Add pseudopotentials from Gaussian output
This commit is contained in:
parent
427514e36e
commit
2d33329c1c
|
|
@ -1,7 +1,7 @@
|
|||
#!/usr/bin/env python3
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# resultsFile is a library which allows to read output files of quantum
|
||||
# chemistry codes and write input files.
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
# Copyright (C) 2007 Anthony SCEMAMA
|
||||
#
|
||||
# This program is free software; you can redistribute it and/or modify
|
||||
# it under the terms of the GNU General Public License as published by
|
||||
|
|
@ -18,11 +18,11 @@
|
|||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
|
||||
#
|
||||
# Anthony Scemama
|
||||
# LCPQ - IRSAMC
|
||||
# LCPQ - IRSAMC
|
||||
# Universite Paul Sabatier
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
# 118, route de Narbonne
|
||||
# 31062 Toulouse Cedex 4
|
||||
# scemama@irsamc.ups-tlse.fr
|
||||
|
||||
|
||||
|
||||
|
|
@ -35,7 +35,7 @@ import re
|
|||
gaussianFile_defined_vars = [ "date", "version", "machine", "memory", "disk",\
|
||||
"cpu_time", "author", "title", "units", "methods", "options", \
|
||||
"spin_restrict", "conv_threshs", "energies", \
|
||||
"ee_pot_energies", \
|
||||
"ee_pot_energies", "pseudo", \
|
||||
"Ne_pot_energies", "pot_energies", \
|
||||
"kin_energies", "point_group", "num_elec", \
|
||||
"charge", "multiplicity","nuclear_energy","dipole","geometry",\
|
||||
|
|
@ -103,7 +103,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
for x in dip:
|
||||
self._dipole.append(float(x))
|
||||
return self._dipole
|
||||
|
||||
|
||||
def get_multiplicity(self):
|
||||
if self._multiplicity is None:
|
||||
self._multiplicity = int(self.options[3][0].split(',')[1])
|
||||
|
|
@ -229,7 +229,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
def get_spin_restrict(self):
|
||||
if self._spin_restrict is None:
|
||||
method = self.methods[0]
|
||||
self._spin_restrict = True
|
||||
self._spin_restrict = True
|
||||
if method.startswith("U"): self._spin_restrict = False
|
||||
return self._spin_restrict
|
||||
|
||||
|
|
@ -266,7 +266,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
|
||||
def get_ee_pot_energies(self):
|
||||
if self._ee_pot_energies is None:
|
||||
self._ee_pot_energies = []
|
||||
self._ee_pot_energies = []
|
||||
for i,e in enumerate(self.kin_energies):
|
||||
self._ee_pot_energies.append(self.energies[i]\
|
||||
-self.nuclear_energy\
|
||||
|
|
@ -299,7 +299,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
def get_point_group(self):
|
||||
if self._point_group is None:
|
||||
self._point_group = self.options[4][-1].split()[0].split('=')[1]
|
||||
return self._point_group
|
||||
return self._point_group
|
||||
|
||||
def get_geometry(self):
|
||||
if self._geometry is None:
|
||||
|
|
@ -323,7 +323,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
temp.charge = float(buffer[1])
|
||||
temp.coord = (float(buffer[3]), float(buffer[4]), float(buffer[5]))
|
||||
self._geometry.append(temp)
|
||||
pos += 1
|
||||
pos += 1
|
||||
for i,line in enumerate(self.options[3][1:]):
|
||||
buffer = line.split(',')
|
||||
self._geometry[i].name = buffer[0]
|
||||
|
|
@ -454,21 +454,21 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
elif basis[k][0] == "G":
|
||||
if not Polar:
|
||||
mylist = [ "ZZZZ", "ZZZY", "YYZZ", "YYYZ", "YYYY", "ZZZX",
|
||||
"ZZXY", "YYXZ","YYYX", "XXZZ", "XXYZ",
|
||||
"ZZXY", "YYXZ","YYYX", "XXZZ", "XXYZ",
|
||||
"XXYY", "XXXZ","XXXY", "XXXX" ]
|
||||
else:
|
||||
mylist = [ "G0", "G1+", "G1-", "G2+", "G2-", "G3+", "G3-",
|
||||
"G4+", "G4-" ]
|
||||
elif basis[k][0] == "H":
|
||||
if not Polar:
|
||||
mylist = [ "ZZZZZ", "YZZZZ", "YYZZZ", "YYYZZ", "YYYYZ", "YYYYY",
|
||||
mylist = [ "ZZZZZ", "YZZZZ", "YYZZZ", "YYYZZ", "YYYYZ", "YYYYY",
|
||||
"XZZZZ", "XYZZZ", "XYYZZ", "XYYYZ", "XYYYY", "XXZZZ", "XXYZZ", "XXYYZ",
|
||||
"XXYYY", "XXXZZ", "XXXYZ", "XXXYY", "XXXXZ", "XXXXY", "XXXXX" ]
|
||||
"XXYYY", "XXXZZ", "XXXYZ", "XXXYY", "XXXXZ", "XXXXY", "XXXXX" ]
|
||||
else:
|
||||
mylist = [ "H0", "H1+", "H1-", "H2+", "H2-", "H3+", "H3-",
|
||||
"H4+", "H4-", "H5+", "H5-" ]
|
||||
elif basis[k][0] == "I":
|
||||
if not Polar:
|
||||
if not Polar:
|
||||
mylist = [ "ZZZZZZ", "YZZZZZ", "YYZZZZ", "YYYZZZ",
|
||||
"YYYYZZ", "YYYYYZ", "YYYYYY", "XZZZZZ", "XYZZZZ", "XYYZZZ",
|
||||
"XYYYZZ", "XYYYYZ", "XYYYYY", "XXZZZZ", "XXYZZZ", "XXYYZZ",
|
||||
|
|
@ -510,7 +510,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
def get_mo_types(self):
|
||||
if self._mo_types is None:
|
||||
self.get_mo_sets()
|
||||
return self._mo_types
|
||||
return self._mo_types
|
||||
|
||||
def get_mo_sets(self):
|
||||
if self._mo_sets is None:
|
||||
|
|
@ -585,7 +585,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
line = line.replace('**********','-99999999.')
|
||||
line = line.split()
|
||||
if line[0].lower() == "unable":
|
||||
pos +=1
|
||||
pos +=1
|
||||
line = line.split()
|
||||
eigval = [ float(k) for k in line ]
|
||||
pos += 1
|
||||
|
|
@ -616,7 +616,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
if self._mo_sets == {}:
|
||||
self._mo_sets = None
|
||||
return self._mo_sets
|
||||
|
||||
|
||||
def get_mulliken_mo(self):
|
||||
if self._mulliken_mo is None:
|
||||
pass
|
||||
|
|
@ -632,6 +632,49 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
pass
|
||||
return self._lowdin_ao
|
||||
|
||||
def get_pseudo(self):
|
||||
if self._pseudo is None:
|
||||
try:
|
||||
self.find_string("Pseudopotential Parameters")
|
||||
except IndexError:
|
||||
return None
|
||||
self._pos += 5
|
||||
pos = self._pos
|
||||
try:
|
||||
self.find_next_string("=======")
|
||||
except IndexError:
|
||||
return None
|
||||
end = self._pos
|
||||
pseudo_read = []
|
||||
text = self.text
|
||||
bdict = {"S": 0, "P": 1, "D": 2, "F": 3, "G": 4, "H": 5}
|
||||
while pos < end:
|
||||
ecp = {}
|
||||
center, _, valence = [int(x) for x in text[pos].split()]
|
||||
ecp["atom"] = center
|
||||
ecp["zcore"] = valence
|
||||
ecp["lmax"] = 0
|
||||
pos += 1
|
||||
l = 0
|
||||
while text[pos][:35].strip() == "":
|
||||
# Read angular momentum
|
||||
line = text[pos].lstrip()
|
||||
buffer = line.split()
|
||||
if buffer[0] in "SPDFGH":
|
||||
contraction = []
|
||||
l = bdict[buffer[0]]
|
||||
ecp["lmax"] = max(ecp["lmax"], l)
|
||||
else:
|
||||
# Read gaussian parameters
|
||||
power, expo, coef = int(buffer[0]), float(buffer[1]), float(buffer[2])
|
||||
contraction.append( (coef, power, expo) )
|
||||
ecp[str(l)] = contraction
|
||||
pos += 1
|
||||
pseudo_read.append(ecp)
|
||||
|
||||
self._pseudo = pseudo_read
|
||||
return self._pseudo
|
||||
|
||||
|
||||
def get_mulliken_atom(self):
|
||||
if self._mulliken_atom is None:
|
||||
|
|
@ -671,14 +714,14 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
self.find_string("alpha electrons")
|
||||
pos = self._pos
|
||||
self._num_alpha = int(self.text[pos].split()[0])
|
||||
return self._num_alpha
|
||||
return self._num_alpha
|
||||
|
||||
def get_num_beta(self):
|
||||
if self._num_beta is None:
|
||||
self.find_string("beta electrons")
|
||||
pos = self._pos
|
||||
self._num_beta = int(self.text[pos].split()[3])
|
||||
return self._num_beta
|
||||
return self._num_beta
|
||||
|
||||
def get_determinants_mo_type(self):
|
||||
if self._determinants_mo_type is None:
|
||||
|
|
@ -890,7 +933,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
for motype in self.mo_types:
|
||||
occ[motype] = [ mo.eigenvalue for mo in self.mulliken_mo ]
|
||||
self._occ_num = occ
|
||||
return self._occ_num
|
||||
return self._occ_num
|
||||
|
||||
def get_num_states(self):
|
||||
if self._num_states is None:
|
||||
|
|
@ -923,7 +966,7 @@ class gaussianFile(resultsFile.resultsFileX):
|
|||
self._file = fortranBinary(filename,"rb")
|
||||
|
||||
def get_form(self):
|
||||
return self._file.form
|
||||
return self._file.form
|
||||
|
||||
def set_form(self,form):
|
||||
self._file.form = form
|
||||
|
|
@ -988,7 +1031,7 @@ def write_vec(res, file):
|
|||
monum = monum[-2:]
|
||||
fields.append ( monum )
|
||||
linum = "%4d"%(line)
|
||||
linum = linum[-3:]
|
||||
linum = linum[-3:]
|
||||
fields.append ( linum )
|
||||
for n in range(5):
|
||||
fields.append ( "%15.8E"%v.pop(0) )
|
||||
|
|
@ -1041,8 +1084,8 @@ def write_data(res, file):
|
|||
print(" $END", file=file)
|
||||
|
||||
|
||||
|
||||
|
||||
resultsFile.fileTypes.append(gaussianFile)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
resultsFile.main(gaussianFile)
|
||||
|
|
|
|||
Loading…
Reference in New Issue