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