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Modify molecule.py to support Q-Chem EDA/FDA calculations. #192

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Modify molecule.py to support Q-Chem EDA/FDA calculations. #192

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37 changes: 28 additions & 9 deletions geometric/molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1381,8 +1381,8 @@ def __deepcopy__(self, memo):
# (Q-Chem input section name) and the second element
# is a list (Q-Chem input section data).
New.Data[key] = []
for SectName, SectData in self.Data[key]:
New.Data[key].append((SectName, SectData[:]))
for SectName, SectData, SectInsert in self.Data[key]:
New.Data[key].append((SectName, SectData[:], SectInsert))
else:
raise RuntimeError("Failed to copy key %s" % key)
return New
Expand Down Expand Up @@ -3595,11 +3595,14 @@ def read_qcin(self, fnm, **kwargs):
mult = 0
Answer = {}
SectionData = []
SectionInsert = {}
template_cut = 0
section_ln = 0 # Line number within a section
readsuf = True
suffix = [] # The suffix, which comes after every atom line in the $molecule section, is for determining the MM atom type and topology.
ghost = [] # If the element in the $molecule section is preceded by an '@' sign, it's a ghost atom for counterpoise calculations.
infsm = False
found_charge_mult = False

# The 'iso-8859-1' prevents some strange errors that show up when reading the Archival summary line
for line in open(fnm, encoding='iso-8859-1').readlines():
Expand All @@ -3610,6 +3613,7 @@ def read_qcin(self, fnm, **kwargs):
zmatrix = True
if re.match(r'^\$',line):
wrd = re.sub(r'\$','',line).lower()
section_ln = 0
if zmatrix:
if wrd == 'end':
zmatrix = False
Expand All @@ -3630,7 +3634,7 @@ def read_qcin(self, fnm, **kwargs):
qcrem = OrderedDict()
if reading_template:
if section != 'external_charges': # Ignore the external charges section because it varies from frame to frame.
template.append((section,SectionData))
template.append((section,SectionData,SectionInsert))
SectionData = []
else:
section = wrd
Expand Down Expand Up @@ -3658,14 +3662,15 @@ def read_qcin(self, fnm, **kwargs):
if readsuf and len(sline) > 4:
whites = re.split('[^ ]+',line)
suffix.append(''.join([whites[j]+sline[j] for j in range(4,len(sline))]))
elif re.match("[+-]?[0-9]+ +[0-9]+$",line.split('!')[0].strip()):
if not found_first_mol:
charge = int(sline[0])
mult = int(sline[1])
elif re.match("[+-]?[0-9]+ +[0-9]+$",line.split('!')[0].strip()) and not found_charge_mult:
charge = int(sline[0])
mult = int(sline[1])
found_charge_mult = True
elif infsm and re.sub(r'\$','',line).lower() != 'end':
pass
else:
SectionData.append(line)
SectionInsert[section_ln] = line
# SectionData.append(line)
elif reading_template:
if section == 'basis':
SectionData.append(line.split('!')[0])
Expand All @@ -3677,6 +3682,7 @@ def read_qcin(self, fnm, **kwargs):
qcrem[S[0].lower()] = ''.join(S[2:])
else:
SectionData.append(line)
section_ln += 1
elif re.match('^@+$', line) and reading_template:
template.append(('@@@', []))
elif re.match('Welcome to Q-Chem', line) and reading_template and found_first_mol:
Expand Down Expand Up @@ -4209,6 +4215,14 @@ def write_qcin(self, **kwargs):
read = kwargs['read']
else:
read = False

def insert_section(linelist, section_ln, sect_insert):
section_ln += 1
while section_ln in sect_insert:
linelist.append(sect_insert[section_ln])
section_ln += 1
return section_ln

for SI, I in enumerate(selection):
fsm = False
remidx = 0
Expand All @@ -4220,7 +4234,7 @@ def write_qcin(self, **kwargs):
for i in range(len(extchg)):
out.append("% 15.10f % 15.10f % 15.10f %15.10f" % (extchg[i,0],extchg[i,1],extchg[i,2],extchg[i,3]))
out.append('$end')
for SectName, SectData in self.qctemplate:
for SectName, SectData, SectInsert in self.qctemplate:
if 'jobtype' in self.qcrems[remidx] and self.qcrems[remidx]['jobtype'].lower() == 'fsm':
fsm = True
if len(selection) != 2:
Expand All @@ -4233,15 +4247,19 @@ def write_qcin(self, **kwargs):
if SectName == 'molecule':
if molecule_printed == False:
molecule_printed = True
section_ln = 0
if read:
out.append("read")
section_ln = insert_section(out, section_ln, SectInsert)
elif self.na > 0:
out.append("%i %i" % (self.charge, self.mult))
section_ln = insert_section(out, section_ln, SectInsert)
an = 0
for e, x in zip(self.elem, self.xyzs[I]):
pre = '@' if ('qm_ghost' in self.Data and self.Data['qm_ghost'][an]) else ''
suf = self.Data['qcsuf'][an] if 'qcsuf' in self.Data else ''
out.append(pre + format_xyz_coord(e, x) + suf)
section_ln = insert_section(out, section_ln, SectInsert)
an += 1
if fsm:
out.append("****")
Expand All @@ -4250,6 +4268,7 @@ def write_qcin(self, **kwargs):
pre = '@' if ('qm_ghost' in self.Data and self.Data['qm_ghost'][an]) else ''
suf = self.Data['qcsuf'][an] if 'qcsuf' in self.Data else ''
out.append(pre + format_xyz_coord(e, x) + suf)
section_ln = insert_section(out, section_ln, SectInsert)
an += 1
if SectName == 'rem':
for key, val in self.qcrems[remidx].items():
Expand Down
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