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supported non-orthogonal cells for amber/md #276

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supported non-orthogonal cells for amber/md #276

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a272a8a
supported non-orthogonal cells for amber/md
njzjz May 8, 2022
e246fbb
Merge branch 'devel' into non-orthogonal-cells-for-amber-md
njzjz Jan 25, 2023
1416786
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 25, 2023
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8 changes: 5 additions & 3 deletions dpdata/amber/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,15 +69,17 @@ def read_amber_traj(parm7_file, nc_file, mdfrc_file=None, mden_file = None, mdou
coords = np.array(f.variables["coordinates"][:])
cell_lengths = np.array(f.variables["cell_lengths"][:])
cell_angles = np.array(f.variables["cell_angles"][:])
shape = cell_lengths.shape
cells = np.zeros((shape[0], 3, 3))
if np.all(cell_angles > 89.99 ) and np.all(cell_angles < 90.01):
# only support 90
# TODO: support other angles
shape = cell_lengths.shape
cells = np.zeros((shape[0], 3, 3))
for ii in range(3):
cells[:, ii, ii] = cell_lengths[:, ii]
else:
raise RuntimeError("Unsupported cells")
from ase.geometry import cellpar_to_cell
for ii in range(cell_lengths.shape[0]):
cells[ii, :, :] = cellpar_to_cell([*cell_lengths[ii], *cell_angles[ii]])

if labeled:
with netcdf.netcdf_file(mdfrc_file, 'r') as f:
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