def test_prettify(self):
"""Test that the prettify function works for an Arkane job"""
benzyl_path = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)),
'examples', 'arkane', 'species', 'Benzyl')
arkane = Arkane(input_file=os.path.join(benzyl_path, 'input.py'), output_directory=benzyl_path)
arkane.plot = False
arkane.execute()
with open(os.path.join(benzyl_path, 'output.py'), 'r') as f:
lines = f.readlines()
self.assertIn('conformer(\n', lines)
self.assertIn(" E0 = (193.749, 'kJ/mol'),\n", lines)
self.assertIn('thermo(\n', lines)
self.assertIn(" Cp0 = (33.2579, 'J/(mol*K)'),\n", lines)
def test_pdep_job(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.input_file = self.input_file
self.tst1.output_directory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.job_list = []
self.tst1.job_list = self.tst1.load_input_file(self.tst1.input_file)
self.tst1.execute()
job = self.tst1.job_list[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimum_grain_count, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.active_j_rotor)
self.assertEquals(job.network.path_reactions[0].label, 'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(job.network.path_reactions[0].transition_state.tunneling.E0_TS.value_si, -24267.2)
self.assertAlmostEquals(job.network.path_reactions[0].transition_state.tunneling.frequency.value_si, -1679.04)
self.assertEquals(len(job.network.net_reactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {'hydroperoxylvinoxy': Species().from_smiles('[CH2]C(=O)OO'),
'acetylperoxy': Species().from_smiles('CC(=O)O[O]')}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = read_reactions_block(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
# Accept a delta of 0.2, which could result from numerical discrepancies
# See RMG-Py #1682 on GitHub for discussion
self.assertAlmostEquals(rxn.kinetics.get_rate_coefficient(1000.0, 1.0), 88.88253229631246, delta=0.2)
files = [f for f in os.listdir(os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'), 'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertAlmostEquals(float(sa_coeff), -8.23e-6, delta=0.02e-6)
def testPDepJob(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.inputFile = self.input_file
self.tst1.outputDirectory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.jobList = []
self.tst1.jobList = self.tst1.loadInputFile(self.tst1.inputFile)
self.tst1.execute()
job = self.tst1.jobList[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimumGrainCount, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.activeJRotor)
self.assertEquals(job.network.pathReactions[0].label,'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.E0_TS.value_si,-24267.2)
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.frequency.value_si,-1679.04)
self.assertEquals(len(job.network.netReactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {'hydroperoxylvinoxy': Species().fromSMILES('[CH2]C(=O)OO'),
'acetylperoxy': Species().fromSMILES('CC(=O)O[O]')}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = readReactionsBlock(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
self.assertAlmostEquals(rxn.kinetics.getRateCoefficient(1000.0, 1.0), 88.879056605)
files = [f for f in os.listdir(os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'), 'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertEquals(float(sa_coeff), -8.24e-6)
def testPDepJob(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.inputFile = self.input_file
self.tst1.outputDirectory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.jobList = []
self.tst1.jobList = self.tst1.loadInputFile(self.tst1.inputFile)
self.tst1.execute()
job = self.tst1.jobList[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimumGrainCount, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.activeJRotor)
self.assertEquals(job.network.pathReactions[0].label,'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.E0_TS.value_si,-24267.2)
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.frequency.value_si,-1679.04)
self.assertEquals(len(job.network.netReactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {'hydroperoxylvinoxy': Species().fromSMILES('[CH2]C(=O)OO'),
'acetylperoxy': Species().fromSMILES('CC(=O)O[O]')}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = readReactionsBlock(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
self.assertAlmostEquals(rxn.kinetics.getRateCoefficient(1000.0, 1.0), 88.879056605)
files = [f for f in os.listdir(os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'), 'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertEquals(float(sa_coeff), -8.24e-6)
def __init__(self,
reaction,
directory=".",
model_chemistry="M06-2X/cc-pVTZ",
freq_scale_factor=0.982):
"""
A class to perform Arkane calculations:
:param: reaction: (Reaction) The reaction of interest
:param: output_directory: (str) The directory where you would like output files written to
:param: model_chemistry: (str) The supported model_chemistry described by http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/input.html#model-chemistry
:param: freq_scale_factor: (float) The scaling factor corresponding to the model chemistry - source:https://comp.chem.umn.edu/freqscale/version3b1.htm
"""
self.reaction = reaction
self.directory = directory
self.kinetics_job = RMGArkane()
self.thermo_job = RMGArkane()
self.model_chemistry = model_chemistry
self.freq_scale_factor = freq_scale_factor
class ArkaneTest(unittest.TestCase):
"""
Contains unit tests for the sensitivity module in Arkane
"""
@classmethod
def setUp(cls):
"""A function that is run ONCE before all unit tests in this class."""
cls.directory = os.path.join(settings['test_data.directory'], 'arkane',
'tst1', '')
cls.input_file = os.path.join(cls.directory, 'pdep_sa.py')
# clean working folder from all previous test output
dirs = [
d for d in os.listdir(cls.directory)
if not os.path.isfile(os.path.join(cls.directory, d))
]
for d in dirs:
shutil.rmtree(
os.path.join(settings['test_data.directory'], 'arkane', 'tst1',
d, ''))
files = [
f for f in os.listdir(cls.directory)
if os.path.isfile(os.path.join(cls.directory, f))
]
for f in files:
if 'pdep_sa' not in f:
os.remove(
os.path.join(settings['test_data.directory'], 'arkane',
'tst1', f))
def test_pdep_job(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.input_file = self.input_file
self.tst1.output_directory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.job_list = []
self.tst1.job_list = self.tst1.load_input_file(self.tst1.input_file)
self.tst1.execute()
job = self.tst1.job_list[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimum_grain_count, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.active_j_rotor)
self.assertEquals(job.network.path_reactions[0].label,
'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(
job.network.path_reactions[0].transition_state.tunneling.E0_TS.
value_si, -24267.2)
self.assertAlmostEquals(
job.network.path_reactions[0].transition_state.tunneling.frequency.
value_si, -1679.04)
self.assertEquals(
len(job.network.net_reactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [
f for f in os.listdir(self.directory)
if os.path.isfile(os.path.join(self.directory, f))
]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {
'hydroperoxylvinoxy': Species().from_smiles('[CH2]C(=O)OO'),
'acetylperoxy': Species().from_smiles('CC(=O)O[O]')
}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = read_reactions_block(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
self.assertAlmostEquals(rxn.kinetics.get_rate_coefficient(1000.0, 1.0),
88.88253229631246)
files = [
f for f in os.listdir(
os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))
]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'),
'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertEquals(float(sa_coeff), -8.23e-6)
@classmethod
def tearDown(cls):
"""A function that is run ONCE after all unit tests in this class."""
cls.directory = os.path.join(settings['test_data.directory'], 'arkane',
'tst1', '')
cls.input_file = os.path.join(cls.directory, 'pdep_sa.py')
# clean working folder from all previous test output
dirs = [
d for d in os.listdir(cls.directory)
if not os.path.isfile(os.path.join(cls.directory, d))
]
for d in dirs:
shutil.rmtree(
os.path.join(settings['test_data.directory'], 'arkane', 'tst1',
d, ''))
files = [
f for f in os.listdir(cls.directory)
if os.path.isfile(os.path.join(cls.directory, f))
]
for f in files:
if 'pdep_sa' not in f:
os.remove(
os.path.join(settings['test_data.directory'], 'arkane',
'tst1', f))
execute. Arkane will run the specified job, writing the output to
``output.py`` and a log to both the console and to ``Arkane.log``, with both
files appearing in the same directory as the input file. Some additional
command-line arguments are available; run the command ::
$ python Arkane.py -h
for more information.
"""
import os
import logging
from arkane.main import Arkane
arkane = Arkane()
# Parse and validate the command-line arguments
arkane.parse_command_line_arguments()
# Execute the job
arkane.execute()
try:
import psutil
process = psutil.Process(os.getpid())
memory_info = process.memory_info()
logging.info('Memory used: %.2f MB' % (memory_info.rss / 1024.0 / 1024.0))
except ImportError:
logging.info(
class ArkaneTest(unittest.TestCase):
"""
Contains unit tests for the sensitivity module in Arkane
"""
@classmethod
def setUp(self):
"""A function that is run ONCE before all unit tests in this class."""
self.directory = os.path.join(settings['test_data.directory'], 'arkane', 'tst1', '')
self.input_file = os.path.join(self.directory, 'pdep_sa.py')
# clean working folder from all previous test output
dirs = [d for d in os.listdir(self.directory) if not os.path.isfile(os.path.join(self.directory, d))]
for d in dirs:
shutil.rmtree(os.path.join(settings['test_data.directory'], 'arkane', 'tst1', d, ''))
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
for f in files:
if not 'pdep_sa' in f:
os.remove(os.path.join(settings['test_data.directory'], 'arkane', 'tst1', f))
def testPDepJob(self):
"""
A general test for a PDep job in Arkane
"""
self.tst1 = Arkane()
self.tst1.inputFile = self.input_file
self.tst1.outputDirectory = self.directory
self.tst1.verbose = logging.WARN
self.tst1.plot = False
self.tst1.jobList = []
self.tst1.jobList = self.tst1.loadInputFile(self.tst1.inputFile)
self.tst1.execute()
job = self.tst1.jobList[0]
self.assertEquals(job.Tmin.value_si, 300.0)
self.assertEquals(job.minimumGrainCount, 100)
self.assertFalse(job.rmgmode)
self.assertTrue(job.activeJRotor)
self.assertEquals(job.network.pathReactions[0].label,'acetylperoxy <=> hydroperoxylvinoxy')
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.E0_TS.value_si,-24267.2)
self.assertAlmostEquals(job.network.pathReactions[0].transitionState.tunneling.frequency.value_si,-1679.04)
self.assertEquals(len(job.network.netReactions[0].reactants[0].conformer.modes), 6)
# self.assertEquals(self.tst1.frequencyScaleFactor, 0.947)
# test that a network pdf was generated
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
self.assertTrue(any(f == 'network.pdf' for f in files))
# Test the generated network reaction
dictionary = {'hydroperoxylvinoxy': Species().fromSMILES('[CH2]C(=O)OO'),
'acetylperoxy': Species().fromSMILES('CC(=O)O[O]')}
with open(os.path.join(self.directory, 'chem.inp'), 'r') as chem:
reaction_list = readReactionsBlock(chem, dictionary)
rxn = reaction_list[0]
self.assertIsInstance(rxn.kinetics, Chebyshev)
self.assertAlmostEquals(rxn.kinetics.getRateCoefficient(1000.0, 1.0), 88.879056605)
files = [f for f in os.listdir(os.path.join(self.directory, 'sensitivity', ''))
if os.path.isfile(os.path.join(self.directory, 'sensitivity', f))]
self.assertTrue(any('hydroperoxylvinoxy.pdf' in f for f in files))
with open(os.path.join(self.directory, 'sensitivity', 'network1.txt'), 'r') as f:
lines = f.readlines()
for line in lines:
if '1000.0' in line:
break
sa_coeff = line.split()[-2]
self.assertEquals(float(sa_coeff), -8.24e-6)
@classmethod
def tearDown(self):
"""A function that is run ONCE after all unit tests in this class."""
self.directory = os.path.join(settings['test_data.directory'], 'arkane', 'tst1', '')
self.input_file = os.path.join(self.directory, 'pdep_sa.py')
# clean working folder from all previous test output
dirs = [d for d in os.listdir(self.directory) if not os.path.isfile(os.path.join(self.directory, d))]
for d in dirs:
shutil.rmtree(os.path.join(settings['test_data.directory'], 'arkane', 'tst1', d, ''))
files = [f for f in os.listdir(self.directory) if os.path.isfile(os.path.join(self.directory, f))]
for f in files:
if not 'pdep_sa' in f:
os.remove(os.path.join(settings['test_data.directory'], 'arkane', 'tst1', f))
class StatMech(Calculator):
def __init__(
self,
reaction,
scratch=".",
output_directory=".",
model_chemistry="M06-2X/cc-pVTZ",
freq_scale_factor=0.982):
"""
A class to perform Arkane calculations:
:param: reaction: (Reaction) The reaction of interest
:param: output_directory: (str) The directory where you would like output files written to
:param: model_chemistry: (str) The supported model_chemistry described by http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/input.html#model-chemistry
:param: freq_scale_factor: (float) The scaling factor corresponding to the model chemistry - source:https://comp.chem.umn.edu/freqscale/version3b1.htm
"""
self.reaction = reaction
self.scratch = scratch
self.arkane_job = RMGArkane()
self.output_directory = output_directory
self.arkane_job.outputDirectory = self.output_directory
self.model_chemistry = model_chemistry
self.freq_scale_factor = freq_scale_factor
def get_atoms(self, conformer):
"""
A method to create an atom dictionary for an rmg molecule
"""
atom_dict = {}
conf = conformer
rmg_mol = conf.rmg_molecule
for atom in rmg_mol.atoms:
if atom.isCarbon():
atom_type = "C"
if atom.isHydrogen():
atom_type = "H"
if atom.isOxygen():
atom_type = "O"
try:
atom_dict[atom_type] += 1
except KeyError:
atom_dict[atom_type] = 1
return atom_dict
def get_bonds(self, conformer):
conf = conformer
rmg_mol = conf.rmg_molecule
bondList = []
for atom in rmg_mol.atoms:
for bond in atom.bonds.values():
bondList.append(bond)
bonds = list(set(bondList))
bondDict = {}
for bond in bonds:
if bond.isSingle():
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C-C'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'H'):
bondType = 'H-H'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol == 'H') or (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'C'):
bondType = 'C-H'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'O'):
bondType = 'O-O'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol == 'O') or (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'C'):
bondType = 'C-O'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'O') or (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'H'):
bondType = 'O-H'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N-N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol == 'N') or (bond.atom1.symbol == 'N' and bond.atom2.symbol == 'C'):
bondType = 'N-C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'N') or (bond.atom1.symbol == 'N' and bond.atom2.symbol == 'O'):
bondType = 'N-O'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'N') or (bond.atom1.symbol == 'N' and bond.atom2.symbol == 'H'):
bondType = 'N-H'
elif bond.atom1.symbol == 'S' and bond.atom2.symbol == 'S':
bondType = 'S-S'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'S') or (bond.atom1.symbol == 'S' and bond.atom2.symbol == 'H'):
bondType = 'S-H'
elif bond.isDouble:
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C=C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'O'):
bondType = 'O=O'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol == 'O') or (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'C'):
bondType = 'C=O'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N=N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol == 'N') or (bond.atom1.symbol == 'N' and bond.atom2.symbol == 'C'):
bondType = 'N=C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'N') or (bond.atom1.symbol == 'N' and bond.atom2.symbol == 'O'):
bondType = 'N=O'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'S') or (bond.atom1.symbol == 'S' and bond.atom2.symbol == 'O'):
bondType = 'S=O'
elif bond.isTriple:
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C#C'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N#N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol == 'N') or (bond.atom1.symbol == 'N' and bond.atom2.symbol == 'C'):
bondType = 'N#C'
try:
bondDict[bondType] += 1
except KeyError:
bondDict[bondType] = 1
return bondDict
def write_arkane_for_reacts_and_prods(self, conformer):
"""
a method to write species to an arkane input file. Mol is an RMGMolecule
"""
conf = conformer
mol = conf.rmg_molecule
output = ['#!/usr/bin/env python',
'# -*- coding: utf-8 -*-', '', 'atoms = {']
atom_dict = self.get_atoms(conf)
for atom, count in atom_dict.iteritems():
output.append(" '{0}': {1},".format(atom, count))
output = output + ['}', '']
bond_dict = self.get_bonds(conf)
if bond_dict != {}:
output.append('bonds = {')
for bond_type, num in bond_dict.iteritems():
output.append(" '{0}': {1},".format(bond_type, num))
output.append("}")
else:
output.append('bonds = {}')
label = Chem.rdinchi.InchiToInchiKey(
Chem.MolToInchi(Chem.MolFromSmiles(mol.toSMILES()))).strip("-N")
external_symmetry = mol.getSymmetryNumber()
output += ["",
"linear = False",
"",
"externalSymmetry = {}".format(external_symmetry),
"",
"spinMultiplicity = {}".format(mol.multiplicity),
"",
"opticalIsomers = 1",
""]
output += ["energy = {", " '{0}': Log('{1}.log'),".format(
self.model_chemistry, label), "}", ""]
output += ["geometry = Log('{0}.log')".format(label), ""]
output += [
"frequencies = Log('{0}.log')".format(label), ""]
output += ["rotors = ["] #TODO for carl
for torsion in conf.torsions:
output += [self.get_rotor_info(conf, torsion)]
output += ["]"]
input_string = ""
for t in output:
input_string += t + "\n"
with open(os.path.join(self.scratch, label + ".py"), "w") as f:
f.write(input_string)
def get_rotor_info(self, conformer, torsion):
"""
Formats and returns info about torsion as it should appear in an Arkane species.py
conformer :: autotst conformer object
torsion :: autotst torsion object
Needed for Arkane species file:
scanLog :: Gaussian output log of freq calculation on optimized geometry
pivots :: torsion center: j,k)
top :: ID of all atoms in one top, starting from 1!),
"""
i,j,k,l = torsion.atom_indices
tor_center = [j,k] #If given i,j,k,l torsion, center is j,k
tor_center_adj = [j+1, k+1] # Adjusted since mol's IDs start from 0 while Arkane's start from 1
# MUST CONTAIN FREQ as well as opt geometry
if isinstance(conformer, TS):
tor_log = os.path.join(
self.scratch,
comformer.reaction_label + "_tor{0}{1}.log".format(j,k)
)
else:
tor_log = os.path.join(
self.scratch,
conformer.rmg_molecule.toAugmentedInChIKey().strip("-N") + '_tor{0}{1}.log'.format(j,k)
)
top_IDs = []
for num, tf in enumerate(torsion.mask):
if tf: top_IDs.append(num)
top_IDs_adj = [ID+1 for ID in top_IDs] # Adjusted to start from 1 instead of 0
info = " HinderedRotor(scanLog=Log('{0}'), pivots={1}, top={2}, fit='fourier'),".format(tor_log, tor_center_adj, top_IDs_adj)
return info
def write_statmech_ts(self, rxn):
conf = find_lowest_energy_conformer(rxn, self.scratch)
output = ['#!/usr/bin/env python',
'# -*- coding: utf-8 -*-', '', 'atoms = {']
atom_dict = self.get_atoms(rxn)
for atom, count in atom_dict.iteritems():
output.append(" '{0}': {1},".format(atom, count))
output = output + ['}', '']
bond_dict = self.get_bonds(rxn)
if bond_dict != {}:
output.append('bonds = {')
for bond_type, num in bond_dict.iteritems():
output.append(" '{0}': {1},".format(bond_type, num))
output.append("}")
else:
output.append('bonds = {}')
conf.rmg_molecule.updateMultiplicity()
external_symmetry = conf.rmg_molecule.getSymmetryNumber()
output += ["",
"linear = False",
"",
"externalSymmetry = {}".format(external_symmetry),
"",
"spinMultiplicity = {}".format(conf.rmg_molecule.multiplicity),
"",
"opticalIsomers = 1",
""]
output += ["energy = {", " '{0}': Log('{1}.log'),".format(
self.model_chemistry, rxn.label), "}", ""]
output += ["geometry = Log('{0}.log')".format(rxn.label), ""]
output += [
"frequencies = Log('{0}.log')".format(rxn.label), ""]
output += ["rotors = []", ""]
input_string = ""
for t in output:
input_string += t + "\n"
with open(os.path.join(self.scratch, rxn.label + ".py"), "w") as f:
f.write(input_string)
def write_arkane_ts(self, rxn):
top = [
"#!/usr/bin/env python",
"# -*- coding: utf-8 -*-",
"",
'modelChemistry = "{0}"'.format(
self.model_chemistry),
"frequencyScaleFactor = {0}".format(
self.freq_scale_factor),
"useHinderedRotors = False",
"useBondCorrections = False",
""]
labels = []
r_smiles = []
p_smiles = []
for react in rxn.reactants:
conf = find_lowest_energy_conformer(react, self.scratch)
r_smiles.append(conf.smiles)
label = Chem.rdinchi.InchiToInchiKey(
Chem.MolToInchi(Chem.MolFromSmiles(conf.smiles))).strip("-N")
if label in labels:
continue
else:
labels.append(label)
line = "species('{0}', '{1}')".format(
conf.smiles, label + ".py")
top.append(line)
for prod in rxn.products:
conf = find_lowest_energy_conformer(prod, self.scratch)
p_smiles.append(conf.smiles)
label = Chem.rdinchi.InchiToInchiKey(
Chem.MolToInchi(Chem.MolFromSmiles(conf.smiles))).strip("-N")
if label in labels:
continue
else:
labels.append(label)
line = "species('{0}', '{1}')".format(
conf.smiles, label + ".py")
top.append(line)
line = "transitionState('TS', '{0}')".format(rxn.label + ".py")
top.append(line)
line = ["",
"reaction(",
" label = '{0}',".format(rxn.label),
" reactants = ['{0}', '{1}'],".format(
r_smiles[0], r_smiles[1]),
" products = ['{0}', '{1}'],".format(
p_smiles[0], p_smiles[1]),
" transitionState = 'TS',",
" tunneling = 'Eckart',",
")",
"",
"statmech('TS')",
"kinetics('{0}')".format(rxn.label)]
top += line
input_string = ""
for t in top:
input_string += t + "\n"
with open(os.path.join(self.scratch, rxn.label + ".ark.py"), "w") as f:
f.write(input_string)
def write_files(self):
for mol in self.reaction.reactants:
self.write_arkane_for_reacts_and_prods(mol)
for mol in self.reaction.products:
self.write_arkane_for_reacts_and_prods(mol)
self.write_statmech_ts(self.reaction)
self.write_arkane_ts(self.reaction)
def run(self):
self.arkane_job.inputFile = os.path.join(
self.scratch, self.reaction.label + ".ark.py")
self.arkane_job.plot = False
# try:
self.arkane_job.execute()
# except IOError:
for job in self.arkane_job.jobList:
if isinstance(job, KineticsJob):
self.kinetics_job = job
elif isinstance(job, ThermoJob)
def set_reactants_and_products(self):
for reactant in self.reaction.rmg_reaction.reactants:
for r in self.kinetics_job.reaction.reactants:
if reactant.toSMILES() == r.label:
r.molecule = [reactant]
for product in self.reaction.rmg_reaction.products:
for p in self.kinetics_job.reaction.products:
if product.toSMILES() == p.label:
p.molecule = [product]
self.reaction.rmg_reaction = self.kinetics_job.reaction
return self.reaction
class StatMech():
def __init__(self,
reaction,
directory=".",
model_chemistry="M06-2X/cc-pVTZ",
freq_scale_factor=0.982):
"""
A class to perform Arkane calculations:
:param: reaction: (Reaction) The reaction of interest
:param: output_directory: (str) The directory where you would like output files written to
:param: model_chemistry: (str) The supported model_chemistry described by http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/input.html#model-chemistry
:param: freq_scale_factor: (float) The scaling factor corresponding to the model chemistry - source:https://comp.chem.umn.edu/freqscale/version3b1.htm
"""
self.reaction = reaction
self.directory = directory
self.kinetics_job = RMGArkane()
self.thermo_job = RMGArkane()
self.model_chemistry = model_chemistry
self.freq_scale_factor = freq_scale_factor
def get_atoms(self, conformer):
"""
A method to create an atom dictionary for an rmg molecule from a `Conformer` object.
Parameters:
- conformer (Conformer): a conformer object that you want atom info from
Returns:
- atom_dict (dict): a dictionary containing counts of different atom types
"""
atom_dict = {}
for atom in conformer.rmg_molecule.atoms:
if atom.isCarbon():
atom_type = "C"
if atom.isHydrogen():
atom_type = "H"
if atom.isOxygen():
atom_type = "O"
try:
atom_dict[atom_type] += 1
except KeyError:
atom_dict[atom_type] = 1
return atom_dict
def get_bonds(self, conformer):
"""
A method to create a bond dictionary for an rmg molecule from a `Conformer` object.
Parameters:
- conformer (Conformer): a conformer object that you want bond info from
Returns:
- bondDict (dict): a dictionary containing counts of different bond types
"""
bonds = conformer.rmg_molecule.getAllEdges()
bondDict = {}
for bond in bonds:
if bond.isSingle():
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C-C'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'H'):
bondType = 'H-H'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'H') or (bond.atom1.symbol == 'H'
and bond.atom2.symbol == 'C'):
bondType = 'C-H'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'O'):
bondType = 'O-O'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'O') or (bond.atom1.symbol == 'O'
and bond.atom2.symbol == 'C'):
bondType = 'C-O'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol
== 'O') or (bond.atom1.symbol == 'O'
and bond.atom2.symbol == 'H'):
bondType = 'O-H'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N-N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'C'):
bondType = 'N-C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'O'):
bondType = 'N-O'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'H'):
bondType = 'N-H'
elif bond.atom1.symbol == 'S' and bond.atom2.symbol == 'S':
bondType = 'S-S'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol
== 'S') or (bond.atom1.symbol == 'S'
and bond.atom2.symbol == 'H'):
bondType = 'S-H'
elif bond.isDouble:
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C=C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'O'):
bondType = 'O=O'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'O') or (bond.atom1.symbol == 'O'
and bond.atom2.symbol == 'C'):
bondType = 'C=O'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N=N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'C'):
bondType = 'N=C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'O'):
bondType = 'N=O'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol
== 'S') or (bond.atom1.symbol == 'S'
and bond.atom2.symbol == 'O'):
bondType = 'S=O'
elif bond.isTriple:
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C#C'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N#N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'C'):
bondType = 'N#C'
try:
bondDict[bondType] += 1
except KeyError:
bondDict[bondType] = 1
return bondDict
def write_species_files(self, species):
"""
A method to write Arkane files for all conformers in a Species object
Parameters:
- species (Species): a species object that you want to write arkane files for
- scratch (str): the directory where you want to write arkane files to, there should be a 'species/SMILES/' subdirectory
Returns:
- None
"""
for smiles, confs in list(species.conformers.items()):
if os.path.exists(
os.path.join(self.directory, "species", smiles,
smiles + ".log")):
logging.info(
"Lowest energy conformer log file exists for {}".format(
smiles))
self.write_conformer_file(conformer=confs[0])
else:
logging.info(
"Lowest energy conformer log file DOES NOT exist for {}".
format(smiles))
def write_conformer_file(self, conformer):
"""
A method to write Arkane files for a single Conformer object
Parameters:
- conformer (Conformer): a Conformer object that you want to write an Arkane file for
- scratch (str): the directory where you want to write arkane files to, there should be a 'species/SMILES/' subdirectory
Returns:
- None
"""
label = conformer.smiles
if not os.path.exists(
os.path.join(self.directory, "species", label,
label + ".log")):
logging.info("There is no lowest energy conformer file...")
return False
if os.path.exists(
os.path.join(self.directory, "species", label, label + '.py')):
logging.info(
"Species input file already written... Not doing anything")
return True
parser = ccread(
os.path.join(self.directory, "species", label, label + ".log"))
symbol_dict = {
35: "Br",
17: "Cl",
9: "F",
8: "O",
7: "N",
6: "C",
1: "H",
}
atoms = []
for atom_num, coords in zip(parser.atomnos, parser.atomcoords[-1]):
atoms.append(Atom(symbol=symbol_dict[atom_num], position=coords))
conformer.ase_molecule = Atoms(atoms)
conformer.update_coords_from("ase")
mol = conformer.rmg_molecule
output = [
'#!/usr/bin/env python', '# -*- coding: utf-8 -*-', '', 'atoms = {'
]
atom_dict = self.get_atoms(conformer=conformer) # Fix this
for atom, count in atom_dict.items():
output.append(" '{0}': {1},".format(atom, count))
output = output + ['}', '']
bond_dict = self.get_bonds(conformer=conformer)
if bond_dict != {}:
output.append('bonds = {')
for bond_type, num in bond_dict.items():
output.append(" '{0}': {1},".format(bond_type, num))
output.append("}")
else:
output.append('bonds = {}')
external_symmetry = conformer.calculate_symmetry_number()
output += [
"", "linear = {}".format(conformer.rmg_molecule.isLinear()), "",
"externalSymmetry = {}".format(external_symmetry), "",
"spinMultiplicity = {}".format(
conformer.rmg_molecule.multiplicity), "", "opticalIsomers = 1",
""
]
output += [
"energy = {",
" '{0}': Log('{1}.log'),".format(self.model_chemistry,
label), "}", ""
] # fix this
output += ["geometry = Log('{0}.log')".format(label), ""]
output += ["frequencies = Log('{0}.log')".format(label), ""]
"""
TODO: add rotor information @carl
output += ["rotors = ["]
for torsion in conf.torsions:
output += [self.get_rotor_info(conf, torsion)]
output += ["]"]
"""
input_string = ""
for t in output:
input_string += t + "\n"
with open(
os.path.join(self.directory, "species", label, label + '.py'),
"w") as f:
f.write(input_string)
return True
def get_rotor_info(self, conformer, torsion_index):
"""
Formats and returns info about torsion as it should appear in an Arkane species.py
The following are needed for an Arkane input file:
- scanLog :: Gaussian output log of freq calculation on optimized geometry
- pivots :: torsion center: j,k of i,j,k,l (Note Arkane begins indexing with 1)
- top :: ID of all atoms in one top (Note Arkane begins indexing with 1)
Parameters:
- conformer (Conformer): autotst conformer object
- torsion (Torsion): autotst torsion object
Returns:
- info (str): a string containing all of the relevant information for a hindered rotor scan
"""
torsion = conformer.torsions[torsion_index]
_, j, k, _ = torsion.atom_indices
# Adjusted since mol's IDs start from 0 while Arkane's start from 1
tor_center_adj = [j + 1, k + 1]
if isinstance(conformer, TS):
tor_log = os.path.join(
scratch, "ts", conformer.reaction_label, "torsions",
comformer.reaction_label + "_36by10_{0}_{1}.log".format(j, k))
else:
tor_log = os.path.join(
scratch, "species", conformer.smiles, "torsions",
conformer.smiles + '_36by10_{0}_{1}.log'.format(j, k))
if not os.path.exists(tor_log):
logging.info(
"Torsion log file does not exist for {}".format(torsion))
return ""
top_IDs = []
for num, tf in enumerate(torsion.mask):
if tf:
top_IDs.append(num)
# Adjusted to start from 1 instead of 0
top_IDs_adj = [ID + 1 for ID in top_IDs]
info = " HinderedRotor(scanLog=Log('{0}'), pivots={1}, top={2}, fit='fourier'),".format(
tor_log, tor_center_adj, top_IDs_adj)
return info
def write_ts_input(self, transitionstate):
"""
A method to write Arkane files for a single TS object
Parameters:
- transitionstate (TS): a TS object that you want to write an Arkane file for
- scratch (str): the directory where you want to write arkane files to, there should be a 'ts/REACTION_LABEL/' subdirectory
Returns:
- None
"""
label = transitionstate.reaction_label
if os.path.exists(
os.path.join(self.directory, "ts", label, label + '.py')):
logging.info("TS input file already written... Not doing anything")
return True
if not os.path.exists(
os.path.join(self.directory, "ts", label, label + ".log")):
logging.info("There is no lowest energy conformer file...")
return False
parser = ccread(
os.path.join(self.directory, "ts", label, label + ".log"))
symbol_dict = {
17: "Cl",
9: "F",
8: "O",
7: "N",
6: "C",
1: "H",
}
atoms = []
for atom_num, coords in zip(parser.atomnos, parser.atomcoords[-1]):
atoms.append(Atom(symbol=symbol_dict[atom_num], position=coords))
transitionstate.ase_molecule = Atoms(atoms)
transitionstate.update_coords_from("ase")
output = [
'#!/usr/bin/env python', '# -*- coding: utf-8 -*-', '', 'atoms = {'
]
atom_dict = self.get_atoms(conformer=transitionstate) # need to fix
for atom, count in atom_dict.items():
output.append(" '{0}': {1},".format(atom, count))
output = output + ['}', '']
bond_dict = self.get_bonds(conformer=transitionstate) # need to fix
if bond_dict != {}:
output.append('bonds = {')
for bond_type, num in bond_dict.items():
output.append(" '{0}': {1},".format(bond_type, num))
output.append("}")
else:
output.append('bonds = {}')
transitionstate.rmg_molecule.updateMultiplicity()
external_symmetry = transitionstate.calculate_symmetry_number()
output += [
"", "linear = False", "",
"externalSymmetry = {}".format(external_symmetry), "",
"spinMultiplicity = {}".format(
transitionstate.rmg_molecule.multiplicity), "",
"opticalIsomers = 1", ""
]
output += [
"energy = {",
" '{0}': Log('{1}.log'),".format(self.model_chemistry,
label), "}", ""
] # fix this
output += ["geometry = Log('{0}.log')".format(label), ""]
output += ["frequencies = Log('{0}.log')".format(label), ""]
output += ["rotors = []", ""] # TODO: Fix this
input_string = ""
for t in output:
input_string += t + "\n"
with open(os.path.join(self.directory, "ts", label, label + '.py'),
"w") as f:
f.write(input_string)
return True
def write_kinetics_input(self):
"""
A method to write Arkane file to obtain kinetics for a Reaction object
Parameters:
- reaction (Reaction): a Reaction object that you want to write an Arkane kinetics job file for.
- scratch (str): the directory where you want to write arkane files to, there should be a 'species/SMILES/' subdirectory
Returns:
- None
"""
top = [
"#!/usr/bin/env python",
"# -*- coding: utf-8 -*-",
"",
'modelChemistry = "{0}"'.format(self.model_chemistry), # fix this
"frequencyScaleFactor = {0}".format(
self.freq_scale_factor), # fix this
"useHinderedRotors = False", # fix this @carl
"useBondCorrections = False",
""
]
labels = []
r_smiles = []
p_smiles = []
for i, react in enumerate(self.reaction.reactants):
lowest_energy = 1e5
lowest_energy_conf = None
if len(list(react.conformers.keys())) > 1:
for smiles in list(react.conformers.keys()):
path = os.path.join(self.directory, "species", smiles,
smiles + ".log")
if not os.path.exists(path):
logging.info(
"It looks like {} doesn't have any optimized geometries"
.format(smiles))
continue
parser = ccread(path)
energy = parser.scfenergies[-1]
if energy < lowest_energy:
lowest_energy = energy
lowest_energy_conf = react.conformers[smiles][0]
else:
smiles = list(react.conformers.keys())[0]
path = os.path.join(self.directory, "species", smiles,
smiles + ".log")
if not os.path.exists(path):
logging.info(
"It looks like {} doesn't have any optimized geometries"
.format(smiles))
continue
parser = ccread(path)
lowest_energy = parser.scfenergies[-1]
lowest_energy_conf = list(react.conformers.values())[0][0]
# r_smiles.append(lowest_energy_conf.smiles)
r_smiles.append("react_{}".format(i))
label = lowest_energy_conf.smiles
if label in labels:
continue
else:
labels.append(label)
line = "species('{0}', '{1}', structure=SMILES('{2}'))".format(
"react_{}".format(i),
os.path.join(self.directory, "species", label, label + ".py"),
label)
top.append(line)
for i, prod in enumerate(self.reaction.products):
lowest_energy = 1e5
lowest_energy_conf = None
if len(list(prod.conformers.keys())) > 1:
for smiles in list(prod.conformers.keys()):
path = os.path.join(self.directory, "species", smiles,
smiles + ".log")
if not os.path.exists(path):
logging.info(
"It looks like {} doesn't have any optimized geometries"
.format(smiles))
continue
parser = ccread(path)
energy = parser.scfenergies[-1]
if energy < lowest_energy:
lowest_energy = energy
lowest_energy_conf = prod.conformers[smiles][0]
else:
smiles = list(prod.conformers.keys())[0]
path = os.path.join(self.directory, "species", smiles,
smiles + ".log")
if not os.path.exists(path):
logging.info(
"It looks like {} doesn't have any optimized geometries"
.format(smiles))
continue
parser = ccread(path)
lowest_energy = parser.scfenergies[-1]
lowest_energy_conf = list(prod.conformers.values())[0][0]
# p_smiles.append(lowest_energy_conf.smiles)
p_smiles.append("prod_{}".format(i))
label = lowest_energy_conf.smiles
if label in labels:
continue
else:
labels.append(label)
line = "species('{0}', '{1}', structure=SMILES('{2}'))".format(
"prod_{}".format(i),
os.path.join(self.directory, "species", label, label + ".py"),
label)
top.append(line)
line = "transitionState('TS', '{0}')".format(
os.path.join(self.directory, "ts", self.reaction.label,
self.reaction.label + ".py"))
top.append(line)
line = [
"", "reaction(", " label = '{0}',".format(self.reaction.label),
" reactants = {},".format(r_smiles),
" products = {},".format(p_smiles),
" transitionState = 'TS',", " tunneling = 'Eckart',", ")",
"", "statmech('TS')", "kinetics('{0}')".format(self.reaction.label)
]
top += line
input_string = ""
for t in top:
input_string += t + "\n"
with open(
os.path.join(self.directory, "ts", self.reaction.label,
self.reaction.label + ".kinetics.py"), "w") as f:
f.write(input_string)
def write_thermo_input(self, conformer):
"""
A method to write Arkane file to obtain thermochemistry for a Conformer object
Parameters:
- conformer (Conformer): a Conformer object that you want to write an Arkane thermo job file for.
- scratch (str): the directory where you want to write arkane files to, there should be a 'species/SMILES/' subdirectory
Returns:
- None
"""
model_chemistry = self.model_chemistry
freq_scale_factor = self.freq_scale_factor
top = [
"#!/usr/bin/env python",
"# -*- coding: utf-8 -*-",
"",
'modelChemistry = "{0}"'.format(model_chemistry), # fix this
"frequencyScaleFactor = {0}".format(freq_scale_factor), # fix this
"useHinderedRotors = False", # fix this @carl
"useBondCorrections = False",
""
]
line = "species('species', '{1}', structure=SMILES('{2}'))".format(
"species", os.path.join(conformer.smiles + ".py"),
conformer.smiles)
top.append(line)
top.append("statmech('species')")
top.append("thermo('species', 'NASA')")
input_string = ""
for t in top:
input_string += t + "\n"
with open(
os.path.join(self.directory, "species", conformer.smiles,
conformer.smiles + ".thermo.py"), "w") as f:
f.write(input_string)
def write_files(self):
"""
A method to write all species, transition state, and kinetics job files to obtain kinetic parameters
Parameters:
- None
Returns:
- None
"""
for mol in self.reaction.reactants:
for smiles, confs in list(mol.conformers.items()):
conf = confs[0]
self.write_conformer_file(conf)
for mol in self.reaction.products:
for smiles, confs in list(mol.conformers.items()):
conf = confs[0]
self.write_conformer_file(conf)
self.write_ts_input(self.reaction.ts["forward"][0])
self.write_kinetics_input()
def run(self):
"""
A method to write run a kinetics job from all of the files written `write_files`
Parameters:
- None
Returns:
- None
"""
self.kinetics_job.inputFile = os.path.join(
self.directory, "ts", self.reaction.label,
self.reaction.label + ".kinetics.py")
self.kinetics_job.plot = False
self.kinetics_job.outputDirectory = os.path.join(
self.directory, "ts", self.reaction.label)
self.kinetics_job.execute()
for job in self.kinetics_job.jobList:
if isinstance(job, KineticsJob):
self.kinetics_job = job
elif isinstance(job, ThermoJob):
self.thermo_job = job
def set_results(self):
"""
A method to set the RMGReaction from the kinetics job to the RMGReaction of the input Reaction
Parameters:
- None
Returns:
- None
"""
for reactant in self.reaction.rmg_reaction.reactants:
for r in self.kinetics_job.reaction.reactants:
if reactant.toSMILES() == r.label:
r.molecule = [reactant]
for product in self.reaction.rmg_reaction.products:
for p in self.kinetics_job.reaction.products:
if product.toSMILES() == p.label:
p.molecule = [product]
self.reaction.rmg_reaction = self.kinetics_job.reaction
return self.reaction
class StatMech(Calculator):
def __init__(self,
reaction,
scratch=".",
output_directory=".",
model_chemistry="M06-2X/cc-pVTZ",
freq_scale_factor=0.982):
"""
A class to perform Arkane calculations:
:param: reaction: (Reaction) The reaction of interest
:param: output_directory: (str) The directory where you would like output files written to
:param: model_chemistry: (str) The supported model_chemistry described by http://reactionmechanismgenerator.github.io/RMG-Py/users/arkane/input.html#model-chemistry
:param: freq_scale_factor: (float) The scaling factor corresponding to the model chemistry - source:https://comp.chem.umn.edu/freqscale/version3b1.htm
"""
self.reaction = reaction
self.scratch = scratch
self.arkane_job = RMGArkane()
self.output_directory = output_directory
self.arkane_job.outputDirectory = self.output_directory
self.model_chemistry = model_chemistry
self.freq_scale_factor = freq_scale_factor
def get_atoms(self, species):
"""
A method to create an atom dictionary for an rmg molecule
"""
atom_dict = {}
conf = find_lowest_energy_conformer(species, self.scratch)
rmg_mol = conf.rmg_molecule
for atom in rmg_mol.atoms:
if atom.isCarbon():
atom_type = "C"
if atom.isHydrogen():
atom_type = "H"
if atom.isOxygen():
atom_type = "O"
try:
atom_dict[atom_type] += 1
except KeyError:
atom_dict[atom_type] = 1
return atom_dict
def get_bonds(self, species):
conf = find_lowest_energy_conformer(species, self.scratch)
rmg_mol = conf.rmg_molecule
bondList = []
for atom in rmg_mol.atoms:
for bond in atom.bonds.values():
bondList.append(bond)
bonds = list(set(bondList))
bondDict = {}
for bond in bonds:
if bond.isSingle():
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C-C'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol == 'H'):
bondType = 'H-H'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'H') or (bond.atom1.symbol == 'H'
and bond.atom2.symbol == 'C'):
bondType = 'C-H'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'O'):
bondType = 'O-O'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'O') or (bond.atom1.symbol == 'O'
and bond.atom2.symbol == 'C'):
bondType = 'C-O'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol
== 'O') or (bond.atom1.symbol == 'O'
and bond.atom2.symbol == 'H'):
bondType = 'O-H'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N-N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'C'):
bondType = 'N-C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'O'):
bondType = 'N-O'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'H'):
bondType = 'N-H'
elif bond.atom1.symbol == 'S' and bond.atom2.symbol == 'S':
bondType = 'S-S'
elif (bond.atom1.symbol == 'H' and bond.atom2.symbol
== 'S') or (bond.atom1.symbol == 'S'
and bond.atom2.symbol == 'H'):
bondType = 'S-H'
elif bond.isDouble:
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C=C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol == 'O'):
bondType = 'O=O'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'O') or (bond.atom1.symbol == 'O'
and bond.atom2.symbol == 'C'):
bondType = 'C=O'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N=N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'C'):
bondType = 'N=C'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'O'):
bondType = 'N=O'
elif (bond.atom1.symbol == 'O' and bond.atom2.symbol
== 'S') or (bond.atom1.symbol == 'S'
and bond.atom2.symbol == 'O'):
bondType = 'S=O'
elif bond.isTriple:
if bond.atom1.symbol == 'C' and bond.atom2.symbol == 'C':
bondType = 'C#C'
elif bond.atom1.symbol == 'N' and bond.atom2.symbol == 'N':
bondType = 'N#N'
elif (bond.atom1.symbol == 'C' and bond.atom2.symbol
== 'N') or (bond.atom1.symbol == 'N'
and bond.atom2.symbol == 'C'):
bondType = 'N#C'
try:
bondDict[bondType] += 1
except KeyError:
bondDict[bondType] = 1
return bondDict
def write_arkane_for_reacts_and_prods(self, species):
"""
a method to write species to an arkane input file. Mol is an RMGMolecule
"""
conf = find_lowest_energy_conformer(species, self.scratch)
mol = conf.rmg_molecule
output = [
'#!/usr/bin/env python', '# -*- coding: utf-8 -*-', '', 'atoms = {'
]
atom_dict = self.get_atoms(species)
for atom, count in atom_dict.iteritems():
output.append(" '{0}': {1},".format(atom, count))
output = output + ['}', '']
bond_dict = self.get_bonds(species)
if bond_dict != {}:
output.append('bonds = {')
for bond_type, num in bond_dict.iteritems():
output.append(" '{0}': {1},".format(bond_type, num))
output.append("}")
else:
output.append('bonds = {}')
label = Chem.rdinchi.InchiToInchiKey(
Chem.MolToInchi(Chem.MolFromSmiles(mol.toSMILES()))).strip("-N")
external_symmetry = mol.getSymmetryNumber()
output += [
"", "linear = False", "",
"externalSymmetry = {}".format(external_symmetry), "",
"spinMultiplicity = {}".format(mol.multiplicity), "",
"opticalIsomers = 1", ""
]
output += [
"energy = {",
" '{0}': Log('{1}.log'),".format(self.model_chemistry,
label), "}", ""
]
output += ["geometry = Log('{0}.log')".format(label), ""]
output += ["frequencies = Log('{0}.log')".format(label), ""]
output += ["rotors = []"]
input_string = ""
for t in output:
input_string += t + "\n"
with open(os.path.join(self.scratch, label + ".py"), "w") as f:
f.write(input_string)
def write_statmech_ts(self, rxn):
conf = find_lowest_energy_conformer(rxn, self.scratch)
output = [
'#!/usr/bin/env python', '# -*- coding: utf-8 -*-', '', 'atoms = {'
]
atom_dict = self.get_atoms(rxn)
for atom, count in atom_dict.iteritems():
output.append(" '{0}': {1},".format(atom, count))
output = output + ['}', '']
bond_dict = self.get_bonds(rxn)
if bond_dict != {}:
output.append('bonds = {')
for bond_type, num in bond_dict.iteritems():
output.append(" '{0}': {1},".format(bond_type, num))
output.append("}")
else:
output.append('bonds = {}')
conf.rmg_molecule.updateMultiplicity()
external_symmetry = conf.rmg_molecule.getSymmetryNumber()
output += [
"", "linear = False", "",
"externalSymmetry = {}".format(external_symmetry), "",
"spinMultiplicity = {}".format(conf.rmg_molecule.multiplicity), "",
"opticalIsomers = 1", ""
]
output += [
"energy = {",
" '{0}': Log('{1}.log'),".format(self.model_chemistry,
rxn.label), "}", ""
]
output += ["geometry = Log('{0}.log')".format(rxn.label), ""]
output += ["frequencies = Log('{0}.log')".format(rxn.label), ""]
output += ["rotors = []", ""]
input_string = ""
for t in output:
input_string += t + "\n"
with open(os.path.join(self.scratch, rxn.label + ".py"), "w") as f:
f.write(input_string)
def write_arkane_ts(self, rxn):
top = [
"#!/usr/bin/env python", "# -*- coding: utf-8 -*-", "",
'modelChemistry = "{0}"'.format(self.model_chemistry),
"frequencyScaleFactor = {0}".format(self.freq_scale_factor),
"useHinderedRotors = False", "useBondCorrections = False", ""
]
labels = []
r_smiles = []
p_smiles = []
for react in rxn.reactants:
conf = find_lowest_energy_conformer(react, self.scratch)
r_smiles.append(conf.smiles)
label = Chem.rdinchi.InchiToInchiKey(
Chem.MolToInchi(Chem.MolFromSmiles(conf.smiles))).strip("-N")
if label in labels:
continue
else:
labels.append(label)
line = "species('{0}', '{1}')".format(conf.smiles, label + ".py")
top.append(line)
for prod in rxn.products:
conf = find_lowest_energy_conformer(prod, self.scratch)
p_smiles.append(conf.smiles)
label = Chem.rdinchi.InchiToInchiKey(
Chem.MolToInchi(Chem.MolFromSmiles(conf.smiles))).strip("-N")
if label in labels:
continue
else:
labels.append(label)
line = "species('{0}', '{1}')".format(conf.smiles, label + ".py")
top.append(line)
line = "transitionState('TS', '{0}')".format(rxn.label + ".py")
top.append(line)
line = [
"", "reaction(", " label = '{0}',".format(rxn.label),
" reactants = ['{0}', '{1}'],".format(r_smiles[0], r_smiles[1]),
" products = ['{0}', '{1}'],".format(p_smiles[0], p_smiles[1]),
" transitionState = 'TS',", " tunneling = 'Eckart',", ")",
"", "statmech('TS')", "kinetics('{0}')".format(rxn.label)
]
top += line
input_string = ""
for t in top:
input_string += t + "\n"
with open(os.path.join(self.scratch, rxn.label + ".ark.py"), "w") as f:
f.write(input_string)
def write_files(self):
for mol in self.reaction.reactants:
print mol
self.write_arkane_for_reacts_and_prods(mol)
for mol in self.reaction.products:
self.write_arkane_for_reacts_and_prods(mol)
self.write_statmech_ts(self.reaction)
self.write_arkane_ts(self.reaction)
def run(self):
self.arkane_job.inputFile = os.path.join(
self.scratch, self.reaction.label + ".ark.py")
print self.arkane_job.inputFile
self.arkane_job.plot = False
#try:
self.arkane_job.execute()
#except IOError:
# print "There was an issue with Cairo..."
for job in self.arkane_job.jobList:
if isinstance(job, KineticsJob):
self.kinetics_job = job
def set_reactants_and_products(self):
for reactant in self.reaction.rmg_reaction.reactants:
for r in self.kinetics_job.reaction.reactants:
if reactant.toSMILES() == r.label:
r.molecule = [reactant]
for product in self.reaction.rmg_reaction.products:
for p in self.kinetics_job.reaction.products:
if product.toSMILES() == p.label:
p.molecule = [product]
self.reaction.rmg_reaction = self.kinetics_job.reaction
return self.reaction