstop=0, num=81, ax=None, **kwargs)
         np.savetxt(file_path, data_to_save, fmt='%4.6e', delimiter='\t\t',  header='\t\t\t'.join(columns), comments='')
 
         ax.grid(True)
-        ax.legend()
+        ax.legend(loc="best", shadow=True)
         ax.set_xlabel('Temperature (K)')
         ax.set_ylabel(r'Thermal Expansion Coefficients ($\alpha$)')
         plt.savefig("thermal_expansion.pdf", format="pdf", bbox_inches="tight")
 
         return fig
 
     @add_fig_kwargs
-    def plot_lattice(self, tstart=800, tstop=0, num=81, ax=None, **kwargs):
+    def plot_lattice(self, tstart=800, tstop=0, num=81, ax=None, **kwargs) -> Figure:
         """
         Plots thermal expansion coefficients along the a-axis, c-axis, and volumetric alpha.
         Uses both QHA and a 9-point stencil for comparison.
@@ -416,16 +422,16 @@ def plot_lattice(self, tstart=800, tstop=0, num=81, ax=None, **kwargs):
 
 
         axs[0].set_ylabel("a")
-        axs[0].legend()
+        axs[0].legend(loc="best", shadow=True)
         axs[0].grid(True)
         axs[0].set_xlabel("Temperature (T)")
         axs[1].set_ylabel("c")
-        axs[1].legend()
+        axs[1].legend(loc="best", shadow=True)
         axs[1].grid(True)
         axs[1].set_xlabel("Temperature (T)")
         axs[2].set_xlabel("Temperature (T)")
         axs[2].set_ylabel("Volume")
-        axs[2].legend()
+        axs[2].legend(loc="best", shadow=True)
         axs[2].grid(True)
 
         # Adjust layout and show the figure