def read_geometries(filename, dir='.'):
txt = os.path.join(dir, filename)
fh = open(txt, 'rb')
table = fh.read()
firstsplit = '(in xyz format):' # TM1R2006 and TM2R2007
dataformat = 'xyz'
if table.find('(Gaussian archive entries):') != -1:
firstsplit = '(Gaussian archive entries):' # TM3R2008
dataformat = 'gaussian'
table = table.split(firstsplit)
table = table[1]
# remove one or two digit numbers (page numbers/numbers of atoms in xyz format)
table = re.sub('\n\d\d\n', '\n', table)
table = re.sub('\n\d\n', '\n', table)
# remove S + two digit numbers (page numbers)
table = re.sub('\nS\d\d\n', '\n', table)
# remove S + one digit (page numbers)
table = re.sub('\nS\d\n', '\n', table)
# remove empty lines
# http://stackoverflow.com/questions/1140958/whats-a-quick-one-liner-to-remove-empty-lines-from-a-python-string
table = os.linesep.join([s for s in table.splitlines() if s])
geometries = []
if dataformat == 'xyz':
# split on new lines
table = table.split('\n')
# mark compound names with ':' tags
for n, line in enumerate(table):
if not (line.find('.') != -1):
# remove method/basis set information
table[n] = table[n].replace(' BP86/qzvp', '')
table[n] = ':' + table[n] + ':'
table = '\n'.join([s for s in table])
# split into compounds
# http://simonwillison.net/2003/Oct/26/reSplit/
# http://stackoverflow.com/questions/647655/python-regex-split-and-special-character
table = re.compile('(:.*:)').split(table)
# remove empty elements
table = [l.strip() for l in table]
table = [l for l in table if len(l) > 1]
# extract compounds
for n in range(0, len(table), 2):
compound = table[n].replace(':', '').replace(' ', '_')
geometry = []
for atom in table[n+1].split('\n'):
geometry.append(Atom(symbol=atom.split()[0], position=atom.split()[1:]))
atoms = Atoms(geometry)
# set the charge and magnetic moment on the heaviest atom (better ideas?)
heaviest = max([a.get_atomic_number() for a in atoms])
heaviest_index = [a.get_atomic_number() for a in atoms].index(heaviest)
charge = 0.0
if abs(charge) > 0.0:
charges = [0.0 for a in atoms]
charges[heaviest_index] = charge
atoms.set_initial_charges(charges)
if compound in [ # see corresponding articles
'Ti(BH4)3', # TM1R2006
'V(NMe2)4', # TM1R2006
'Cu(acac)2', # TM1R2006
'Nb(Cp)(C7H7)_Cs', # TM2R2007
'CdMe_C3v', # TM2R2007
]:
multiplicity = 2.0
else:
multiplicity = 1.0
if multiplicity > 1.0:
magmoms = [0.0 for a in atoms]
magmoms[heaviest_index] = multiplicity - 1
atoms.set_initial_magnetic_moments(magmoms)
geometries.append((compound, atoms))
elif dataformat == 'gaussian':
# remove new lines
table = table.replace('\n', '')
# fix: MeHg(Cl) written as MeHg(CN)
table = table.replace(
'MeHg(CN), qzvp (SDD/def-qzvp for metal)\\\\0,1\\Hg,0.,0.,0.1975732257',
'MeHg(Cl), qzvp (SDD/def-qzvp for metal)\\\\0,1\\Hg,0.,0.,0.1975732257')
# split on compound end marks
table = table.split('\\\@')
# remove empty elements
table = [l.strip() for l in table]
table = [l for l in table if len(l) > 1]
# extract compounds
for n, line in enumerate(table):
# split on gaussian separator '\\'
entries = line.split('\\\\')
compound = entries[2].split(',')[0].split(' ')[0]
# charge and multiplicity from gaussian archive
charge, multiplicity = entries[3].split('\\')[0].split(',')
charge = float(charge)
multiplicity = float(multiplicity)
if compound in ['Au(Me)PMe3']: # in gzmat format!
# check openbabel version (babel >= 2.2 needed)
cmd = popen3('babel -V')[1]
output = cmd.read().strip()
cmd.close()
v1, v2, v3 = output.split()[2].split('.')
v1, v2, v3 = int(v1), int(v2), int(v3)
if not (v1 > 2 or ((v1 == 2) and (v2 >= 2))):
print(compound + ': skipped - version of babel does not support gzmat format')
continue # this one is given in z-matrix format
finame = compound.replace('(', '').replace(')', '') + '.orig'
foname = finame.split('.')[0] + '.xyz'
fi = open(finame, 'w')
fo = open(foname, 'w')
if 1: # how to extract zmat by hand
zmat = ['#'] # must start with gaussian input start
zmat.extend('@') # separated by newline
zmat.extend([compound])
zmat.extend('@') # separated by newline
zmat.extend([str(int(charge)) + ' ' + str(int(multiplicity))])
zmat.extend(entries[3].replace(',', ' ').split('\\')[1:])
zmat.extend('@') # atom and variable definitions separated by newline
zmat.extend(entries[4].split('\\'))
zmat.extend('@') # end with newline
for l in zmat:
fi.write(l.replace('@', '').replace('=', ' ') + '\n')
fi.close()
if 0:
# or use the whole gausian archive entry
entries = ''.join(entries)
fi.write(entries)
# convert gzmat into xyz using openbabel (babel >= 2.2 needed)
cmd = popen3('babel -i gzmat ' + finame + ' -o xyz ' + foname)[2]
error = cmd.read().strip()
cmd.close()
fo.close()
if not (error.find('0 molecules') != -1):
atoms = ase.io.read(foname)
else:
print(compound + ': babel conversion failed')
continue # conversion failed
else:
positions = entries[3].replace(',', ' ').split('\\')[1:]
geometry = []
for k, atom in enumerate(positions):
geometry.append(Atom(symbol=atom.split()[0],
position=[float(p) for p in atom.split()[1:]]))
atoms = Atoms(geometry)
#
# set the charge and magnetic moment on the heaviest atom (better ideas?)
heaviest = max([a.get_atomic_number() for a in atoms])
heaviest_index = [a.get_atomic_number() for a in atoms].index(heaviest)
if abs(charge) > 0.0:
charges = [0.0 for a in atoms]
charges[heaviest_index] = charge
atoms.set_initial_charges(charges)
if multiplicity > 1.0:
magmoms = [0.0 for a in atoms]
magmoms[heaviest_index] = multiplicity - 1
atoms.set_initial_magnetic_moments(magmoms)
geometries.append((compound, atoms))
return geometries
def read_geometries(filename, dir='.'):
txt = os.path.join(dir, filename)
fh = open(txt, 'rb')
table = fh.read()
firstsplit = '(in xyz format):' # TM1R2006 and TM2R2007
dataformat = 'xyz'
if table.find('(Gaussian archive entries):') != -1:
firstsplit = '(Gaussian archive entries):' # TM3R2008
dataformat = 'gaussian'
table = table.split(firstsplit)
table = table[1]
# remove one or two digit numbers (page numbers/numbers of atoms in xyz format)
table = re.sub('\n\d\d\n', '\n', table)
table = re.sub('\n\d\n', '\n', table)
# remove S + two digit numbers (page numbers)
table = re.sub('\nS\d\d\n', '\n', table)
# remove S + one digit (page numbers)
table = re.sub('\nS\d\n', '\n', table)
# remove empty lines
# http://stackoverflow.com/questions/1140958/whats-a-quick-one-liner-to-remove-empty-lines-from-a-python-string
table = os.linesep.join([s for s in table.splitlines() if s])
geometries = []
if dataformat == 'xyz':
# split on new lines
table = table.split('\n')
# mark compound names with ':' tags
for n, line in enumerate(table):
if not (line.find('.') != -1):
# remove method/basis set information
table[n] = table[n].replace(' BP86/qzvp', '')
table[n] = ':' + table[n] + ':'
table = '\n'.join([s for s in table])
# split into compounds
# http://simonwillison.net/2003/Oct/26/reSplit/
# http://stackoverflow.com/questions/647655/python-regex-split-and-special-character
table = re.compile('(:.*:)').split(table)
# remove empty elements
table = [l.strip() for l in table]
table = [l for l in table if len(l) > 1]
# extract compounds
for n in range(0, len(table), 2):
compound = table[n].replace(':', '').replace(' ', '_')
geometry = []
for atom in table[n + 1].split('\n'):
geometry.append(
Atom(symbol=atom.split()[0], position=atom.split()[1:]))
atoms = Atoms(geometry)
# set the charge and magnetic moment on the heaviest atom (better ideas?)
heaviest = max([a.get_atomic_number() for a in atoms])
heaviest_index = [a.get_atomic_number()
for a in atoms].index(heaviest)
charge = 0.0
if abs(charge) > 0.0:
charges = [0.0 for a in atoms]
charges[heaviest_index] = charge
atoms.set_charges(charges)
if compound in [ # see corresponding articles
'Ti(BH4)3', # TM1R2006
'V(NMe2)4', # TM1R2006
'Cu(acac)2', # TM1R2006
'Nb(Cp)(C7H7)_Cs', # TM2R2007
'CdMe_C3v', # TM2R2007
]:
multiplicity = 2.0
else:
multiplicity = 1.0
if multiplicity > 1.0:
magmoms = [0.0 for a in atoms]
magmoms[heaviest_index] = multiplicity - 1
atoms.set_initial_magnetic_moments(magmoms)
geometries.append((compound, atoms))
elif dataformat == 'gaussian':
# remove new lines
table = table.replace('\n', '')
# fix: MeHg(Cl) written as MeHg(CN)
table = table.replace(
'MeHg(CN), qzvp (SDD/def-qzvp for metal)\\\\0,1\\Hg,0.,0.,0.1975732257',
'MeHg(Cl), qzvp (SDD/def-qzvp for metal)\\\\0,1\\Hg,0.,0.,0.1975732257'
)
# split on compound end marks
table = table.split('\\\@')
# remove empty elements
table = [l.strip() for l in table]
table = [l for l in table if len(l) > 1]
# extract compounds
for n, line in enumerate(table):
# split on gaussian separator '\\'
entries = line.split('\\\\')
compound = entries[2].split(',')[0].split(' ')[0]
# charge and multiplicity from gaussian archive
charge, multiplicity = entries[3].split('\\')[0].split(',')
charge = float(charge)
multiplicity = float(multiplicity)
if compound in ['Au(Me)PMe3']: # in gzmat format!
# check openbabel version (babel >= 2.2 needed)
cmd = popen3('babel -V')[1]
output = cmd.read().strip()
cmd.close()
v1, v2, v3 = output.split()[2].split('.')
v1, v2, v3 = int(v1), int(v2), int(v3)
if not (v1 > 2 or ((v1 == 2) and (v2 >= 2))):
print compound + ': skipped - version of babel does not support gzmat format'
continue # this one is given in z-matrix format
finame = compound.replace('(', '').replace(')', '') + '.orig'
foname = finame.split('.')[0] + '.xyz'
fi = open(finame, 'w')
fo = open(foname, 'w')
if 1: # how to extract zmat by hand
zmat = ['#'] # must start with gaussian input start
zmat.extend('@') # separated by newline
zmat.extend([compound])
zmat.extend('@') # separated by newline
zmat.extend(
[str(int(charge)) + ' ' + str(int(multiplicity))])
zmat.extend(entries[3].replace(',', ' ').split('\\')[1:])
zmat.extend(
'@'
) # atom and variable definitions separated by newline
zmat.extend(entries[4].split('\\'))
zmat.extend('@') # end with newline
for l in zmat:
fi.write(l.replace('@', '').replace('=', ' ') + '\n')
fi.close()
if 0:
# or use the whole gausian archive entry
entries = ''.join(entries)
fi.write(entries)
# convert gzmat into xyz using openbabel (babel >= 2.2 needed)
cmd = popen3('babel -i gzmat ' + finame + ' -o xyz ' +
foname)[2]
error = cmd.read().strip()
cmd.close()
fo.close()
if not (error.find('0 molecules') != -1):
atoms = ase.io.read(foname)
else:
print compound + ': babel conversion failed'
continue # conversion failed
else:
positions = entries[3].replace(',', ' ').split('\\')[1:]
geometry = []
for k, atom in enumerate(positions):
geometry.append(
Atom(symbol=atom.split()[0],
position=[float(p) for p in atom.split()[1:]]))
atoms = Atoms(geometry)
#
# set the charge and magnetic moment on the heaviest atom (better ideas?)
heaviest = max([a.get_atomic_number() for a in atoms])
heaviest_index = [a.get_atomic_number()
for a in atoms].index(heaviest)
if abs(charge) > 0.0:
charges = [0.0 for a in atoms]
charges[heaviest_index] = charge
atoms.set_charges(charges)
if multiplicity > 1.0:
magmoms = [0.0 for a in atoms]
magmoms[heaviest_index] = multiplicity - 1
atoms.set_initial_magnetic_moments(magmoms)
geometries.append((compound, atoms))
return geometries