def read_gaussian_log(filename,target_level=None):
'''
xcc,gcc,Fcc and symbols --> returned without dummy atoms
'''
if not os.path.exists(filename): return
# split lines into blocks (in case of Link1)
blocks = split_gaulog_into_gaublocks(filename)
# Get info of each block
data = [get_data_from_gaublock(block) for block in blocks]
# There is nothing to return
if data == []: return [None]*12
# Localize data with hessian matrix
IDX = -1
for idx,data_i in enumerate(data):
Fcc = data_i[7]
if Fcc is not None:
IDX = idx
break
# Return the best set of data (the last with the hessian or the last block)
commands,comment,ch,mtp,symbols,xcc,gcc,Fcc,energies,E_oniom,num_imag,zmat = data[IDX]
# Recalculating xcc from z-matrix (do not trust the orientation read from output)
if zmat is not None:
(lzmat,zmatvals,zmatatoms),symbols = convert_zmat(zmat)
xcc = zmat2xcc(lzmat,zmatvals)
# Correct symbols (just in case)
symbols,atonums = symbols_and_atonums(symbols)
# Remove dummies from xcc, gcc and Fcc!
if xcc is not None: xcc = clean_dummies(symbols,xcc=xcc)[1]
if gcc is not None: gcc = clean_dummies(symbols,gcc=gcc)[1]
if Fcc is not None: Fcc = clean_dummies(symbols,Fcc=Fcc)[1]
symbols = clean_dummies(symbols)
# If user does not ask for level, send one of lowest energy
if target_level is None:
energies.sort()
energy,level = energies[0]
else:
IDX = None
exception = Exc.LevelNotFound()
exception._var = target_level
for idx,(energy,level) in enumerate(energies):
if level.lower() == target_level.lower():
IDX = idx
break
if IDX is None: raise exception
energy, level = energies[IDX]
# oniom?
if E_oniom is not None:
energy = E_oniom
level = "ONIOM"
# Return data
return commands,comment,ch,mtp,symbols,xcc,gcc,Fcc,energy,num_imag,zmat,level
def read_gaussian_log(filename, target_level=None):
if not os.path.exists(filename): return
# split lines into blocks (in case of Link1)
blocks = split_gaulog_into_gaublocks(filename)
# Get info of each block
data = [get_data_from_gaublock(block) for block in blocks]
# There is nothing to return
if data == []: return [None] * 12
# Localize data with hessian matrix
IDX = -1
for idx, data_i in enumerate(data):
Fcc = data_i[7]
if Fcc is not None:
IDX = idx
break
# Return the best set of data (the last with the hessian or the last block)
commands, comment, ch, mtp, symbols, xcc, gcc, Fcc, energies, E_oniom, num_imag, zmat = data[
IDX]
# If user does not ask for level, send one of lowest energy
if target_level is None:
energies.sort()
energy, level = energies[0]
else:
IDX = None
exception = Exc.LevelNotFound()
exception._var = target_level
for idx, (energy, level) in enumerate(energies):
if level.lower() == target_level.lower():
IDX = idx
break
if IDX is None: raise exception
energy, level = energies[IDX]
# oniom?
if E_oniom is not None:
energy = E_oniom
level = "ONIOM"
# Return data
return commands, comment, ch, mtp, symbols, xcc, gcc, Fcc, energy, num_imag, zmat, level