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Added some parameter in eval_mu_alpha.py #636

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Added some parameter in eval_mu_alpha.py #636

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20 changes: 10 additions & 10 deletions mace/cli/eval_mu_alpha.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ def main():

# Load data and prepare input
if args.configs.endswith(".xyz"):
atoms_list = ase.io.read(args.configs, index=":")
atoms_list = ase.io.read(args.configs, index=":", format='extxyz')
if args.output_SFG:
velocities = np.array(
[atoms.arrays[args.velocity_key] for atoms in atoms_list]
Expand Down Expand Up @@ -166,12 +166,12 @@ def main():
dmu_dr = np.split(
torch_tools.to_numpy(output["dmu_dr"]),
indices_or_sections=batch.ptr[1:],
axis=0,
axis=1,
)[:-1]
dalpha_dr = np.split(
torch_tools.to_numpy(output["dalpha_dr"]),
indices_or_sections=batch.ptr[1:],
axis=0,
axis=1,
)[:-1]
dmu_dr_collection.append(dmu_dr)
dalpha_dr_collection.append(dalpha_dr)
Expand Down Expand Up @@ -261,14 +261,18 @@ def main():

if args.compute_dielectric_derivatives:
dmu_dr_list = [
dmu_dr for dmu_dr_list in dmu_dr_collection for dmu_dr in dmu_dr_list
dmu_dr
for dmu_dr_list in dmu_dr_collection
for dmu_dr in dmu_dr_list
]
dalpha_dr_list = [
dalpha_dr
for dalpha_dr_list in dalpha_dr_collection
for dalpha_dr in dalpha_dr_list
]

assert len(atoms_list) == len(dmu_dr_list) == len(dalpha_dr_list)

# Store data in atoms objects
if args.configs.endswith(".xyz"):
for i, (atoms, dmu_dr, dalpha_dr) in enumerate(
Expand All @@ -277,12 +281,8 @@ def main():
atoms.calc = None # crucial
if args.velocity_key in atoms.arrays.keys():
atoms.arrays.pop(args.velocity_key)
atoms.arrays[args.info_prefix + "dmu_dr"] = dmu_dr.reshape(
dmu_dr.shape[0], 9
)
atoms.arrays[args.info_prefix + "dalpha_dr"] = dalpha_dr_list[
i
].reshape(dalpha_dr_list[i].shape[0], 27)
atoms.arrays[args.info_prefix + "dmu_dr"] = dmu_dr.reshape(-1, 9)
atoms.arrays[args.info_prefix + "dalpha_dr"] = dalpha_dr.reshape(-1, 27)
# Write atoms to output path
ase.io.write(args.output, images=atoms_list, format="extxyz")
else:
Expand Down