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Enable loading of virials for 'qe/cp/traj' if prefix.str file is present #583

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Enable loading of virials for 'qe/cp/traj' if prefix.str file is present #583

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6ed8779
Enable loading of virials for 'qe/cp/traj' if prefix.str file is present
rashidrafeek Nov 30, 2023
dbe6699
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 30, 2023
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8 changes: 7 additions & 1 deletion dpdata/plugins/qe.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
import numpy as np

import dpdata.md.pbc
import dpdata.qe.scf
import dpdata.qe.traj
Expand Down Expand Up @@ -26,9 +28,13 @@ def from_labeled_system(self, file_name, begin=0, step=1, **kwargs):
data["coords"],
data["cells"],
)
data["energies"], data["forces"], es = dpdata.qe.traj.to_system_label(
data["energies"], data["forces"], stress, es = dpdata.qe.traj.to_system_label(
file_name + ".in", file_name, begin=begin, step=step
)
if stress is not None:
# Compute virials of all frames by: virial = stress * volume
virial = stress * np.linalg.det(data["cells"])[:, np.newaxis, np.newaxis]
data["virials"] = virial
assert cs == es, "the step key between files are not consistent"
return data

Expand Down
13 changes: 11 additions & 2 deletions dpdata/qe/traj.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#!/usr/bin/python3
import os
import warnings

import numpy as np
Expand All @@ -16,6 +17,7 @@
length_convert = LengthConversion("bohr", "angstrom").value()
energy_convert = EnergyConversion("hartree", "eV").value()
force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
stress_convert = PressureConversion("GPa", "eV/angstrom^3").value()


def load_key(lines, key):
Expand Down Expand Up @@ -233,8 +235,15 @@ def to_system_label(input_name, prefix, begin=0, step=1):
step=step,
convert=force_convert,
)
assert esteps == fsteps, "the step key between files are not consistent "
return energy, force, esteps
# Load stress from .str file if it exists
if os.path.isfile(prefix + ".str"):
stress, vsteps = load_data(
prefix + ".str", 3, begin=begin, step=step, convert=stress_convert
)
else:
stress, vsteps = None, esteps
assert esteps == fsteps == vsteps, "the step key between files are not consistent "
return energy, force, stress, esteps


if __name__ == "__main__":
Expand Down