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Merge pull request #1571 from ReactionMechanismGenerator/auto_optical…
…_isomer_ex_symmetry_arkane Auto optical isomer and external symmetry to Arkane
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| #!/usr/bin/env python2 | ||
| # -*- coding: utf-8 -*- | ||
| """ | ||
| A general class for parsing quantum mechanical log files | ||
| """ | ||
| import os.path | ||
| import logging | ||
| import shutil | ||
|
|
||
| from rmgpy.qm.qmdata import QMData | ||
| from rmgpy.qm.symmetry import PointGroupCalculator | ||
|
|
||
| class Log(object): | ||
| """ | ||
| Represent a general log file. | ||
| The attribute `path` refers to the location on disk of the log file of interest. | ||
| """ | ||
| def __init__(self, path): | ||
| self.path = path | ||
|
|
||
| def getNumberOfAtoms(self): | ||
| """ | ||
| Return the number of atoms in the molecular configuration used in | ||
| the MolPro log file. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadForceConstantMatrix(self): | ||
| """ | ||
| Return the force constant matrix (in Cartesian coordinates) from the | ||
| QChem log file. If multiple such matrices are identified, | ||
| only the last is returned. The units of the returned force constants | ||
| are J/m^2. If no force constant matrix can be found in the log file, | ||
| ``None`` is returned. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadGeometry(self): | ||
| """ | ||
| Return the optimum geometry of the molecular configuration from the | ||
| log file. If multiple such geometries are identified, only the | ||
| last is returned. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadConformer(self, symmetry=None, spinMultiplicity=0, opticalIsomers=None, label=''): | ||
| """ | ||
| Load the molecular degree of freedom data from an output file created as the result of a | ||
| QChem "Freq" calculation. As QChem's guess of the external symmetry number is not always correct, | ||
| you can use the `symmetry` parameter to substitute your own value; | ||
| if not provided, the value in the QChem output file will be adopted. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadEnergy(self, frequencyScaleFactor=1.): | ||
| """ | ||
| Load the energy in J/mol from a QChem log file. Only the last energy | ||
| in the file is returned. The zero-point energy is *not* included in | ||
| the returned value. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadZeroPointEnergy(self,frequencyScaleFactor=1.): | ||
| """ | ||
| Load the unscaled zero-point energy in J/mol from a QChem output file. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadScanEnergies(self): | ||
| """ | ||
| Extract the optimized energies in J/mol from a QChem log file, e.g. the | ||
| result of a QChem "PES Scan" quantum chemistry calculation. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def loadNegativeFrequency(self): | ||
| """ | ||
| Return the imaginary frequency from a transition state frequency | ||
| calculation in cm^-1. | ||
| """ | ||
| raise NotImplementedError("loadGeometry is not implemented for the Log class") | ||
|
|
||
| def get_optical_isomers_and_symmetry_number(self): | ||
| """ | ||
| This method uses the symmetry package from RMG's QM module | ||
| and returns a tuple where the first element is the number | ||
| of optical isomers and the second element is the symmetry number. | ||
| """ | ||
| coordinates, atom_numbers, _ = self.loadGeometry() | ||
| unique_id = '0' # Just some name that the SYMMETRY code gives to one of its jobs | ||
| scr_dir = os.path.join(os.path.abspath('.'), str('scratch')) # Scratch directory that the SYMMETRY code writes its files in | ||
| if not os.path.exists(scr_dir): | ||
| os.makedirs(scr_dir) | ||
| try: | ||
| qmdata = QMData( | ||
| groundStateDegeneracy=1, # Only needed to check if valid QMData | ||
| numberOfAtoms=len(atom_numbers), | ||
| atomicNumbers=atom_numbers, | ||
| atomCoords=(coordinates, str('angstrom')), | ||
| energy=(0.0, str('kcal/mol')) # Only needed to avoid error | ||
| ) | ||
| settings = type(str(''), (), dict(symmetryPath=str('symmetry'), scratchDirectory=scr_dir))() # Creates anonymous class | ||
| pgc = PointGroupCalculator(settings, unique_id, qmdata) | ||
| pg = pgc.calculate() | ||
| if pg is not None: | ||
| optical_isomers = 2 if pg.chiral else 1 | ||
| symmetry = pg.symmetryNumber | ||
| logging.debug("Symmetry algorithm found {0} optical isomers and a symmetry number of {1}".format(optical_isomers,symmetry)) | ||
| else: | ||
| logging.error("Symmetry algorithm errored when computing point group\nfor log file located at{0}.\nManually provide values in Arkane input.".format(self.path)) | ||
| return optical_isomers, symmetry | ||
| finally: | ||
| shutil.rmtree(scr_dir) |
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