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fix(abacus): fix bug to read the data when relax job not set cal_stress #549

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Merged
wanghan-iapcm merged 4 commits into from
Oct 11, 2023
Merged

fix(abacus): fix bug to read the data when relax job not set cal_stress #549

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0158a48
fix(abacus): fix bug to read the data when relax job not set cal_stress
pxlxingliang Oct 10, 2023
3039c86
fix
pxlxingliang Oct 10, 2023
8036cfc
add ut
pxlxingliang Oct 10, 2023
7d8495b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 10, 2023
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14 changes: 9 additions & 5 deletions dpdata/abacus/relax.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,10 +158,13 @@ def get_coords_from_log(loglines, natoms):
cells *= bohr2ang
coords *= bohr2ang

virial = np.zeros([len(cells), 3, 3])
for i in range(len(cells)):
volume = np.linalg.det(cells[i, :, :].reshape([3, 3]))
virial[i] = stress[i] * kbar2evperang3 * volume
if len(stress) > 0:
virial = np.zeros([len(cells), 3, 3])
for i in range(len(cells)):
volume = np.linalg.det(cells[i, :, :].reshape([3, 3]))
virial[i] = stress[i] * kbar2evperang3 * volume
else:
virial = None

return energy, cells, coords, force, stress, virial

Expand Down Expand Up @@ -203,7 +206,8 @@ def get_frame(fname):
data["coords"] = coords
data["energies"] = energy
data["forces"] = force
data["virials"] = virial
if isinstance(virial, np.ndarray):
data["virials"] = virial
data["stress"] = stress
data["orig"] = np.zeros(3)

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