Source code for scm.plams.interfaces.adfsuite.mopac

from ...core.basejob import SingleJob
from .scmjob import SCMResults

__all__ = ['MOPACJob', 'MOPACResults']

[docs]class MOPACResults(SCMResults): """A class for results of computation done with MOPAC. This class inherits all methods from |SCMResults|. .. technical:: In case of a MOPAC job, preparation is much different from other programs of AMSuite, but the result handling is quite similar due to presence of KF files. Therefore |MOPACResults| is a subclass of |SCMResults|, but |MOPACJob| is not a subclass of |SCMJob|. """ _rename_map = {'results.rkf':'$JN.rkf', '$':'$JN.aux', '$':'$JN.arc', '$':'$JN.out' } _kfext = '.rkf' def _int2inp(self): return list(range(1, 1+len(self.job.molecule)))
[docs] def _atomic_numbers_input_order(self): return self.readkf('Molecule', 'AtomicNumbers')
[docs]class MOPACJob(SingleJob): """A class representing a single computational job with MOPAC.""" _result_type = MOPACResults _command = 'MOPAC2016-SCM.exe'
[docs] def get_input(self): """Transform the contents of ``input`` branch of ``settings`` into the first line of MOPAC input. Print the molecular coordinates together with frozen coordinate flags.""" aux = self.settings.input.find_case('aux') if aux not in self.settings.input: self.settings.input[aux] = [0,'PRECISION=9'] keylist = [] for key, value in self.settings.input.items(): if value is True: keylist.append(key) elif isinstance(value, tuple): keylist.append(key + '=(' + ','.join(map(str, value)) + ')' ) elif isinstance(value, list): keylist.append(key + '(' + ','.join(map(str, value)) + ')' ) else: keylist.append(key + '=' + str(value)) ret = ' '.join(keylist) + '\n\n\n' for at in self.molecule: line = '{:7}'.format(at.symbol) for c in ['x', 'y', 'z']: num = at.__getattribute__(c) frz = 0 if ('mopac_freeze' in and c in else 1 line += ' {: 11.8f} {:d}'.format(num,frz) ret += line + '\n' return ret
[docs] def get_runscript(self): """Generate a MOPAC runscript. The name of the MOPAC executable is taken from class attribute ``MOPACJob._command``. If you experience problems running MOPAC, check if that value corresponds to the name of the executable and this executable is visible in your ``$PATH`` (in case of AMSuite it's in ``$AMSBIN``). Note that a bare MOPAC executable should be used here, please avoid using any wrappers. The execution of MOPAC binary is followed by calling a simple command line tool ``tokf`` which reads various output text files produced by MOPAC and collects all the data in a binary KF file. See :ref:`kf-files` for details. """ ret = self._command + ' ' + self._filename('inp') if self.settings.runscript.stdout_redirect: ret += ' >'+self._filename('out') ret += '\n\n' ret += 'cp {} {}.stdout\n'.format(self._filename('err'), self._filename('inp')) ret += 'tokf mopac {} {}.rkf\n'.format(self._filename('inp'), ret += 'rm {}.stdout\n\n'.format(self._filename('inp')) ret += 'rm {}\n\n'.format(self._filename('out')) return ret
[docs] def check(self): """Grep standard output for ``* JOB ENDED NORMALLY *``.""" s = self.results.grep_output('* JOB ENDED NORMALLY *') return len(s) > 0