Fix bug in Qha2dFlow.finalize

abipy/dfpt/qha_2D.py

@@ -65,8 +65,8 @@ def from_gsr_ddb_paths(cls,
 
         Args:
             nqsmall_or_qppa: Define the q-mesh for the computation of the PHDOS.
-                if > 0, it is interpreted as nqsmall
-                if < 0, it is interpreted as qppa.
+                if > 0, it is interpreted as nqsmall.
+                if < 0, it is interpreted as q-point per atom qppa.
             gsr_paths: list of paths to GSR files.
             ddb_paths: list of paths to DDB files.
             bo_strains_ac: List of strains for the a and the c lattice vector.

abipy/dfpt/tests/test_vzsisa.py

@@ -138,7 +138,7 @@ def test_vzsisa(self):
             assert qha.plot_abc_vs_t_4th(tstop=tstop, tstart=tstart, num=101, lattice="a", show=False)
             assert qha.plot_abc_vs_t_4th(tstop=tstop, tstart=tstart, show=False)
             assert qha.plot_thermal_expansion_coeff_4th(tref=293, show=False)
-            assert qha.plot_thermal_expansion_coeff_abc_4th(tstop=tstop, tstart=tstart ,num=101, tref=293, show=False)
+            assert qha.plot_thermal_expansion_coeff_abc_4th(tstop=tstop, tstart=tstart, num=101, tref=293, show=False)
             assert qha.plot_angles_vs_t_4th(tstop=tstop, tstart=tstart, num=101, angle=3, show=False)
 
             plotter = qha.get_phdos_plotter()

abipy/dfpt/vzsisa.py

@@ -489,7 +489,7 @@ def vol_E2Vib1(self, tstart=0, tstop=1000, num=101) -> tuple:
             vols[i] = V0 - (dfe_dV1[i] + self.pressure / abu.eVA3_GPa) / E2D
 
         # Calculate total energies (Eq 15, 16)
-        # FIXME The consntant term F_V0(T) is missing
+        # FIXME The constant term F_V0(T) is missing
         gibbs_vt = (self.bo_energies[self.iv0]
                   + 0.5 * (bo_volumes[np.newaxis, :].T - V0)**2 * E2D
                   + (bo_volumes[np.newaxis, :].T - V0) * dfe_dV1

abipy/examples/flows/run_qha_2d.py

@@ -75,7 +75,10 @@ def build_flow(options):
     bo_strains_c = [-5, 0, 5, 10, 15]
     #bo_strains_a = [0, 5, 10, 15, 20]
     #bo_strains_c = [0, 5, 10, 15, 20]
-    bo_strains_a = [0, 5]
+    # This is just for testing purposes
+    #bo_strains_a = [0, 5]
+    #bo_strains_c = [0, 5]
+    bo_strains_a = [0, ]
     bo_strains_c = [0, 5]
     bo_strains_a = np.array(bo_strains_a) / 100
     bo_strains_c = np.array(bo_strains_c) / 100

abipy/examples/plot/plot_qha_vzsisa.py

@@ -4,7 +4,7 @@
 =========================================
 
 This example shows how to use the GSR.nc and PHDOS.nc files computed with different volumes
-to compute thermodynamic properties within the v-ZSISA method.
+to compute thermodynamic properties within the v-ZSISA approximation.
 """
 import os
 import abipy.data as abidata

abipy/flowtk/qha_2d.py

@@ -1,6 +1,7 @@
 # coding: utf-8
 """
-Workflows for calculations within the quasi-harmonic approximation.
+Workflows for calculations within the quasi-harmonic approximation
+with two degrees of freedom. The main entry point is Qha2dFlow.
 """
 from __future__ import annotations
 
@@ -89,10 +90,10 @@ def finalize(self):
                 gsr_relax_volumes.append(gsr.structure.volume)
 
         data["gsr_relax_entries"] = gsr_relax_entries
-
         data["ddb_relax_paths"] = [ph_work.outdir.has_abiext("DDB") for ph_work in work.ph_works]
         data["gsr_relax_edos_paths"] = [] if not work.edos_work else [task.gsr_path for task in work.edos_work]
-        data["gsr_relax_ebands_paths"] = [] if work.ndivsm == 0 else [ph_work.ebands_task.gsr_path for ph_work in work.ph_works]
+        data["gsr_relax_ebands_paths"] = [] if work.ndivsm == 0 else \
+            [ph_work.ebands_task.gsr_path for ph_work in work.ph_works if ph_work.ebands_task is not None]
 
         # Write json file
         mjson_write(data, self.outdir.path_in("qha_2d.json"), indent=4)
@@ -146,7 +147,7 @@ def from_scf_input(cls,
         # Create input for relaxation and register the relaxation task.
         work.relax_template = relax_template = scf_input.deepcopy()
 
-        # optcell = 3: constant-volume optimization of cell geometry
+        # optcell = 3 --> constant-volume optimization of cell geometry.
         relax_template.pop_tolerances()
         relax_template.set_vars(optcell=3, ionmov=ionmov, tolvrs=1e-8, tolmxf=1e-6)
         relax_template.set_vars_ifnotin(ecutsm=1.0, dilatmx=1.05)
@@ -215,7 +216,7 @@ def on_all_ok(self):
                 self.ph_works.append(ph_work)
                 self.flow.register_work(ph_work)
 
-            # Add task for electron DOS calculation to edos_work
+            # Add task for electron DOS calculation to edos_work.
             if self.edos_ngkpt is not None:
                 edos_input = scf_input.make_edos_input(self.edos_ngkpt)
                 self.edos_work.register_nscf_task(edos_input, deps={ph_work[0]: "DEN"}).set_name(deformationname)

abipy/flowtk/zsisa.py

@@ -17,7 +17,7 @@
 
 class ZsisaFlow(Flow):
     """
-    Flow for QHA calculations with the VZSISA approach.
+    Flow for QHA calculations with the ZSISA approach.
 
     .. rubric:: Inheritance Diagram
     .. inheritance-diagram:: ZsisaFlow

requirements-tests.txt

@@ -1,6 +1,6 @@
 # Libraries required for running unit tests.
-python-coveralls
 pytest
+python-coveralls
 pytest-cov
 pytest-xdist
 pytest-sugar