def __init__(self, qmout=None, **kwargs):
GaussianBasisOutput.__init__(self, qmout, **kwargs)
if qmout:
self.program = 'nwchem'
outfile = open(qmout, 'r')
data = outfile.readlines()
outfile.close()
Et = filter(lambda x: 'Total' in x and 'energy' in x, data)
try:
self.Et = float(Et[-1].split( )[-1])
except:
self.Et = np.nan
try:
_Et = filter(lambda x: 'total' in x and 'energy' in x, data)
_Et = float(_Et[-1].split( )[-1])
self.Et = _Et
except:
pass
# necessary for opening *.movecs file
n_basis = filter(lambda x: 'functions' in x, data)
if ':' in n_basis[-1]:
try:
self.n_basis = int(n_basis[-1].split(':')[1])
except:
self.n_basis = np.nan
elif '=' in n_basis[-1]:
try:
self.n_basis = int(n_basis[-1].split('=')[1])
except:
self.n_basis = np.nan
nuclear = filter(lambda x: 'repulsion' in x, data)[-1]
self.nuclear_repulsion = float(nuclear.split(' ')[-1])
def getBasis():
######################################
# extract basis function information #
######################################
basis_dict = {"S":0, "P":1, "D":2, "F":3, "G":4, "H":5}
basis_P = re.compile(r" *[0-9]+ [A-Z] [0-9]\.[0-9]{8}")
batom_P = re.compile(r"^ [0-9A-Za-z\-_\.]+ *\([A-Z][a-z]*\)")
bname_P = re.compile(r"\((.*)\)")
coord_P = re.compile(r"^ [0-9A-Za-z\.\-_]+ +[- ][0-9\.]{9,}")
basisStr = filter(basis_P.match, data)
batomStr = filter(batom_P.match, data)
coordStr = filter(coord_P.match, data)
# change 'Sulphur' to 'Sulfur' for NWChem format
# 'Sulphur' 'Sulfur'
def atomNameConv(old, new):
_matched = filter(lambda x: old in x, batomStr)
if _matched:
_matched = _matched[0]
_s = batomStr.index(_matched)
batomStr[_s] = re.sub(old, new, batomStr[_s])
_s = data.index(_matched)
data[_s] = re.sub(old, new, data[_s])
atomNameConv('Sulphur', 'Sulfur')
atomNameConv('Aluminium', 'Aluminum')
_exponents = [float(filter(None, s.split(' '))\
[2]) for s in basisStr]
_coefficients = [float(filter(None, s.split(' '))\
[3]) for s in basisStr]
_N = [int(filter(None, s.split(' '))[0])\
for s in basisStr]
_type = [filter(None, s.split(' '))[1]\
for s in basisStr]
_bfnInd = [data.index(batom) for batom in batomStr]
_bfnEndPtn = re.compile(r" Summary of \"")
_bfnEndStr = filter(_bfnEndPtn.match, data)[0]
_bfnInd.append(data.index(_bfnEndStr))
_ao_keys = [0]
for ind in range(len(_bfnInd)-1):
_key = _ao_keys[-1]
for i in range(_bfnInd[ind]+4, _bfnInd[ind+1]):
if len(data[i]) > 1:
_key = _key + 1
_ao_keys.append(_key)
_atoms = [getattr(pt, bname_P.match(
filter(None, s.split(' '))[1]).group(1).lower()).symbol\
for s in batomStr]
self.type_list = [re.split(r'[\._]',
filter(None, s.split(' '))[0])[0].title()\
for s in coordStr]
self.type_list_unique = list(
collections.OrderedDict.fromkeys(self.type_list)
)
self.R = np.array([filter(None, s.split(' '))[1:4]\
for s in coordStr]).astype(float)
self.N = len(self.R)
self.Z = [qtk.n2Z(e) for e in self.type_list]
self.R_bohr = 1.889725989 * self.R
ZR = []
for i in range(self.N):
vec = [self.Z[i]]
vec.extend(self.R[i])
ZR.append(vec)
self.molecule = qtk.Molecule()
self.molecule.build(ZR)
_N.append(0)
self.basis = []
for i in range(len(self.type_list)):
e = self.type_list[i]
center = self.R_bohr[i]
ind = self.type_list_unique.index(e)
bfn_base = {}
bfn_base['atom'] = e
bfn_base['center'] = center
bfn_base['index'] = i
exp = []
cef = []
for g in range(_ao_keys[ind], _ao_keys[ind+1]):
exp.append(_exponents[g])
cef.append(_coefficients[g])
if _N[g] != _N[g+1] or g+1 >= _ao_keys[ind+1]:
bfn = copy.deepcopy(bfn_base)
bfn['exponents'] = copy.deepcopy(exp)
bfn['coefficients'] = copy.deepcopy(cef)
if _type[g] in basis_dict:
_bfnList = self.basisList(basis_dict[_type[g]])
for bStr in _bfnList:
bfn['type'] = _type[g].lower() + bStr
self.basis.append(copy.deepcopy(bfn))
exp = []
cef = []
try:
getBasis()
except AttributeError as err:
qtk.warning('failed to get basis information with error: %s.'\
% err + ' Weird atom names?')
movecs = os.path.join(self.path, self.stem) + '.modat'
if os.path.exists(movecs):
self.getMO(movecs)
def __init__(self, qmout=None, **kwargs):
GaussianBasisOutput.__init__(self, qmout, **kwargs)
if qmout:
self.program = 'nwchem'
outfile = open(qmout, 'r')
data = outfile.readlines()
outfile.close()
Et = filter(lambda x: 'Total' in x and 'energy' in x, data)
try:
self.Et = float(Et[-1].split()[-1])
except:
self.Et = np.nan
try:
_Et = filter(lambda x: 'total' in x and 'energy' in x, data)
_Et = float(_Et[-1].split()[-1])
self.Et = _Et
except:
pass
# necessary for opening *.movecs file
n_basis = filter(lambda x: 'functions' in x, data)
if ':' in n_basis[-1]:
try:
self.n_basis = int(n_basis[-1].split(':')[1])
except:
self.n_basis = np.nan
elif '=' in n_basis[-1]:
try:
self.n_basis = int(n_basis[-1].split('=')[1])
except:
self.n_basis = np.nan
nuclear = filter(lambda x: 'repulsion' in x, data)[-1]
self.nuclear_repulsion = float(nuclear.split(' ')[-1])
def getBasis():
######################################
# extract basis function information #
######################################
basis_dict = {"S": 0, "P": 1, "D": 2, "F": 3, "G": 4, "H": 5}
basis_P = re.compile(r" *[0-9]+ [A-Z] [0-9]\.[0-9]{8}")
batom_P = re.compile(r"^ [0-9A-Za-z\-_\.]+ *\([A-Z][a-z]*\)")
bname_P = re.compile(r"\((.*)\)")
coord_P = re.compile(r"^ [0-9A-Za-z\.\-_]+ +[- ][0-9\.]{9,}")
basisStr = filter(basis_P.match, data)
batomStr = filter(batom_P.match, data)
coordStr = filter(coord_P.match, data)
# change 'Sulphur' to 'Sulfur' for NWChem format
# 'Sulphur' 'Sulfur'
def atomNameConv(old, new):
_matched = filter(lambda x: old in x, batomStr)
if _matched:
_matched = _matched[0]
_s = batomStr.index(_matched)
batomStr[_s] = re.sub(old, new, batomStr[_s])
_s = data.index(_matched)
data[_s] = re.sub(old, new, data[_s])
atomNameConv('Sulphur', 'Sulfur')
atomNameConv('Aluminium', 'Aluminum')
_exponents = [float(filter(None, s.split(' '))\
[2]) for s in basisStr]
_coefficients = [float(filter(None, s.split(' '))\
[3]) for s in basisStr]
_N = [int(filter(None, s.split(' '))[0])\
for s in basisStr]
_type = [filter(None, s.split(' '))[1]\
for s in basisStr]
_bfnInd = [data.index(batom) for batom in batomStr]
_bfnEndPtn = re.compile(r" Summary of \"")
_bfnEndStr = filter(_bfnEndPtn.match, data)[0]
_bfnInd.append(data.index(_bfnEndStr))
_ao_keys = [0]
for ind in range(len(_bfnInd) - 1):
_key = _ao_keys[-1]
for i in range(_bfnInd[ind] + 4, _bfnInd[ind + 1]):
if len(data[i]) > 1:
_key = _key + 1
_ao_keys.append(_key)
_atoms = [getattr(pt, bname_P.match(
filter(None, s.split(' '))[1]).group(1).lower()).symbol\
for s in batomStr]
self.type_list = [re.split(r'[\._]',
filter(None, s.split(' '))[0])[0].title()\
for s in coordStr]
self.type_list_unique = list(
collections.OrderedDict.fromkeys(self.type_list))
self.R = np.array([filter(None, s.split(' '))[1:4]\
for s in coordStr]).astype(float)
self.N = len(self.R)
self.Z = [qtk.n2Z(e) for e in self.type_list]
self.R_bohr = 1.889725989 * self.R
ZR = []
for i in range(self.N):
vec = [self.Z[i]]
vec.extend(self.R[i])
ZR.append(vec)
self.molecule = qtk.Molecule()
self.molecule.build(ZR)
_N.append(0)
self.basis = []
for i in range(len(self.type_list)):
e = self.type_list[i]
center = self.R_bohr[i]
ind = self.type_list_unique.index(e)
bfn_base = {}
bfn_base['atom'] = e
bfn_base['center'] = center
bfn_base['index'] = i
exp = []
cef = []
for g in range(_ao_keys[ind], _ao_keys[ind + 1]):
exp.append(_exponents[g])
cef.append(_coefficients[g])
if _N[g] != _N[g + 1] or g + 1 >= _ao_keys[ind + 1]:
bfn = copy.deepcopy(bfn_base)
bfn['exponents'] = copy.deepcopy(exp)
bfn['coefficients'] = copy.deepcopy(cef)
if _type[g] in basis_dict:
_bfnList = self.basisList(basis_dict[_type[g]])
for bStr in _bfnList:
bfn['type'] = _type[g].lower() + bStr
self.basis.append(copy.deepcopy(bfn))
exp = []
cef = []
try:
getBasis()
except AttributeError as err:
qtk.warning('failed to get basis information with error: %s.'\
% err + ' Weird atom names?')
movecs = os.path.join(self.path, self.stem) + '.modat'
if os.path.exists(movecs):
self.getMO(movecs)
def __init__(self, qmout=None, **kwargs):
GaussianBasisOutput.__init__(self, qmout, **kwargs)
if qmout:
outfile = open(qmout)
data = outfile.readlines()
pattern = re.compile(" *R *M *S *D *=")
try:
report = filter(lambda x: "\\" in x, data)
except Exception as e:
qtk.exit("error when access final report with message %s" %
str(e))
final_str = ''.join(report)
final_str = final_str.replace('\n', '')
final_list = final_str.split('\\')
try:
rmsd = filter(pattern.match, final_list)[0]
except Exception as e:
qtk.exit("something wrong when accessing final energy" +\
" with error message: %s" % str(e))
ind = final_list.index(rmsd) - 1
Et_str = final_list[ind]
term = Et_str.split('=')[0].replace(' ', '')
E_list = [
'HF', 'CCSD', 'CCSD(T)', 'MP4SDQ', 'MP4DQ'
'MP4D', 'MP3', 'MP2', 'HF'
]
while term not in E_list:
ind = ind - 1
Et_str = final_list[ind]
term = Et_str.split('=')[0].replace(' ', '')
self.Et = float(Et_str.split('=')[1].replace(' ', ''))
self.detail = final_list
EJStr = filter(lambda x: 'EJ=' in x, data)
if len(EJStr) > 0:
EJStr = EJStr[-1]
EJind = data.index(EJStr)
EJStr = data[EJind].replace(' ', '')
EComponents = filter(None, EJStr.split('E'))
tags_dict = {
'T': 'Ekin',
'V': 'Eext',
'J': 'Eee',
'K': 'Ex',
'Nuc': 'Enn',
}
for EStr in EComponents:
tag, E = EStr.split('=')
try:
self.energies[tags_dict[tag]] = float(E)
except Exception as e:
qtk.warning("FORTRAN float overflow " + \
"when extracting energy components for " +\
qmout + " with error message %s" % str(e))
self.energies[tags_dict[tag]] = np.nan
crdStr = filter(lambda x: 'Angstroms' in x, data)[-1]
ind = len(data) - data[::-1].index(crdStr) + 2
ZR = []
while True:
if not data[ind].startswith(' ---'):
crdData = [
float(c) for c in filter(None, data[ind].split(' '))
]
crd = [crdData[1]]
crd.extend(crdData[3:])
ZR.append(crd)
ind = ind + 1
else:
break
self.molecule = qtk.Molecule()
self.molecule.build(ZR)
self.nuclear_repulsion = self.molecule.nuclear_repulsion()
force = []
fStr_list = filter(lambda x: 'Forces (Hartrees' in x, data)
if len(fStr_list) > 0:
fStr = fStr_list[-1]
ind = len(data) - data[::-1].index(fStr) + 2
for i in range(self.molecule.N):
fLst = filter(None, data[ind + i].split(' '))[2:]
force.append([float(s) for s in fLst])
self.force = np.array(force)
else:
self.force = np.nan
dipole = []
uStr_list = filter(lambda x: 'Debye)' in x, data)
if len(uStr_list) > 0:
uStr = uStr_list[-1]
ind = len(data) - data[::-1].index(uStr)
dipoleStr = filter(None, data[ind].split(' '))
for i in [1, 3, 5]:
dipole.append(float(dipoleStr[i]))
self.dipole = np.array(dipole)
else:
self.dipole = np.nan
qp = []
qStr_list = filter(lambda x: ' Quadrupole moment' in x, data)
if len(qStr_list) > 0:
qStr = qStr_list[-1]
ind = len(data) - data[::-1].index(qStr)
for i in range(2):
tmp = dipoleStr = filter(None, data[ind + i].split(' '))
for j in [1, 3, 5]:
qp.append(float(tmp[j]))
xx, yy, zz, xy, xz, yz = qp
self.quadrupole = np.array([
[xx, xy, xz],
[xy, yy, yz],
[xz, yz, zz],
])
else:
self.quadrupole = np.nan
read_fchk = True
if 'read_fchk' in kwargs:
read_fchk = kwargs['read_fchk']
if read_fchk:
fchk = os.path.join(self.path, self.stem) + ".fchk"
if os.path.exists(fchk):
if 'debug' in kwargs and kwargs['debug']:
self.getMO(fchk)
else:
try:
self.getMO(fchk)
except Exception as e:
qtk.warning("something wrong while loading fchk file"+\
" with error message: %s" % str(e))
def __init__(self, qmout=None, **kwargs):
GaussianBasisOutput.__init__(self, qmout, **kwargs)
if qmout:
outfile = open(qmout)
data = outfile.readlines()
pattern = re.compile(" *R *M *S *D *=")
try:
report = filter(lambda x: "\\" in x, data)
except Exception as e:
qtk.exit("error when access final report with message %s" % str(e))
final_str = ''.join(report)
final_str = final_str.replace('\n', '')
final_list = final_str.split('\\')
try:
rmsd = filter(pattern.match, final_list)[0]
except Exception as e:
qtk.exit("something wrong when accessing final energy" +\
" with error message: %s" % str(e))
ind = final_list.index(rmsd) - 1
Et_str = final_list[ind]
term = Et_str.split('=')[0].replace(' ', '')
E_list = ['HF', 'CCSD', 'CCSD(T)', 'MP4SDQ', 'MP4DQ'
'MP4D', 'MP3', 'MP2', 'HF']
while term not in E_list:
ind = ind - 1
Et_str = final_list[ind]
term = Et_str.split('=')[0].replace(' ', '')
self.Et = float(Et_str.split('=')[1].replace(' ',''))
self.detail = final_list
EJStr = filter(lambda x: 'EJ=' in x, data)
if len(EJStr) > 0:
EJStr = EJStr[-1]
EJind = data.index(EJStr)
EJStr = data[EJind].replace(' ', '')
EComponents = filter(None, EJStr.split('E'))
tags_dict = {
'T':'Ekin',
'V':'Eext',
'J':'Eee',
'K':'Ex',
'Nuc':'Enn',
}
for EStr in EComponents:
tag, E = EStr.split('=')
try:
self.energies[tags_dict[tag]] = float(E)
except Exception as e:
qtk.warning("FORTRAN float overflow " + \
"when extracting energy components for " +\
qmout + " with error message %s" % str(e))
self.energies[tags_dict[tag]] = np.nan
crdStr = filter(lambda x: 'Angstroms' in x, data)[-1]
ind = len(data) - data[::-1].index(crdStr) + 2
ZR = []
while True:
if not data[ind].startswith(' ---'):
crdData = [float(c)
for c in filter(None, data[ind].split(' '))]
crd = [crdData[1]]
crd.extend(crdData[3:])
ZR.append(crd)
ind = ind + 1
else:
break
self.molecule = qtk.Molecule()
self.molecule.build(ZR)
self.nuclear_repulsion = self.molecule.nuclear_repulsion()
force = []
fStr_list = filter(lambda x: 'Forces (Hartrees' in x, data)
if len(fStr_list) > 0:
fStr = fStr_list[-1]
ind = len(data) - data[::-1].index(fStr) + 2
for i in range(self.molecule.N):
fLst = filter(None, data[ind+i].split(' '))[2:]
force.append([float(s) for s in fLst])
self.force = np.array(force)
else:
self.force = np.nan
dipole = []
uStr_list = filter(lambda x: 'Debye)' in x, data)
if len(uStr_list) > 0:
uStr = uStr_list[-1]
ind = len(data) - data[::-1].index(uStr)
dipoleStr = filter(None, data[ind].split(' '))
for i in [1,3,5]:
dipole.append(float(dipoleStr[i]))
self.dipole = np.array(dipole)
else:
self.dipole = np.nan
qp = []
qStr_list = filter(lambda x: ' Quadrupole moment' in x, data)
if len(qStr_list) > 0:
qStr = qStr_list[-1]
ind = len(data) - data[::-1].index(qStr)
for i in range(2):
tmp = dipoleStr = filter(None, data[ind+i].split(' '))
for j in [1,3,5]:
qp.append(float(tmp[j]))
xx, yy, zz, xy, xz, yz = qp
self.quadrupole = np.array([
[xx, xy, xz],
[xy, yy, yz],
[xz, yz, zz],
])
else:
self.quadrupole = np.nan
read_fchk = True
if 'read_fchk' in kwargs:
read_fchk = kwargs['read_fchk']
if read_fchk:
fchk = os.path.join(self.path, self.stem) + ".fchk"
if os.path.exists(fchk):
if 'debug' in kwargs and kwargs['debug']:
self.getMO(fchk)
else:
try:
self.getMO(fchk)
except Exception as e:
qtk.warning("something wrong while loading fchk file"+\
" with error message: %s" % str(e))
