qha_aproximation.py --> vzsisa.py

abipy/dfpt/deformation_utils.py

@@ -1,11 +1,14 @@
 # deformation_utils.py
+from __future__ import annotations
 
 import numpy as np
-from pymatgen.core import Structure, Lattice, Element
+import re
+
+from pymatgen.core import Lattice, Element
+#from abipy.core.structure import Structure
 from abipy.core.symmetries import AbinitSpaceGroup
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from abipy.abio.inputs import AbinitInput
-import re
 
 
 def generate_deformations_volumic(structure, eps_V=0.02, scales=None):

abipy/dfpt/qha_aproximation.py → abipy/dfpt/vzsisa.py

@@ -1,6 +1,6 @@
 # coding: utf-8
 """
-Classes for V-ZSISA approximation.
+Classes  for post-processing QHA results obtained with the V-ZSISA approximation.
 See PHYSICAL REVIEW B 110, 014103 (2024)
 """
 from __future__ import annotations
@@ -19,7 +19,7 @@
 from abipy.dfpt.phonons import PhdosFile, PhononDosPlotter
 
 
-class QHA_App:
+class Vzsisa:
     """
     Class for the approximations on QHA analysis.
     Provides some basic methods and plotting utils.
@@ -31,7 +31,7 @@ def from_gsr_ddb_files(cls,
                            gsr_paths: list[PathLike],
                            ddb_paths: list[PathLike],
                            verbose: int = 0,
-                           **extra_kwargs) -> QHA_App:
+                           **extra_kwargs) -> Vzsisa:
         """
         Creates an instance from a list of GSR files and a list of DDB files.
         This is a simplified interface that computes the PHDOS.nc files automatically
@@ -71,7 +71,7 @@ def from_gsr_ddb_files(cls,
         return cls.from_gsr_phdos_files(gsr_paths, phdos_paths)
 
     @classmethod
-    def from_gsr_phdos_files(cls, gsr_paths: list[str], phdos_paths: list[str]) -> QHA_App:
+    def from_gsr_phdos_files(cls, gsr_paths: list[str], phdos_paths: list[str]) -> Vzsisa:
         """
         Creates an instance from a list of GSR files and a list of PHDOS.nc files.
 
@@ -112,11 +112,8 @@ def from_gsr_phdos_files(cls, gsr_paths: list[str], phdos_paths: list[str]) -> Q
 
         return cls(structures, structures_from_phdos, index_list, phdoses, energies, pressures)
 
-    # FIXME: This to maintain previous interface. It should be removed
-    from_files_app = from_gsr_phdos_files
-
     @classmethod
-    def from_ddb_phdos_files(cls, ddb_paths: list[str], phdos_paths: list[str]) -> QHA_App:
+    def from_ddb_phdos_files(cls, ddb_paths: list[str], phdos_paths: list[str]) -> Vzsisa:
         """
         Creates an instance from a list of DDB files and a list of PHDOS.nc files.
 
@@ -158,9 +155,6 @@ def from_ddb_phdos_files(cls, ddb_paths: list[str], phdos_paths: list[str]) -> Q
 
         return cls(structures, structures_from_phdos, index_list, phdoses, energies, pressures)
 
-    # FIXME: This to maintain previous interface. It should be removed
-    from_files_app_ddb = from_ddb_phdos_files
-
     def __init__(self, structures, structures_from_phdos, index_list, phdoses, energies, pressures,
                  eos_name: str = 'vinet', pressure: float = 0.0):
         """
@@ -529,6 +523,8 @@ def plot_energies(self, tstart=0, tstop=1000, num=1, ax=None, fontsize=10, **kwa
         ax.plot(f.min_vol, f.min_en - self.energies[self.iv0], color='r', linestyle='dashed' , lw=1, marker='o', ms=5)
         set_grid_legend(ax, fontsize, xlabel=r'V (${\AA}^3$)', ylabel='E (eV)', legend=False)
 
+        fig.suptitle("Energies as a function of volume for different T")
+
         return fig
 
     def get_phdos_plotter(self) -> PhononDosPlotter:
@@ -605,6 +601,8 @@ def plot_vol_vs_t(self, tstart=0, tstop=1000, num=101, fontsize=10, ax=None, **k
         set_grid_legend(ax, fontsize, xlabel='T (K)', ylabel=r'V (${\AA}^3$)')
         ax.set_xlim(tstart, tstop)
 
+        fig.suptitle("Volume as a function of T")
+
         return fig
 
     def get_thermal_expansion_coeff(self, tstart=0, tstop=1000, num=101, tref=None) -> Function1D:
@@ -775,6 +773,8 @@ def plot_thermal_expansion_coeff(self, tstart=0, tstop=1000, num=101, tref=None,
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Volumetric thermal expansion coefficient as a function of T")
+
         return fig
 
     def get_abc(self, volumes, num=101) -> tuple:
@@ -924,6 +924,8 @@ def plot_thermal_expansion_coeff_abc(self, tstart=0, tstop=1000, num=101, tref=N
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Thermal expansion coefficient as a function of T")
+
         return fig
 
     @add_fig_kwargs
@@ -1107,6 +1109,8 @@ def plot_abc_vs_t(self, tstart=0, tstop=1000, num=101, lattice=None, tref=None,
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Lattice as a function of T")
+
         return fig
 
     @add_fig_kwargs
@@ -1181,6 +1185,8 @@ def plot_angles_vs_t(self, tstart=0, tstop=1000, num=101, angle=None, tref=None,
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Angles as a function of T")
+
         return fig
 
     def fit_forth(self, tstart=0, tstop=1000, num=1, energy="energy", volumes="volumes"):
@@ -1434,6 +1440,8 @@ def plot_vol_vs_t_4th(self, tstart=0, tstop=1000, num=101, ax=None, fontsize=10,
         set_grid_legend(ax, fontsize, xlabel='T (K)', ylabel=r'V (${\AA}^3$)')
         ax.set_xlim(tstart, tstop)
 
+        fig.suptitle("Volume as a function of T")
+
         return fig
 
     def get_thermal_expansion_coeff_4th(self, tstart=0, tstop=1000, num=101, tref=None) -> np.ndarray:
@@ -1558,7 +1566,7 @@ def plot_thermal_expansion_coeff_4th(self, tstart=0, tstop=1000, num=101, tref=N
             ds_dv = ds_dv + (df_t[:,iv0+2]-2*df_t[:,iv0+1]+df_t[:,iv0])/dV**2 * (vol3_4th[:]-volumes[iv0+1])
             if tref is None:
                 alpha_3 = - 1/vol3_4th[:] * ds_dv / (E2D_V[:]+dfe_dV2[:])
-            else :
+            else:
                 vol3_4th_ref = self.vol_Einf_Vib2_forth(num=1, tstop=tref, tstart=tref)
                 alpha_3 = - 1/vol3_4th_ref * ds_dv / (E2D_V[:]+dfe_dV2[:])
 
@@ -1602,6 +1610,8 @@ def plot_thermal_expansion_coeff_4th(self, tstart=0, tstop=1000, num=101, tref=N
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Volumetric thermal expansion coefficient as a function of T")
+
         return fig
 
     @add_fig_kwargs
@@ -1676,6 +1686,8 @@ def plot_abc_vs_t_4th(self, tstart=0, tstop=1000, num=101, lattice=None, tref=No
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Lattice as a function of T")
+
         return fig
 
     @add_fig_kwargs
@@ -1750,6 +1762,8 @@ def plot_angles_vs_t_4th(self, tstart=0, tstop=1000, num=101, angle=None, tref=N
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Angles as a function of T")
+
         return fig
 
     @add_fig_kwargs
@@ -1858,6 +1872,8 @@ def plot_thermal_expansion_coeff_abc_4th(self, tstart=0, tstop=1000, num=101, tr
         ax.set_xlim(tstart, tstop)
         ax.get_yaxis().get_major_formatter().set_powerlimits((0, 0))
 
+        fig.suptitle("Thermal expansion coefficient as a function of T")
+
         return fig
 
     @add_fig_kwargs

abipy/examples/flows/run_qha_vzsisa.py

@@ -10,7 +10,7 @@
 import abipy.data as abidata
 
 from abipy import flowtk
-from abipy.flowtk.qha import VzsisaFlow
+from abipy.flowtk.vzsisa import VzsisaFlow
 
 
 def build_flow(options):

abipy/examples/plot/plot_qha_v-ZSISA.py → abipy/examples/plot/plot_qha_vzsisa.py

@@ -9,7 +9,7 @@
 import os
 import abipy.data as abidata
 
-from abipy.dfpt.qha_aproximation import QHA_App
+from abipy.dfpt.vzsisa import Vzsisa
 
 # Root points to the directory in the git submodule with the output results.
 root = os.path.join(abidata.dirpath, "data_v-ZSISA-QHA.git", "Si_v_ZSISA_approximation")
@@ -23,64 +23,64 @@
 ddb_paths = [os.path.join(root, "scale_{:d}_GSR_DDB".format(s)) for s in strains]
 dos_paths = [os.path.join(root, "scale_{:d}_PHDOS.nc".format(s)) for s in strains2]
 
-qha = QHA_App.from_files_app_ddb(ddb_paths, dos_paths)
+qha = Vzsisa.from_files_app_ddb(ddb_paths, dos_paths)
 tstart, tstop = 0, 800
 
 #%%
-qha.plot_energies(tstop=tstop, tstart=tstart, num=11,
-                  title="Energies as a function of volume for different T")
+# Plot Energies as a function of volume for different T
+qha.plot_energies(tstop=tstop, tstart=tstart, num=11)
 
 #%%
-qha.plot_vol_vs_t(tstop=tstop, tstart=tstart, num=101,
-                  title="Volume as a function of T")
+# Plot Volume as a function of T
+qha.plot_vol_vs_t(tstop=tstop, tstart=tstart, num=101)
 
 #%%
-qha.plot_abc_vs_t(tstop=tstop, tstart=tstart, num=101,
-                  title="Lattice as a function of T")
-
+# Plot Lattice as a function of T
+qha.plot_abc_vs_t(tstop=tstop, tstart=tstart, num=101)
 
 #%%
-qha.plot_abc_vs_t(tstop=tstop, tstart=tstart, num=101, lattice="b",
-                  title="Lattice as a function of T")
+# Plot Lattice as a function of T")
+qha.plot_abc_vs_t(tstop=tstop, tstart=tstart, num=101, lattice="b")
 
 #%%
-qha.plot_thermal_expansion_coeff(tstop=tstop, tstart=tstart ,num=101,
-                                 title="Volumetric thermal expansion coefficient as a function of T")
+# Plot Volumetric thermal expansion coefficient as a function of T
+qha.plot_thermal_expansion_coeff(tstop=tstop, tstart=tstart ,num=101)
 
 #%%
-qha.plot_thermal_expansion_coeff_abc(tstop=tstop, tstart=tstart ,num=101,
-                                     title="Thermal expansion coefficient as a function of T")
+# Plot Thermal expansion coefficient as a function of T
+qha.plot_thermal_expansion_coeff_abc(tstop=tstop, tstart=tstart ,num=101)
 
 #%%
-qha.plot_angles_vs_t(tstop=tstop, tstart=tstart, num=101,
-                     title="Angles as a function of T")
+# Plot Angles as a function of T
+qha.plot_angles_vs_t(tstop=tstop, tstart=tstart, num=101)
 
 #%%
-# 4th order polinomial
-qha.plot_vol_vs_t_4th(tstop=tstop, tstart=tstart, num=101,
-                      title="Volume as a function of T")
+#
+# Plot Volume as a function of T. 4th order polinomial
+qha.plot_vol_vs_t_4th(tstop=tstop, tstart=tstart, num=101)
 
 #%%
-qha.plot_abc_vs_t_4th(tstop=tstop, tstart=tstart, num=101, lattice="a",
-                      title="Lattice as a function of T")
+# Plot Lattice as a function of T. 4th order polinomial
+qha.plot_abc_vs_t_4th(tstop=tstop, tstart=tstart, num=101, lattice="a")
 
 #%%
-qha.plot_abc_vs_t_4th(tstop=tstop, tstart=tstart,
-                      title="Lattice as a function of T")
+# Plot Lattice as a function of T. 4th order polinomial
+qha.plot_abc_vs_t_4th(tstop=tstop, tstart=tstart)
 
 #%%
-qha.plot_thermal_expansion_coeff_4th(tref=293,
-                                     title="Volumetric thermal expansion coefficient as a function of T")
+# Plot Volumetric thermal expansion coefficient as a function of T
+qha.plot_thermal_expansion_coeff_4th(tref=293)
 
 #%%
-qha.plot_thermal_expansion_coeff_abc_4th(tstop=tstop, tstart=tstart ,num=101, tref=293,
-                                         title="Thermal expansion coefficient as a function of T")
+# Plot Thermal expansion coefficient as a function of T
+qha.plot_thermal_expansion_coeff_abc_4th(tstop=tstop, tstart=tstart ,num=101, tref=293)
 
 #%%
-qha.plot_angles_vs_t_4th(tstop=tstop, tstart=tstart, num=101, angle=3,
-                         title="Angles as a function of T")
+# Plot Angles as a function of T.
+qha.plot_angles_vs_t_4th(tstop=tstop, tstart=tstart, num=101, angle=3)
 
 
 #%%
+# Create plotter to plot all the phonon DOS.
 phdos_plotter = qha.get_phdos_plotter()
 phdos_plotter.combiplot()

abipy/flowtk/psrepos.py

@@ -56,7 +56,13 @@ def get_oncvpsp_pseudos(xc_name: str, version: str, relativity_type: str = "SR",
     ps_generator, project_name = OncvpspRepo.ps_generator, OncvpspRepo.project_name
     repo_name = f"{ps_generator}-{xc_name}-{relativity_type}-{project_name}v{version}"
 
-    return get_repo_from_name(repo_name).get_pseudos(accuracy)
+    repo = get_repo_from_name(repo_name)
+
+    # Istall it at runtime if needed.
+    if not repo.is_installed():
+        repo.install()
+
+    return repo.get_pseudos(accuracy)
 
 
 # Installation directory.