def read_gaussian_out(filename, index=-1, quantity='atoms'):
""""Interface to GaussianReader and returns various quantities"""
energy = 0.0
data = GR(filename)[index]
formula = data['Chemical_formula']
positions = np.array(data['Positions'])
method = data['Method']
version = data['Version']
charge = data['Charge']
multiplicity = data['Multiplicity']
if method.lower()[1:] in allowed_dft_functionals:
method = 'HF'
atoms = Atoms(formula, positions=positions)
for key, value in data.items():
if (key in method):
energy = value
try:
# Re-read in the log file
f = open(filename, 'r')
lines = f.readlines()
f.close()
forces = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
for j in range(len(atoms)):
forces += [[
float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])
]]
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(forces) * convert
except:
forces = None
energy *= ase.units.Hartree # Convert the energy from a.u. to eV
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
if (quantity == 'energy'):
return energy
elif (quantity == 'forces'):
return forces
elif (quantity == 'dipole'):
return np.array(data['Dipole'])
elif (quantity == 'atoms'):
return atoms
elif (quantity == 'version'):
return version
elif (quantity == 'multiplicity'):
return multiplicity
elif (quantity == 'charge'):
return charge
def read_gaussian_out(filename, index=-1, quantity='atoms'):
""""Interface to GaussianReader and returns various quantities"""
energy = 0.0
data = GR(filename)[index]
formula = data['Chemical_formula']
positions = np.array(data['Positions'])
method = data['Method']
version = data['Version']
if method.lower()[1:] in allowed_dft_functionals:
method = 'HF'
atoms = Atoms(formula, positions=positions)
for key, value in data.items():
if (key in method):
energy = value
try:
# Re-read in the log file
f = open(filename, 'r')
lines = f.readlines()
f.close()
forces = list()
charges = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
for j in range(len(atoms)):
forces += [[float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])]]
if ('Mulliken charges:' in line):
for j in range(len(atoms)):
charges += [-float(lines[n+j+2].split()[2])+int(Atoms(str(lines[n+j+2].split()[1])).get_atomic_numbers())]
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(forces) * convert
except:
forces = None
energy *= ase.units.Hartree # Convert the energy from a.u. to eV
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
if (quantity == 'energy'):
return energy
elif (quantity == 'forces'):
return forces
elif (quantity == 'dipole'):
return data['Dipole']
elif (quantity == 'atoms'):
return atoms
elif (quantity == 'version'):
return version
elif (quantity == 'charges'):
return charges
def read_gaussian_out(filename, index=-1, quantity='atoms'):
""""Interface to GaussianReader and returns various quantities"""
energy = 0.0
data = GR(filename)[index]
if isinstance(data, list):
msg = 'Cannot parse multiple images from Gaussian out files at this'
msg += ' time. Please select a single image.'
raise RuntimeError(msg)
atomic_numbers = data['Atomic_numbers']
formula = str()
for number in atomic_numbers:
formula += chemical_symbols[number]
positions = np.array(data['Positions'])
method = data['Method']
version = data['Version']
charge = data['Charge']
multiplicity = data['Multiplicity']
if method.lower()[1:] in allowed_dft_functionals:
method = 'HF'
atoms = Atoms(formula, positions=positions)
for key, value in data.items():
if (key in method):
energy = value
try:
if isinstance(filename, str):
fileobj = open(filename, 'r')
else:
fileobj = filename
# Re-wind the file in case it was previously read.
fileobj.seek(0)
lines = fileobj.readlines()
iforces = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
forces = list()
for j in range(len(atoms)):
forces += [[float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])]]
iforces.append(np.array(forces))
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(iforces) * convert
except:
forces = None
energy *= ase.units.Hartree # Convert the energy from a.u. to eV
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
if (quantity == 'energy'):
return energy
elif (quantity == 'forces'):
return forces[index]
elif (quantity == 'dipole'):
return np.array(data['Dipole'])
elif (quantity == 'atoms'):
return atoms
elif (quantity == 'version'):
return version
elif (quantity == 'multiplicity'):
return multiplicity
elif (quantity == 'charge'):
return charge
def read_gaussian_out(filename, index=-1, quantity='atoms'):
""""Interface to GaussianReader and returns various quantities"""
energy = 0.0
data = GR(filename)[index]
if isinstance(data, list):
msg = 'Cannot parse multiple images from Gaussian out files at this'
msg += ' time. Please select a single image.'
raise RuntimeError(msg)
atomic_numbers = data['Atomic_numbers']
formula = str()
for number in atomic_numbers:
formula += chemical_symbols[number]
positions = np.array(data['Positions'])
method = data['Method']
version = data['Version']
charge = data['Charge']
multiplicity = data['Multiplicity']
if method.lower()[1:] in allowed_dft_functionals:
method = 'HF'
atoms = Atoms(formula, positions=positions)
for key, value in data.items():
if (key in method):
energy = value
try:
if isinstance(filename, basestring):
fileobj = open(filename, 'r')
else:
fileobj = filename
# Re-wind the file in case it was previously read.
fileobj.seek(0)
lines = fileobj.readlines()
iforces = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
forces = list()
for j in range(len(atoms)):
forces += [[
float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])
]]
iforces.append(np.array(forces))
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(iforces) * convert
except:
forces = None
energy *= ase.units.Hartree # Convert the energy from a.u. to eV
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
if (quantity == 'energy'):
return energy
elif (quantity == 'forces'):
return forces[index]
elif (quantity == 'dipole'):
return np.array(data['Dipole'])
elif (quantity == 'atoms'):
return atoms
elif (quantity == 'version'):
return version
elif (quantity == 'multiplicity'):
return multiplicity
elif (quantity == 'charge'):
return charge
def read_gaussian_out(filename, index=-1, quantity='atoms'):
"""
Interface to GaussianReader and returns various quantities.
No support for multiple images in one file!
- quantity = 'structures' -> all structures from the file
- quantity = 'atoms' -> structure from the archive section
- quantity = 'energy' -> from the archive section
- quantity = 'force' -> last entry from the file
- quantity = 'dipole' -> from the archive section
- quantity = 'version' -> from the archive section
- quantity = 'multiplicity' -> from the archive section
- quantity = 'charge' -> from the archive section
"""
energy = 0.0
tmpGR = GR(filename, read_structures=bool(quantity == 'structures'))
if quantity == 'structures':
structures = tmpGR.get_structures()
data = tmpGR[index]
#fix: io.formats passes a slice as index, resulting in data beeing a list
if isinstance(data, list) and len(data) > 1:
msg = 'Cannot parse multiple images from Gaussian out files at this'
msg += ' time. Please select a single image.'
raise RuntimeError(msg)
elif isinstance(data, list):
data = data[-1]
atomic_numbers = data['Atomic_numbers']
formula = str()
for number in atomic_numbers:
formula += chemical_symbols[number]
positions = np.array(data['Positions'])
method = data['Method']
version = data['Version']
charge = data['Charge']
multiplicity = data['Multiplicity']
if method.lower()[1:] in allowed_dft_functionals:
method = 'HF'
if method.lower()[1:] in semi_empirical_methods:
method = 'HF'
atoms = Atoms(formula, positions=positions)
for key, value in data.items():
if (key in method):
energy = value
try:
if isinstance(filename, basestring):
fileobj = open(filename, 'r')
else:
fileobj = filename
# Re-wind the file in case it was previously read.
fileobj.seek(0)
lines = fileobj.readlines()
iforces = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
forces = list()
for j in range(len(atoms)):
forces += [[
float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])
]]
iforces.append(np.array(forces))
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(iforces) * convert
except:
forces = None
energy *= ase.units.Hartree # Convert the energy from a.u. to eV
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
if (quantity == 'energy'):
return energy
elif (quantity == 'dipole'):
return np.array(data['Dipole'])
elif (quantity == 'atoms'):
return atoms
elif (quantity == 'version'):
return version
elif (quantity == 'multiplicity'):
return multiplicity
elif (quantity == 'charge'):
return charge
elif (quantity == 'structures'):
return structures
# forces not included in all calculations
try:
if (quantity == 'forces'):
return forces[index]
except:
pass
def read_gaussian_out(filename, index=-1, quantity='atoms'):
""""Interface to GaussianReader and returns various quantities"""
energy = 0.0
all_data = GR(filename)
if len(all_data) == 0:
# no archive was found, TODO use other reader methods
if isinstance(filename, basestring):
fileobj = open(filename, 'r')
else:
fileobj = filename
# Re-wind the file in case it was previously read.
fileobj.seek(0)
lines = fileobj.readlines()
#read the positions:
positions = []
for ind, line in enumerate(reversed(lines)):
if re.search('Input orientation:', line) != None:
j = 0
while 1:
if '---------' in lines[-ind + 4 + j]:
break
else:
pos = np.array(lines[-ind + 4 +
j].split()[3:6]).astype(float)
positions.append(pos)
j += 1
break
natom = len(positions)
#read the forces
iforces = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
forces = list()
for j in range(natom):
forces += [[
float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])
]]
iforces.append(np.array(forces))
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(iforces) * convert
#read the energy
for line in reversed(lines):
if re.search('SCF Done', line) != None:
energy = float(line.split()[4])
break
#todo: read other quantities (dipole, multiplicity, atoms, version, charge)
if (quantity == 'energy'):
return energy
elif (quantity == 'positions'):
return positions
elif (quantity == 'forces'):
return forces[index]
elif (quantity == 'dipole'):
#todo
return []
elif (quantity == 'multiplicity'):
#todo
return 1
else:
data = GR(filename)[index]
if isinstance(data, list):
msg = 'Cannot parse multiple images from Gaussian out files at this'
msg += ' time. Please select a single image.'
raise RuntimeError(msg)
atomic_numbers = data['Atomic_numbers']
formula = str()
for number in atomic_numbers:
formula += chemical_symbols[number]
positions = np.array(data['Positions'])
method = data['Method']
version = data['Version']
charge = data['Charge']
multiplicity = data['Multiplicity']
if method.lower()[1:] in allowed_dft_functionals:
method = 'HF'
atoms = Atoms(formula, positions=positions)
for key, value in data.items():
if (key in method):
energy = value
try:
if isinstance(filename, basestring):
fileobj = open(filename, 'r')
else:
fileobj = filename
# Re-wind the file in case it was previously read.
fileobj.seek(0)
lines = fileobj.readlines()
iforces = list()
for n, line in enumerate(lines):
if ('Forces (Hartrees/Bohr)' in line):
forces = list()
for j in range(len(atoms)):
forces += [[
float(lines[n + j + 3].split()[2]),
float(lines[n + j + 3].split()[3]),
float(lines[n + j + 3].split()[4])
]]
iforces.append(np.array(forces))
if ('SCF Done' in line):
energy = float(line.split()[4])
convert = ase.units.Hartree / ase.units.Bohr
forces = np.array(iforces) * convert
except:
forces = None
energy *= ase.units.Hartree # Convert the energy from a.u. to eV
calc = SinglePointCalculator(atoms, energy=energy, forces=forces)
atoms.set_calculator(calc)
if (quantity == 'energy'):
return energy
elif (quantity == 'positions'):
return positions
elif (quantity == 'forces'):
return forces[index]
elif (quantity == 'dipole'):
if 'Dipole' in data:
return np.array(data['Dipole'])
else:
#todo
return []
elif (quantity == 'atoms'):
return atoms
elif (quantity == 'version'):
return version
elif (quantity == 'multiplicity'):
return multiplicity
elif (quantity == 'charge'):
return charge
