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Add pseudo
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@ -38,7 +38,7 @@ gamessFile_defined_vars = [ "date", "version", "machine", "memory", "disk",\
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"Ne_pot_energies", "pot_energies", \
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"kin_energies", "virials", "point_group", "num_elec", \
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"charge", "multiplicity","nuclear_energy","dipole","geometry",\
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"basis","mo_sets","mo_types","mulliken_mo","mulliken_ao",\
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"basis","pseudo", "mo_sets","mo_types","mulliken_mo","mulliken_ao",\
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"mulliken_atom","lowdin_ao", "mulliken_atom","lowdin_atom",\
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"two_e_int_ao", "determinants", "num_alpha", "num_beta",\
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"closed_mos", "active_mos", "virtual_mos", \
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@ -1348,6 +1348,59 @@ class gamessFile(resultsFile):
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pass
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return self._num_states
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def get_pseudo(self):
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try:
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self.find_string('ECP POTENTIALS')
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except IndexError:
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raise TypeError('No ECP')
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else:
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pos_begin = self._pos
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try:
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self.find_string('THE ECP RUN REMOVES')
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except IndexError:
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raise TypeError('Cannot parse ECP')
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else:
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pos_end = self._pos
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raw_str = ''.join(self.text[pos_begin+2:pos_end])
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l_param_atom = raw_str.split('\n\n')
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import re
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regex = r"PARAMETERS FOR \"(.*)\" ON ATOM\s+(\d+) WITH ZCORE\s+(\d+) AND LMAX\s+(\d+) ARE"
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regex_l = r"FOR L=\s+\d+\s+COEFF\s+N\s+ZETA\s*"
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regex_already_existing_atom = r"PARAMETERS FOR \"(.*)\" ON ATOM\s+(\d+) ARE THE SAME AS ATOM\s+(\d+)\s*$"
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d = dict()
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for param in [i for i in l_param_atom if i]:
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matches = re.findall(regex, param)
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if matches:
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name, label,zcore, lmax = matches[0]
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l_str = ['{0} GEN {1} {2}'.format(name, zcore, lmax)]
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#l_bloc
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l_lblock = re.split(regex_l,param)[1:]
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for l in l_lblock:
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lignes = [i.strip() for i in l.split('\n') if i.strip()]
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l_str.append(len(lignes))
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l_str += lignes
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l_str.append('')
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d[int(label)] = '\n'.join(map(str,l_str))
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else:
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matches = re.findall(regex_already_existing_atom, param)
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name, label, label_ref = matches[0]
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d[int(label)] = d[int(label_ref)]
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result = ""
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for i in range(len(d)):
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result+= d[i+1]
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result+= '\n'
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return result
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# Properties
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# ----------
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to_remove = []
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@ -69,19 +69,21 @@ local_vars = [ \
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( 'quadrupole' , "Quadrupole moment"),
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( 'num_states' , "Number of electronic states"),
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# Geometry properties
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( 'point_group' , "Symmetry used."),
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( 'geometry' , "Atom types and coordinates."),
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( 'symmetries' , "Irreducible representations"),
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( 'num_elec' , "Number of electrons."),
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( 'num_alpha' , "Number of Alpha electrons."),
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( 'num_beta' , "Number of Beta electrons."),
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( 'charge' , "Charge of the system."),
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( 'multiplicity' , "Spin multiplicity of the system."),
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( 'nuclear_energy', "Repulsion of the nuclei."),
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( 'point_group' , "Symmetry used."),
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( 'geometry' , "Atom types and coordinates."),
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( 'symmetries' , "Irreducible representations"),
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( 'num_elec' , "Number of electrons."),
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( 'num_alpha' , "Number of Alpha electrons."),
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( 'num_beta' , "Number of Beta electrons."),
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( 'charge' , "Charge of the system."),
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( 'multiplicity' , "Spin multiplicity of the system."),
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( 'nuclear_energy ', "Repulsion of the nuclei."),
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( 'gradient_energy', "Gradient of the Energy wrt nucl coord."),
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# Basis set
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( 'basis' , "Basis set definition"),
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( 'basis' , "Basis set definition"),
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( 'uncontracted_basis', "Uncontracted Basis set"),
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# Pseudo
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('pseudo' , 'Pseudopotential (gamess input format)'),
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# Orbitals
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( 'mo_sets' , "List of molecular orbitals"),
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( 'mo_types' , "Types of molecular orbitals (canonical, natural,...)"),
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