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reading the MD_dump file of ABACUS3.2 #461

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reading the MD_dump file of ABACUS3.2 #461

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3a64a07
reading the MD_dump file of ABACUS3.2
lauthirteen Apr 27, 2023
ba961a8
reading the MD_dump file of ABACUS3.2
lauthirteen Apr 27, 2023
5f9c6cf
reading the MD_dump file of ABACUS3.2, add new MD_dump file
lauthirteen Apr 27, 2023
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12 changes: 5 additions & 7 deletions dpdata/abacus/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ def get_coords_from_dump(dumplines, natoms):
for iline in range(nlines):
if "MDSTEP" in dumplines[iline]:
# read in LATTICE_CONSTANT
celldm = float(dumplines[iline + 1].split(" ")[-1])
celldm = float(dumplines[iline + 1].split(" ")[-2])
# read in LATTICE_VECTORS
for ix in range(3):
cells[iframe, ix] = (
Expand All @@ -98,7 +98,7 @@ def get_coords_from_dump(dumplines, natoms):
[
float(i)
for i in re.split("\s+", dumplines[iline + 11 + iat])[
-6:-3
3:6
]
]
)
Expand All @@ -107,7 +107,7 @@ def get_coords_from_dump(dumplines, natoms):
forces[iframe, iat] = np.array(
[
float(i)
for i in re.split("\s+", dumplines[iline + 11 + iat])[-3:]
for i in re.split("\s+", dumplines[iline + 11 + iat])[6:9]
]
)
else:
Expand All @@ -116,7 +116,7 @@ def get_coords_from_dump(dumplines, natoms):
[
float(i)
for i in re.split("\s+", dumplines[iline + 7 + iat])[
-6:-3
3:6
]
]
)
Expand All @@ -125,16 +125,14 @@ def get_coords_from_dump(dumplines, natoms):
forces[iframe, iat] = np.array(
[
float(i)
for i in re.split("\s+", dumplines[iline + 7 + iat])[-3:]
for i in re.split("\s+", dumplines[iline + 7 + iat])[6:9]
]
)
iframe += 1
assert iframe == nframes_dump, (
"iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."
% (iframe, nframes_dump)
)
cells *= bohr2ang
coords *= bohr2ang
stresses *= kbar2evperang3
return coords, cells, forces, stresses

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