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

from scm.plams.core.basejob import SingleJob
from scm.plams.interfaces.adfsuite.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.in.aux": "$JN.aux", "$JN.in.arc": "$JN.arc", "$JN.in.out": "$JN.out"} _kfext = ".rkf" def _int2inp(self): return list(range(1, 1 + len(self.job.molecule)))
[docs] def _atomic_numbers_input_order(self): return self.readkf("Molecule", "AtomicNumbers")
[docs]class MOPACJob(SingleJob): """A class representing a single computational job with MOPAC.""" _result_type = MOPACResults _command = "MOPAC2016-SCM.exe"
[docs] def get_input(self): """Transform the contents of ``input`` branch of ``settings`` into the first line of MOPAC input. Print the molecular coordinates together with frozen coordinate flags.""" aux = self.settings.input.find_case("aux") if aux not in self.settings.input: self.settings.input[aux] = [0, "PRECISION=9"] keylist = [] for key, value in self.settings.input.items(): if value is True: keylist.append(key) elif isinstance(value, tuple): keylist.append(key + "=(" + ",".join(map(str, value)) + ")") elif isinstance(value, list): keylist.append(key + "(" + ",".join(map(str, value)) + ")") else: keylist.append(key + "=" + str(value)) ret = " ".join(keylist) + "\n\n\n" for at in self.molecule: line = "{:7}".format(at.symbol) for c in ["x", "y", "z"]: num = at.__getattribute__(c) frz = 0 if ("mopac_freeze" in at.properties and c in at.properties.mopac_freeze) else 1 line += " {: 11.8f} {:d}".format(num, frz) ret += line + "\n" return ret
[docs] def get_runscript(self): """Generate a MOPAC runscript. The name of the MOPAC executable is taken from class attribute ``MOPACJob._command``. If you experience problems running MOPAC, check if that value corresponds to the name of the executable and this executable is visible in your ``$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"), self.name) 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