Merge pull request #170 from JaGeo/fix_order_forces_error

Fix born error in phonon workflow

Author: utf

src/atomate2/vasp/flows/phonons.py

@@ -167,9 +167,6 @@ def make(
             these values can also be provided manually.
             if born, epsilon_static are provided, the born
             run will be skipped
-            this matrix can be provided in the phonopy convention
-            with born charges for symmetrically
-            inequivalent atoms only or
             it can be provided in the VASP convention with information for
             every atom in unit cell. Please be careful when converting
             structures within in this workflow as this could lead to errors

src/atomate2/vasp/jobs/phonons.py

@@ -287,6 +287,7 @@ def run_phonon_displacements(
         "forces": [],
         "uuids": [],
         "dirs": [],
+        "displaced_structures": [],
     }
 
     for i, displacement in enumerate(displacements):
@@ -298,6 +299,7 @@ def run_phonon_displacements(
             "displacement_number": i,
             "original_structure": structure,
             "supercell_matrix": supercell_matrix,
+            "displaced_structure": displacement,
         }
         phonon_job.update_maker_kwargs(
             {"_set": {"write_additional_data->phonon_info:json": info}}, dict_mod=True
@@ -307,6 +309,7 @@ def run_phonon_displacements(
         outputs["uuids"].append(phonon_job.output.uuid)
         outputs["dirs"].append(phonon_job.output.dir_name)
         outputs["forces"].append(phonon_job.output.output.forces)
+        outputs["displaced_structures"].append(displacement)
 
     displacement_flow = Flow(phonon_jobs, outputs)
     return Response(replace=displacement_flow)

src/atomate2/vasp/schemas/phonons.py

@@ -5,7 +5,7 @@
 import numpy as np
 from phonopy import Phonopy
 from phonopy.phonon.band_structure import get_band_qpoints_and_path_connections
-from phonopy.structure.symmetry import elaborate_borns_and_epsilon
+from phonopy.structure.symmetry import symmetrize_borns_and_epsilon
 from phonopy.units import VaspToTHz
 from pydantic import BaseModel, Field
 from pymatgen.core import Structure
@@ -258,17 +258,19 @@ def from_forces_born(
 
         if born is not None and epsilon_static is not None:
             if len(structure) == len(born):
-                borns, epsilon, atom_indices = elaborate_borns_and_epsilon(
-                    ucell=get_phonopy_structure(structure),
+                borns, epsilon = symmetrize_borns_and_epsilon(
+                    ucell=phonon.unitcell,
                     borns=np.array(born),
                     epsilon=np.array(epsilon_static),
                     symprec=symprec,
                     primitive_matrix=phonon.primitive_matrix,
                     supercell_matrix=phonon.supercell_matrix,
+                    is_symmetry=kwargs.get("symmetrize_born", True),
                 )
             else:
-                borns = np.array(born)
-                epsilon = np.array(epsilon_static)
+                raise ValueError(
+                    "Number of born charges does not agree with number of atoms"
+                )
             if code == "vasp":
                 if not np.all(np.isclose(borns, 0.0)):
                     phonon.nac_params = {

tests/test_data/vasp/Mg3Sb2_phonons/dielectric/inputs/INCAR

@@ -0,0 +1,28 @@
+ALGO = Fast
+EDIFF = 1e-05
+EDIFFG = -0.02
+ENAUG = 1360
+ENCUT = 680
+GGA = Ps
+IBRION = 8
+ISIF = 3
+ISMEAR = -5
+ISPIN = 2
+KSPACING = 0.22
+LAECHG = True
+LASPH = True
+LCHARG = True
+LELF = False
+LEPSILON = True
+LMAXMIX = 4
+LMIXTAU = True
+LORBIT = 11
+LPEAD = True
+LREAL = False
+LVTOT = True
+LWAVE = False
+MAGMOM = 5*0.6
+NELM = 200
+NSW = 1
+PREC = Accurate
+SIGMA = 0.2

tests/test_data/vasp/Mg3Sb2_phonons/dielectric/inputs/POSCAR

@@ -0,0 +1,13 @@
+Mg3 Sb2
+1.0
+   2.3003714889113014   -3.9843602950772401    0.0000000000000000
+   2.3003714889113014    3.9843602950772401    0.0000000000000000
+   0.0000000000000000    0.0000000000000000    7.2813299999999996
+Mg Sb
+3 2
+direct
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Mg
+   0.3333333333333333    0.6666666666666666    0.3683249999999999 Mg
+   0.6666666666666667    0.3333333333333334    0.6316750000000001 Mg
+   0.3333333333333333    0.6666666666666666    0.7747489999999999 Sb
+   0.6666666666666667    0.3333333333333334    0.2252510000000001 Sb

tests/test_data/vasp/Mg3Sb2_phonons/dielectric/inputs/POTCAR.spec

@@ -0,0 +1,2 @@
+Mg
+Sb