def main():
try:
input_file = sys.argv[1]
except IndexError:
print('To use KinBot, supply one argument being the input file!')
sys.exit(-1)
# print the license message to the console
print(license_message.message)
# initialize the parameters for this run
masterpar = Parameters(input_file)
par = masterpar.par
input_file = masterpar.input_file
# set up the logging environment
if par['verbose']:
logging.basicConfig(filename='kinbot.log', level=logging.DEBUG)
else:
logging.basicConfig(filename='kinbot.log', level=logging.INFO)
# write the license message to the log file
logging.info(license_message.message)
logging.info('Input parameters')
for param in par:
logging.info('{} {}'.format(param, par[param]))
# time stamp of the KinBot start
logging.info('Starting KinBot at {}'.format(datetime.datetime.now()))
# Make the necessary directories
if not os.path.exists('perm'):
os.makedirs('perm')
if not os.path.exists('scratch'):
os.makedirs('scratch')
if not os.path.exists(par['single_point_qc']):
os.mkdir(par['single_point_qc'])
if par['rotor_scan'] == 1:
if not os.path.exists('hir'):
os.mkdir('hir')
if not os.path.exists('hir_profiles'):
os.mkdir('hir_profiles')
if not os.path.exists('perm/hir/'):
os.makedirs('perm/hir/')
if par['conformer_search'] == 1:
if not os.path.exists('conf'):
os.mkdir('conf')
if not os.path.exists('perm/conf'):
os.makedirs('perm/conf')
if not os.path.exists('me'):
os.mkdir('me')
# initialize the reactant
well0 = StationaryPoint('well0',
par['charge'],
par['mult'],
smiles=par['smiles'],
structure=par['structure'])
well0.short_name = 'w1'
# write the initial reactant geometry to a file for visualization
geom_out = open('geometry.xyz', 'w')
geom_out.write('{}\n\n'.format(well0.natom))
for i, at in enumerate(well0.atom):
x, y, z = well0.geom[i]
geom_out.write('{} {:.6f} {:.6f} {:.6f}\n'.format(at, x, y, z))
geom_out.write('\n\n')
geom_out.close()
# characterize the initial reactant
well0.characterize(dimer=par['dimer'])
well0.name = str(well0.chemid)
start_name = well0.name
# initialize the qc instance
qc = QuantumChemistry(par)
# only run filecopying if PES is turned on
# if par['pes']:
# check if this well was calcualted before in another directory
# this flag indicates that this kinbot run
# should wait for the information from another
# kinbot run to become available and copy the necessary information
# wait_for_well = 1
# while wait_for_well:
# wait_for_well = filecopying.copy_from_database_folder(well0.chemid, well0.chemid, qc)
# if wait_for_well:
# time.sleep(1)
# start the initial optimization of the reactant
logging.info('Starting optimization of intial well')
qc.qc_opt(well0, well0.geom)
err, well0.geom = qc.get_qc_geom(str(well0.chemid) + '_well',
well0.natom,
wait=1)
err, well0.freq = qc.get_qc_freq(str(well0.chemid) + '_well',
well0.natom,
wait=1)
if err < 0:
logging.error('Error with initial structure optimization.')
return
if any(well0.freq[i] <= 0 for i in range(len(well0.freq))):
logging.error('Found imaginary frequency for initial structure.')
return
# characterize again and look for differences
well0.characterize(dimer=par['dimer'])
well0.name = str(well0.chemid)
if well0.name != start_name:
logging.error(
'The first well optimized to a structure different from the input.'
)
return
# do an MP2 optimization of the reactant,
# to compare some scan barrier heigths to
if par['families'] == ['all'] or \
'birad_recombination_R' in par['families'] or \
'r12_cycloaddition' in par['families'] or \
'r14_birad_scission' in par['families'] or \
'R_Addition_MultipleBond' in par['families'] or \
(par['skip_families'] != ['none'] and \
('birad_recombination_R' not in par['skip_families'] or \
'r12_cycloaddition' not in par['skip_families'] or \
'r14_birad_scission' not in par['skip_families'] or \
'R_Addition_MultipleBond' not in par['skip_families'])) or \
par['reaction_search'] == 0:
logging.info('Starting MP2 optimization of intial well')
qc.qc_opt(well0, well0.geom, mp2=1)
err, geom = qc.get_qc_geom(
str(well0.chemid) + '_well_mp2', well0.natom, 1)
# comparison for barrierless scan
if par['barrierless_saddle']:
logging.info(
'Optimization of intial well for barrierless at {}/{}'.format(
par['barrierless_saddle_method'],
par['barrierless_saddle_basis']))
qc.qc_opt(well0, well0.geom, bls=1)
err, geom = qc.get_qc_geom(
str(well0.chemid) + '_well_bls', well0.natom, 1)
# characterize again and look for differences
well0.characterize(dimer=par['dimer'])
well0.name = str(well0.chemid)
err, well0.energy = qc.get_qc_energy(str(well0.chemid) + '_well', 1)
err, well0.zpe = qc.get_qc_zpe(str(well0.chemid) + '_well', 1)
well_opt = Optimize(well0, par, qc, wait=1)
well_opt.do_optimization()
if well_opt.shigh == -999:
logging.error(
'Error with high level optimization of initial structure.')
return
if par['pes']:
filecopying.copy_to_database_folder(well0.chemid, well0.chemid, qc)
if par['reaction_search'] == 1:
logging.info('Starting reaction searches of intial well')
rf = ReactionFinder(well0, par, qc)
rf.find_reactions()
rg = ReactionGenerator(well0, par, qc, input_file)
rg.generate()
if par['homolytic_scissions'] == 1:
logging.info('Starting the search for homolytic scission products')
well0.homolytic_scissions = HomolyticScissions(well0, par, qc)
well0.homolytic_scissions.find_homolytic_scissions()
if par['me'] > 0: # it will be 2 for kinbots when the mess file is needed but not run
mess = MESS(par, well0)
mess.write_input(qc)
if par['me'] == 1:
logging.info('Starting Master Equation calculations')
if par['me_code'] == 'mess':
mess.run()
postprocess.createSummaryFile(well0, qc, par)
postprocess.createPESViewerInput(well0, qc, par)
postprocess.creatMLInput(well0, qc, par)
logging.info('Finished KinBot at {}'.format(datetime.datetime.now()))
print("Done!")
def main():
try:
input_file = sys.argv[1]
except IndexError:
print('To use KinBot, supply one argument being the input file!')
sys.exit(-1)
# print the license message to the console
print(license_message.message)
# initialize the parameters for this run
par = Parameters(input_file)
# set up the logging environment
if par.par['verbose']:
logging.basicConfig(filename='kinbot.log', level=logging.DEBUG)
else:
logging.basicConfig(filename='kinbot.log', level=logging.INFO)
# write the license message to the log file
logging.info(license_message.message)
# time stamp of the KinBot start
logging.info('Starting KinBot at {}'.format(datetime.datetime.now()))
# Make the necessary directories
if not os.path.exists('perm'):
os.makedirs('perm')
if not os.path.exists('scratch'):
os.makedirs('scratch')
if not os.path.exists(par.par['single_point_qc']):
os.mkdir(par.par['single_point_qc'])
if par.par['rotor_scan'] == 1:
if not os.path.exists('hir'):
os.mkdir('hir')
if not os.path.exists('hir_profiles'):
os.mkdir('hir_profiles')
if not os.path.exists('perm/hir/'):
os.makedirs('perm/hir/')
if par.par['conformer_search'] == 1:
if not os.path.exists('conf'):
os.mkdir('conf')
if not os.path.exists('perm/conf'):
os.makedirs('perm/conf')
if not os.path.exists('me'):
os.mkdir('me')
if par.par['pes'] and par.par['specific_reaction']:
logging.error('Specific reaction cannot be searched in PES mode.')
return
# initialize the reactant
well0 = StationaryPoint('well0',
par.par['charge'],
par.par['mult'],
smiles=par.par['smiles'],
structure=par.par['structure'])
well0.short_name = 'w1'
# wrtie the initial reactant geometry to a file for visualization
geom_out = open('geometry.xyz', 'w')
geom_out.write('{}\n\n'.format(well0.natom))
for i, at in enumerate(well0.atom):
x, y, z = well0.geom[i]
geom_out.write('{} {:.6f} {:.6f} {:.6f}\n'.format(at, x, y, z))
geom_out.write('\n\n')
geom_out.close()
# characterize the initial reactant
well0.characterize(par.par['dimer'])
well0.name = str(well0.chemid)
start_name = well0.name
# initialize the qc instance
qc = QuantumChemistry(par)
# start the initial optimization of the reactant
logging.info('Starting optimization of intial well')
qc.qc_opt(well0, well0.geom)
err, well0.geom = qc.get_qc_geom(str(well0.chemid) + '_well',
well0.natom, wait=1)
err, well0.freq = qc.get_qc_freq(str(well0.chemid) + '_well',
well0.natom, wait=1)
if err < 0:
logging.error('Error with initial structure optimization.')
return
if any(well0.freq[i] <= 0 for i in range(len(well0.freq))):
logging.error('Found imaginary frequency for initial structure.')
return
# characterize again and look for differences
well0.characterize(par.par['dimer'])
well0.name = str(well0.chemid)
if well0.name != start_name:
logging.error('The first well optimized to a structure different from the input.')
return
# do an MP2 optimization of the reactant,
# to compare Beta scission barrier heigths to
logging.info('Starting MP2 optimization of intial well')
qc.qc_opt(well0, well0.geom, mp2=1)
err, geom = qc.get_qc_geom(str(well0.chemid) + '_well_mp2', well0.natom, 1)
# characterize again and look for differences
well0.characterize(par.par['dimer'])
well0.name = str(well0.chemid)
# read the energy and the zpe corrected energy
err, well0.energy = qc.get_qc_energy(str(well0.chemid) + '_well', 1)
err, well0.zpe = qc.get_qc_zpe(str(well0.chemid) + '_well', 1)
well_opt = Optimize(well0, par, qc, wait=1)
well_opt.do_optimization()
if well_opt.shigh == -999:
logging.error('Error with high level optimization of initial structure.')
return
# do the reaction search using heuristics
if par.par['reaction_search'] == 1:
logging.info('Starting reaction searches of intial well')
rf = ReactionFinder(well0, par, qc)
rf.find_reactions()
rg = ReactionGenerator(well0, par, qc)
rg.generate()
# do the homolytic scission products search
if par.par['homolytic_scissions'] == 1:
logging.info('Starting the search for homolytic scission products')
well0.homolytic_scissions = HomolyticScissions(well0, par, qc)
well0.homolytic_scissions.find_homolytic_scissions()
# initialize the master equation instance
mess = MESS(par, well0)
mess.write_input()
mesmer = MESMER(par, well0)
mesmer.write_input()
if par.par['me'] == 1:
logging.info('Starting Master Equation calculations')
if par.par['me_code'] == 'mess':
mess.run()
elif par.par['me_code'] == 'mesmer':
mesmer.run()
else:
logging.error('Cannot recognize me code {}'.format(par.par['me_code']))
# postprocess the calculations
postprocess.createSummaryFile(well0, qc, par)
postprocess.createPESViewerInput(well0, qc, par)
postprocess.creatMLInput(well0, qc, par)
logging.info('Finished KinBot at {}'.format(datetime.datetime.now()))
print("Done!")