scm.plams.interfaces.thirdparty.orca.的源代码

from ...core.basejob import SingleJob
from ...core.settings import Settings


[docs]class ORCAJob(SingleJob): """ A class representing a single computational job with ORCA `Orca <//orcaforum.cec.mpg.de>` """
[docs] def get_input(self): """ Transform all contents of ``input`` branch of ``settings`` into string with blocks, subblocks, keys and values. The branch self.settings.input.main corresponds to the lines starting with the special character ! in the ORCA input. Orca *end* keyword is mandatory for only a subset of sections. For instance the following orca input shows the keywords *methods* and *basis* use of end:: ! UKS B3LYP/G SV(P) SV/J TightSCF Direct Grid3 FinalGrid4 %method SpecialGridAtoms 26 SpecialGridIntAcc 7 end %basis NewGTO 26 "CP(PPP)" end NewAuxGTO 26 "TZV/J" end end In order to specify when the *end* keyword must be used, the following syntax can be used:: job = ORCAJob(molecule=Molecule(<Path/to/molecule>)) job.settings.input.main = "UKS B3LYP/G SV(P) SV/J TightSCF Direct Grid3 FinalGrid4" job.settings.input.method.SpecialGridAtoms = 26 job.settings.input.method.SpecialGridIntAcc = 7 job.settings.input.basis.NewGTO._end = '26 "CP(PPP)"' job.settings.input.basis.NewAuxGTO._end = '26 "TZV/J"' """ def get_end(s): if (不是 isinstance(s, Settings)) or ('_end' 不是 in s): return s else: return '{} end'.format(s['_end']) def pretty_print_inner(s, indent): inp = '' for i, (key, value) in enumerate(s.items()): end = get_end(value) if i == 0: inp += ' {} {}\n'.format(key, end) else: inp += '{}{} {}\n'.format(indent, key, end) return inp def pretty_print_orca(s, indent=''): inp = '' if isinstance(s, Settings): for k, v in s.items(): if k == 'main': inp += '! {}\n\n'.format(pretty_print_orca(v, indent)) else: indent2 = (len(k) + 2) * ' ' if 不是 isinstance(v, Settings): block = pretty_print_orca(v) else: block = pretty_print_inner(v, indent2) inp += '%{}{}{}end\n\n'.format(k, block, indent2) elif isinstance(s, list): for elem in s: inp += '{}'.format(elem) else: inp += '{}'.format(s) return inp inp = pretty_print_orca(self.settings.input) inp_mol = self.print_molecule() return inp + inp_mol
[docs] def print_molecule(self): """Print a molecule in the ORCA format.""" mol = self.molecule if mol: if 'charge' in mol.properties and isinstance(mol.properties.charge, int): charge = mol.properties.charge else: charge = 0 if 'multiplicity' in mol.properties and isinstance(mol.properties.multiplicity, int): multi = mol.properties.multiplicity else: multi = 1 xyz = '\n'.join(at.str(symbol=True, space=11, decimal=5) for at in mol.atoms) return '* xyz {} {}\n{}\n*\n\n'.format(charge, multi, xyz) else: return ''
[docs] def get_runscript(self): """Returned runscript is just one line: ``orca myinput.inp`` """ return 'orca {}'.format(self._filename('inp'))
[docs] def check(self): """Look for the normal termination signal in the output.""" s = self.results.grep_output("ORCA TERMINATED NORMALLY") return len(s) > 0