def get_electronic_zpe(filepath):
"""
:return: float elec_zpe (Hartrees/atom) if found.
False if nothing found
"""
return get_descriptor(filepath,
r'Sum of electronic and zero-point Energies=[ ]*(-?\d+\.?\d+)',
"electronic energy")
def get_zpe(filepath):
"""
:return: float zero point correction (Hartrees/atom) if found.
False if nothing found
"""
return get_descriptor(filepath,
r'Zero-point correction=[ ]*(-?\d+\.?\d+)',
"Zero point correction")
def get_enthalpy(filepath):
"""
:return: float Enthalpy in Hartree/ atom if found.
Prints ('No enthalpy found') and returns False if none found.
"""
return get_descriptor(filepath,
r'Sum of electronic and thermal Enthalpies=[ ]*(-?\d+\.?\d+)',
"enthalpy")
def get_free_energy(filepath):
"""
:return: float free energy in Hartree/ atom if found.
Prints ('No free energy found') and returns False if none found.
"""
return get_descriptor(filepath,
r'Sum of electronic and thermal Free Energies=[ ]*(-?\d+\.?\d+)',
"free energy")
def get_A_P_A_bond_angles(filename, atomids, phosid):
"""
"""
return [
get_descriptor(
filename, # A1 P A2
r' ! A.*A\({},{},{}\)\s*?(.?..\.....).*?'.format(
atomids[0], phosid, atomids[1]),
"A{}-P-A{} bond length".format(atomids[0], atomids[1])),
get_descriptor(
filename, # A1 P A3
r' ! A.*A\({},{},{}\)\s*?(.?..\.....).*?'.format(
atomids[0], phosid, atomids[2]),
"A{}-P-A{} bond length".format(atomids[0], atomids[2])),
get_descriptor(
filename, # A2 P A3
r' ! A.*A\({},{},{}\)\s*?(.?..\.....).*?'.format(
atomids[1], phosid, atomids[2]),
"A{}-P-A{} bond length".format(atomids[1], atomids[2]))
]
def get_A_P_bond_lengths(filename, atomids, phosid):
"""
atom id's is the array of strings containing the gaussian atom ID (find using helper_function
get_phosphine_carbon_numbers)
Assumes that phosphorus is the first atom
:return: arrray of float bond lengths in Angstroms of the central P to
surrounding Atom
"""
return [
get_descriptor(
filename,
r' ! R.*R\({},{}\)\s*?(.\.....).*?'.format(phosid, atomids[0]),
"P-A{} bond length".format(atomids[0])),
get_descriptor(
filename,
r' ! R.*R\({},{}\)\s*?(.\.....).*?'.format(phosid, atomids[1]),
"P-A{} bond length".format(atomids[1])),
get_descriptor(
filename,
r' ! R.*R\({},{}\)\s*?(.\.....).*?'.format(phosid, atomids[2]),
"P-A{} bond length".format(atomids[2]))
]
def get_APT_charges(filename, atomids, phosid):
"""
Be sure to truncate file with both truncate functions before entry,
as desired APT charges are listed first AFTER optimization
"""
return [
get_descriptor(
filename, # P
r' {} P\s*?(.?.\.......)\n'.format(phosid),
"P{} APT charge".format(phosid)),
get_descriptor(
filename, # A1
r'\s*?{} [A-Z][a-z]?\s*?(.?.\.......)\n'.format(atomids[0]),
"C{} APT charge".format(atomids[0])),
get_descriptor(
filename, # A2
r'\s*?{} [A-Z][a-z]?\s*?(.?.\.......)\n'.format(atomids[1]),
"C{} APT charge".format(atomids[1])),
get_descriptor(
filename, # A3
r'\s*?{} [A-Z][a-z]?\s*?(.?.\.......)\n'.format(atomids[2]),
"C{} APT charge".format(atomids[2]))
]
def get_mulliken_charges(filename, atomids, phosid):
"""
Be sure to truncate file before entry, as desired mulliken charges are listed first AFTER optimization
"""
#print(r'\s*?{}\s*?C\s*?(.?.\.......)\s*?'.format(atomids[2]))
return [
get_descriptor(
filename, # P
r' {} P\s*?(.?.\.......)\n'.format(phosid),
"P{} mulliken charge".format(phosid)),
get_descriptor(
filename, # A1
r'\s*?{} [A-Z][a-z]?\s*?(.?.\.......)\n'.format(atomids[0]),
"A{} mulliken charge".format(atomids[0])),
get_descriptor(
filename, #A2
r'\s*?{} [A-Z][a-z]?\s*?(.?.\.......)\n'.format(atomids[1]),
"A{} mulliken charge".format(atomids[1])),
get_descriptor(
filename, # A3
r'\s*?{} [A-Z][a-z]?\s*?(.?.\.......)\n'.format(atomids[2]),
"A{} mulliken charge".format(atomids[2]))
]