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Fix bug in abacus MD support #214

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Merged
amcadmus merged 7 commits into from
Nov 13, 2021
Merged

Fix bug in abacus MD support #214

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db083f3
add ABACUS MD interface.
Liu-RX Oct 15, 2021
2efaaab
Merge branch 'deepmodeling:devel' into devel
Liu-RX Oct 15, 2021
9b9e180
Update system.py
Liu-RX Oct 15, 2021
f543885
Add files via upload
Liu-RX Oct 15, 2021
18080fe
Merge branch 'deepmodeling:devel' into devel
Liu-RX Nov 9, 2021
ffd20e0
Update md.py
Liu-RX Nov 9, 2021
0d7b8ef
Update md.py
Liu-RX Nov 9, 2021
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4 changes: 3 additions & 1 deletion dpdata/abacus/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ def get_frame (fname):
atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines)
# This coords is not to be used.
dump_freq = get_coord_dump_freq(inlines = inlines)
ndump = int(os.popen("ls --l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0])
ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0])
# number of dumped geometry files
coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell)

Expand All @@ -185,6 +185,8 @@ def get_frame (fname):
data['energies'] = energy
data['forces'] = force
data['virials'] = stress
if type(data['virials']) != np.ndarray:
del data['virials']
data['orig'] = np.zeros(3)

return data