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fix reading SQM minimization output #288

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Merged
wanghan-iapcm merged 1 commit into from
May 23, 2022
Merged

fix reading SQM minimization output #288

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8 changes: 7 additions & 1 deletion dpdata/amber/sqm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,15 +25,18 @@ def parse_sqm_out(fname):
for line in f:
if line.startswith(" Total SCF energy"):
energy = float(line.strip().split()[-2])
energies.append(energy)
energies = [energy]
elif line.startswith(" Atom Element Mulliken Charge"):
flag = READ_CHARGE
charges = []
elif line.startswith(" Total Mulliken Charge"):
flag = START
elif line.startswith(" Final Structure"):
flag = READ_COORDS_START
coords = []
elif line.startswith("QMMM: Forces on QM atoms"):
flag = READ_FORCES
forces = []
elif flag == READ_CHARGE:
ls = line.strip().split()
atom_symbols.append(ls[-2])
Expand All @@ -46,6 +49,9 @@ def parse_sqm_out(fname):
flag = START
elif flag == READ_FORCES:
ll = line.strip()
if not ll.startswith("QMMM: Atm "):
flag = START
continue
forces.append([float(ll[-60:-40]), float(ll[-40:-20]), float(ll[-20:])])
if len(forces) == len(charges):
flag = START
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