def check_hrs(n, typ):
"""
Checks MC geoms to make sure they are the same inchii as the starting species
"""
import sys
msg = 'Checking me_files/{1}{0}_hr.me'.format(str(n), typ)
filename = 'data/' + typ + str(n) + '.dat'
nrotors = 0
md = False
if io.check_file(filename):
data = io.read_file(filename)
tmp = data.split('nhind')
if len(tmp) > 2:
nrotors = tmp[1].split('\n')[1]
if len(tmp) > 3:
md = True
data = ''
filename = 'me_files/' + typ + str(n) + '_hr.me'
if io.check_file(filename):
data = io.read_file(filename)
else:
msg = '\nNo hr me_file found'
log.error(msg)
return
if md:
if 'MultiRotor' in data:
msg = '\nMDTau successfully completed'
log.info(msg)
else:
msg = '\nMD scan incomplete'
log.error(msg)
filename = 'me_files/' + typ + str(n) + '_1dhr.me'
if io.check_file(filename):
data = io.read_file(filename)
else:
msg += '\nNo 1dhr me_file found'
log.error(msg)
return
data = data.split('Rotor')
ncomplete = len(data) - 1
msg = '\n{0} out of {1} rotors successfully scanned'.format(
str(ncomplete), nrotors)
if int(nrotors) == ncomplete:
msg = '\n1DTau has completed successfully'
else:
msg = '\nScan incomplete'
log.error(msg)
log.info(msg)
return
def parse_thermo(self, n, species, d):
printstr = '\n=====================\n '+species+'\n=====================\n'
optprog, optmethod, optbasis = self.optlevel.split('/')
if self.enlevel == 'optlevel':
prog = optprog
method = optmethod
basis = optbasis
else:
prog, method, basis = self.enlevel.split('/')
d[ 'prog'] = prog
d['method'] = method
d[ 'basis'] = basis
if self.args.anharm != 'false':
anpfr = ', '.join('%4.4f' % freq for freq in self.anfreqs[n-1])
pxmat =('\n\t'.join(['\t'.join(['%3.3f'%item for item in row])
for row in self.anxmat[n-1]]))
printstr += '\nAnharmonic Frequencies (cm-1):\t' + anpfr
printstr += '\nX matrix:\n\t' + pxmat #+ anxmat[i-1]
d['panharm'] = anpfr
d[ 'pxmat'] = pxmat
printstr += '\nHeat of formation( 0K): {0:.2f} kcal / {1:.2f} kJ\n'.format(self.dH0[n-1], self.dH0[n-1]/.00038088/ 627.503)
printstr += 'Heat of formation(298K): {0:.2f} kcal / {1:.2f} kJ\n'.format(float(self.dH298[n-1]), float(self.dH298[n-1])/.00038088/ 627.503)
d[ 'dH0K'] = self.dH0
d[ 'dH298K'] = self.dH298
if self.args.store:
database = self.args.database
if self.args.anharm != 'false':
anprog, anmethod, anbasis = anlevel.split('/')
io.db_store_sp_prop(anpfr, species, 'panhrm', database, anprog, anmethod, anbasis, optprog, optmethod, optbasis)
io.db_store_sp_prop(pxmat, species, 'pxmat', database, anprog, anmethod, anbasis, optprog, optmethod, optbasis)
if not io.check_file(io.db_sp_path(prog, method, basis, database, species, optprog, optmethod, optbasis) + '/' + species + '.hf298k'):
io.db_store_sp_prop('Energy (kcal)\tBasis\n----------------------------------\n',species,'hf298k',database, prog,method,basis, optprog, optmethod, optbasis)
if len(self.hfbases) >= n+1:
io.db_append_sp_prop(str(self.dH298[n-1]) + '\t' + ', '.join(self.hfbases[n]) + '\n', species, 'hf298k',database, prog,method,basis, optprog, optmethod, optbasis)
return printstr, d
def extract_mess(filename):
"""
Extracts necessary EStokTP output for MESS
"""
lines = ''
if io.check_file(filename):
lines = io.read_file(filename)
if lines == '':
log.error(filename + ' is empty, check estoktp.log')
return lines
def get_results(self):
msg = printheader()
d = {}
for i,reac in enumerate(self.args.reacs, start=1):
lines = ''
if io.check_file('geoms/reac' + str(i) + '_l1.log'):
lines = io.read_file('geoms/reac' + str(i) + '_l1.log')
lines2 = ''
if io.check_file('me_files/reac' + str(i) + '_fr.me'):
lines2 = io.read_file('me_files/reac' + str(i) + '_fr.me')
if lines:
printstr, d[reac] = self.parse(i, reac, lines, lines2)
msg += printstr
else:
log.warning('No geom for ' + reac + ' in geoms/reac' + str(i) + '_l1.log')
for j,prod in enumerate(self.args.prods, start=1):
lines = ''
if io.check_file('geoms/prod' + str(i) + '_l1.log'):
lines = io.read_file('geoms/prod' + str(j) + '_l1.log')
lines2 = ''
if io.check_file('me_files/reac' + str(j) + '_fr.me'):
lines2 = io.read_file('me_files/prod' + str(j) + '_fr.me')
if lines:
printstr, d[prod] = self.parse(i+j-1, prod, lines, lines2)
msg += printstr
else:
log.warning('No geom for ' + prod + ' in geoms/prod' + str(j) + '_l1.log')
#if args.nTS > 0:
# lines = io.read_file('geoms/tsgta_l1.log')
# printstr += ts_parse(0,lines)
# if args.nTS > 1:
# lines = io.read_file('geoms/wellr_l1.log')
# printstr += ts_parse(1,lines)
# if args.nTS > 2:
# lines = io.read_file('geoms/wellp_l1.log')
# printstr += ts_parse(2,lines)
log.info(msg)
self.d = d
return
def me_file_abs_path():
"""
Replaces relative path in mdhr file with absolute path
"""
if io.check_file('me_files/reac1_hr.me'):
lines = io.read_file('me_files/reac1_hr.me')
if "PotentialEnergySurface[kcal/mol]" in lines:
before, after = lines.split("PotentialEnergySurface[kcal/mol]")
after = after.split('\n')
after[0] = after[0].replace('./', io.pwd() + '/')
lines = before + "PotentialEnergySurface[kcal/mol]" + '\n'.join(
after)
io.write_file(lines, 'me_files/reac1_hr.me')
return
def get_hlen(self):
hlen = []
msg = ''
for i in range(len(self.args.reacs)):
if io.check_file('me_files/reac'+str(i+1) + '_en.me'):
hlen.append(float(io.read_file('me_files/reac'+str(i+1) + '_en.me')))
for meth in self.args.meths:
if 'hlevel' in meth:
self.enlevel = '{}/{}'.format(meth[1],meth[2])
else:
msg += 'No energy found for reac{:g}\n'.format(i+1)
for i in range(len(self.args.prods)):
if io.check_file('me_files/prod'+str(i+1) + '_en.me'):
hlen.append(float(io.read_file('me_files/prod'+str(i+1) + '_en.me')))
else:
msg += 'No energy found for prod{:g}\n'.format(i+1)
if self.args.reactype:
if io.check_file('me_files/ts_en.me'):
hlen.append(float(io.read_file('me_files/ts_en.me')))
else:
msg += 'No energy found for ts\n'
if self.args.wellr and self.args.wellr.lower() != 'false':
if io.check_file('me_files/wellr_en.me'):
hlen.append(float(io.read_file('me_files/wellr_en.me')))
else:
msg += 'No energy found for wellr\n'
if self.args.wellp and self.args.wellp.lower() != 'false':
if io.check_file('me_files/wellp_en.me'):
hlen.append(float(io.read_file('me_files/wellp_en.me')))
else:
msg += 'No energy found for wellp\n'
log.warning(msg)
self.hlen = hlen
return hlen
def get_anharm(rorp,
i,
natom,
node,
anlevel,
anovrwrt,
species,
optlevel,
paths=''):
"""
Runs the anharm module to project out torsional modes from xmatrix and
find the updated vpt2 frequencies
"""
opts = {}
species = species.split('_m')[0]
opts['smiles'] = species
opts['node'] = node
opts['theory'] = anlevel
opts['optlevel'] = optlevel
opts['anlevel'] = anlevel
opts['natoms'] = natom
if 'ts' in rorp:
opts['logfile'] = 'geoms/' + 'tsgta_l1.log'
opts['freqfile'] = 'me_files/ts_fr.me'
opts['unprojfreq'] = 'me_files/ts_unpfr.me'
else:
opts['logfile'] = 'geoms/' + rorp + i + '_l1.log'
opts['freqfile'] = 'me_files/' + rorp + i + '_fr.me'
opts['unprojfreq'] = 'me_files/' + rorp + i + '_unpfr.me'
if io.check_file(ob.get_smiles_filename(species) +
'anharm.log') and not anovrwrt.lower() == 'true':
opts['anharmlog'] = ob.get_smiles_filename(species) + 'anharm'
opts['writegauss'] = 'false'
opts['rungauss'] = 'false'
else:
opts['writegauss'] = 'true'
opts['rungauss'] = 'true'
opts['anharmlog'] = ob.get_smiles_filename(species) + 'anharm'
return anharm.main(opts)
def check_geoms(name, nsamps):
"""
Checks MC geoms to make sure they are the same inchii as the starting species
"""
import sys
msg = 'Checking level0 geometries'
log.debug(msg)
n = 2
filename = 'geoms/' + name + '_' + '1'.zfill(n) + '.xyz'
lowfilename = filename
coords = io.read_file(filename)
lowcoords = coords
mol = ob.get_mol(coords)
inchi = ob.get_inchi_key(mol)
energy = float(coords.split('\n')[1])
for i in range(2, int(nsamps) + 1):
filename = 'geoms/' + name + '_' + '{}'.format(i).zfill(n) + '.xyz'
log.info(filename)
if io.check_file(filename):
coords = io.read_file(filename)
mol = ob.get_mol(coords)
if inchi == ob.get_inchi_key(mol):
if float(coords.split('\n')[1]) < energy:
energy = float(coords.split('\n')[1])
log.info('Lower energy of {:.2f} found in {}'.format(
energy, filename))
lowcoords = coords
lowfilename = filename
else:
log.info(
'Connectivity change after torsional optimization. (InChI mismatch) in {}.'
.format(filename))
io.cp(lowfilename, 'torsopt.xyz')
#io.write_file("\n".join(lowcoords.split("\n")),'geom.xyz')
io.write_file("\n".join(lowcoords.split("\n")[2:]), 'geom.xyz')
msg = '\nMonte Carlo sampling successfully found geom.xyz!\n'
log.info(msg)
return lowfilename
def run(args, paths, d={}):
"""
Runs heatform, partition_function, thermp, pac99, and write chemkin file
"""
import shutil
import re
reacs = args.reacs
prods = args.prods
anharm = args.anharm
anovrwrt = args.anovrwrt
node = args.nodes[0]
meths = args.meths
hfbasis = args.hfbasis
qtchf = args.qtchf
enlevel = args.enlevel
hlen = args.hlen
hfbases = []
speciess, speclist, anfreqs, anxmat = build_pfinput(args, d)
dH0 = []
dH298 = []
anharmbool = False
deltaH = 0
if anharm.lower() != 'false':
anharmbool = True
for i, species in enumerate(speciess):
if len(species.split('_m')) > 1:
species, mult = species.split('_m')[0], species.split('_m')[1]
if qtchf[0].lower() not in ['false', 'auto']:
if len(qtchf) >= i:
deltaH = float(qtchf[i])
hfbasis = ['N/A']
hfbases.append(hfbasis)
else:
logfile = 'geoms/' + speclist[i] + '_l1.log'
if speclist[i] == 'ts':
logfile = 'geoms/' + speclist[i] + 'gta_l1.log'
if io.check_file(logfile):
lines = io.read_file(logfile)
energy = pa.energy(lines)[1]
zpve = pa.zpve(lines)
printE = '{}- E: {:5g} pulled from: {}'.format(
species, energy, logfile)
printzpve = '{}- zpve: {:5g} pulled from: {}'.format(
species, zpve, logfile)
if enlevel != 'optlevel':
energy = hlen[i]
printE = '{}- E: {:5g} pulled from: {}'.format(
species, energy, 'me_files/' + speclist[i] + '_en.me')
if io.check_file('me_files/' + speclist[i] + '_zpe.me'):
zpve = float(
io.read_file('me_files/' + speclist[i] + '_zpe.me'))
printzpve = '{}- ZPVE: {:5g} pulled from: {}'.format(
species, zpve, 'me_files/' + speclist[i] + '_zpe.me')
if zpve:
energy = energy + zpve
log.info(printE + '\n' + printzpve)
deltaH, hfbasis = hf.main(species,
logfile,
E=energy,
basis=hfbasis,
anharm=anharmbool,
enlevel=enlevel)
hfbases.append(hfbasis)
else:
deltaH = 0.00
dH0.append(deltaH)
if not speclist[i] == 'ts':
log.debug('Running mess')
tc.run_pf('messpf', species + '.pf')
log.info('Completed')
log.debug('Generating thermp input.\n')
log.info('Completed')
stoich = ob.get_formula(ob.get_mol(species))
inp = tc.get_thermp_input(stoich, deltaH)
log.debug('Running thermp.\n')
if io.check_file(species + '.pf.dat'):
os.rename(species + '.pf.dat', 'pf.dat')
else:
log.error('No pf.dat produced, Restart at: 7!')
return [], [], [], [], []
tc.run_thermp(inp, 'thermp.dat', 'pf.dat', 'thermp')
lines = io.read_file('thermp.out')
log.info('Completed')
deltaH298 = ' h298 final\s*([\d,\-,\.]*)'
deltaH298 = re.findall(deltaH298, lines)[-1]
dH298.append(deltaH298)
log.debug('Running pac99.\n')
shutil.copyfile('/home/elliott/Packages/therm/new.groups',
'./new.groups')
shutil.copyfile(stoich + '.i97', species + '.i97')
tc.run_pac99(species, 'pac99')
c97file = species + '.c97'
if io.check_file(c97file):
c97text = io.read_file(c97file)
las, has, msg = tc.get_coefficients(c97text)
log.info('Completed')
else:
log.error('No {} produced'.format(c97file))
chemkinfile = stoich + '.ckin'
log.debug('Writing chemkin file {0}.\n'.format(chemkinfile))
method = meths[-1][2]
chemininput = tc.write_chemkin_file(species, method, deltaH,
float(deltaH298), stoich, 0,
las, has, chemkinfile)
log.info('Completed')
return dH0, dH298, hfbases, anfreqs, anxmat
def run_zero(args, paths, ists=False, restartts=False):
stoichs, symnums = build_files(args, paths, ists, len(args.nodes),
restartts)
successful = True
if not 'd' in args.nodes[0]:
if len(args.nodes) > 1:
import time
for i, node in enumerate(args.nodes):
if not ists:
io.rmrf(node)
io.mkdir(node)
io.cd(node)
shutil.copytree('../data', 'data')
else:
io.cd(node)
shutil.copy('../data/estoktp.dat', 'data/estoktp.dat')
for i in range(len(args.reacs)):
filename = 'output/reac' + str(i + 1) + '_opt.out'
if io.check_file('../' + filename):
shutil.copy('../' + filename, filename)
time.sleep(5)
execute(paths, node, '&')
io.cd('..')
running = True
outlength = {}
for node in args.nodes:
outlength[node] = 0
while (running):
running = False
for node in args.nodes:
filename = node + '/geom.log'
if not io.check_file(filename):
running = True
#log.debug( 'waiting on node {}'.format(node))
else:
lines = io.read_file(filename)
newlength = len(lines)
if 'termination' in lines and newlength == outlength[
node]:
pass
else:
running = True
outlength[node] = newlength
#log.debug( 'waiting on node {}'.format(node))
time.sleep(30)
log.info('Jobs Completed')
io.mkdir('geoms')
else:
execute(paths, args.nodes[0])
j, k = gather_mcgeoms(args.nodes)
for i in range(len(args.reacs)):
filename = check_geoms('reac' + str(i + 1), j[i])
filename = filename.split('/')[1].split(
'_')[0] + '_opt_' + filename.split('_')[1]
filename = 'output/' + filename.replace('.xyz', '.out')
shutil.copy(filename, 'output/reac' + str(i + 1) + '_opt.out')
for i in range(len(args.prods)):
filename = check_geoms('prod' + str(i + 1), j[i + 2])
filename = filename.split('/')[1].split(
'_')[0] + '_opt_' + filename.split('_')[1]
filename = 'output/' + filename.replace('.xyz', '.out')
shutil.copy(filename, 'output/prod' + str(i + 1) + '_opt.out')
if ists:
if not io.check_file('geoms/ts_01.xyz'):
successful = False
if io.check_file('output/ts_opt_01.out'):
shutil.copy('output/ts_opt_01.out', 'output/ts_opt.out')
# filename = filename.split('/')[1].split('_')[0] + '_opt_' + filename.split('_')[1]
# filename = 'output/' + filename.replace('.xyz','.out')
# shutil.copy(filename, 'output/ts_opt.out')
# if args.wellp and args.wellp.lower() != 'false' and 'find' not in args.wellp.lower():
# filename = check_geoms(paths['qtc'], 'wellp', j[6])
# filename = filename.split('/')[1].split('_')[0] + '_opt_' + filename.split('_')[1]
# filename = 'output/' + filename.replace('.xyz','.out')
# shutil.copy(filename, 'output/wellp_opt.out')
# if args.wellr and args.wellr.lower() != 'false' and 'find' not in args.wellr.lower():
# filename = check_geoms(paths['qtc'], 'wellr', j[5])
# filename = filename.split('/')[1].split('_')[0] + '_opt_' + filename.split('_')[1]
# filename = 'output/' + filename.replace('.xyz','.out')
# shutil.copy(filename, 'output/wellr_opt.out')
return successful
def build_files(args, paths, ists=False, nodes=1, restartts=False):
"""
Runs the build functions for reacn.dat, prodn.dat, theory.dat, and estoktp.dat
Requirements: QTC, Openbabel, Pybel (OR prepared cartesian coordinate files) and x2z
"""
import sys
build_subdirs()
os.chdir('./data')
stoichs = []
symnums = []
mdtype = args.mdtype
if not 'MdTau' in args.jobs:
mdtype = ''
#Create Read, Prod, and TS objects from parameters
params = (args.nsamps, args.abcd, nodes, args.interval, args.nsteps,
args.XYZ, args.xyzstart, mdtype)
Reac = build.MOL(params, 'reac', args.reactype)
Prod = build.MOL(params, 'prod')
params = (args.nsamps, args.abcd, nodes, args.interval, args.nsteps,
args.XYZ, args.xyzstart, mdtype)
TS = build.MOL(params, 'ts', args.reactype)
reacs = args.reacs
prods = args.prods
key = set_keys(args.reactype)
i, j, k = 0, 0, 0
TSprops = [0, 0, [], [], [], '',
0] #charge, spin, angles, atoms, sort, bond, babs
foundlist = []
#Build reacn.dat
for i, reac in enumerate(reacs, start=1):
msg = 'Building reac{:g}.dat'.format(i)
log.debug(msg)
args.reacs, angles, atoms, args.jobs, foundlist, stoichs, symnums = build_mol_dat(
Reac, reacs, i, stoichs, symnums, args.jobs, foundlist,
args.select[i - 1], mdtype)
TSprops = prep_reacs4TS(Reac, reac, i, key, angles, atoms, Reac.sort,
TSprops, args.reactype, paths)
nsamps = Reac.nsamps
msg = 'Completed'
log.info(msg)
#Build prodn.dat
for j, prod in enumerate(prods, start=1):
msg = 'Building prod{:g}.dat'.format(j)
log.debug(msg)
args.prods, angles, atoms, args.jobs, foundlist, stoichs, symnums = build_mol_dat(
Prod, prods, j, stoichs, symnums, args.jobs, foundlist,
args.select[i + j - 1], mdtype)
msg = 'Completed'
log.info(msg)
#Build TS, wellr, and wellp.dat
tstype = ['ts', 'wellr', 'wellp']
tss = ['false', args.wellr.lower(), args.wellp.lower()]
if args.reactype:
tss[0] = 'true'
TS.ijk = Reac.ijk
TS.sort = TSprops[4]
TS.bond = TSprops[5]
TS.babs = TSprops[6]
for k in range(3):
if tss[k] and tss[k] != 'false':
if k == 1 and 'true' in args.wellr.lower():
if len(args.reacs) > 1:
spin = 0
reac1 = args.reacs[0].split('_m')
if len(reac1) > 1:
spin += (float(reac1[1]) - 1) / 2
reac2 = args.reacs[1].split('_m')
if len(reac2) > 1:
spin += (float(reac2[1]) - 1) / 2
else:
spin = 0
reac3 = reac1[0] + '.' + reac2[0]
if spin:
reac3 += '_m' + str(int(2 * spin + 1))
log.info('Building {} '.format(reac3))
angles, atoms = build_well_dat(Reac, reac3, 3, args.jobs,
restartts)
else:
log.info(
'Two reactants are required when finding a reactant well'
)
elif k == 2 and (args.reactype.lower() == 'addition_well'
or args.reactype.lower() == 'isomerization_well'):
if io.check_file('prod1.dat'):
msg = 'moving prod1.dat to wellp.dat for {} reaction'.format(
args.reactype.lower())
log.info(msg)
io.mv('prod1.dat', 'wellp.dat')
j = 0
args.prods = []
msg = 'Completed'
log.info(msg)
elif k == 2 and 'true' in args.wellp.lower():
if len(args.prods) > 1:
spin = 0
prod1 = args.prods[0].split('_m')
if len(prod1) > 1:
spin += (float(prod1[1]) - 1) / 2
prod2 = args.prods[1].split('_m')
if len(prod2) > 1:
spin += (float(prod2[1]) - 1) / 2
else:
spin = 0
prod3 = prod1[0] + '.' + prod2[0]
if spin:
prod3 += '_m' + str(int(2 * spin + 1))
log.info('Building {} '.format(prod3))
angles, atoms = build_well_dat(Prod, prod3, 4, args.jobs,
restartts)
else:
log.info(
'Two products are required when finding a product well'
)
else:
msg = 'Building ' + tstype[k] + '.dat'
log.debug(msg)
TS.charge = TSprops[0]
TS.mult = int(2. * TSprops[1] + 1)
TS.symnum = ' 1'
if k == 0:
if 'geomdir' in args.XYZ and io.check_file(
'../geomdir/ts.xyz'):
angles, atoms = build_well_dat(TS, args.reactype, 'ts',
args.jobs, restartts)
else:
zmatstring = TS.build(tstype[k], args.reactype,
args.jobs, False, TSprops[2],
TSprops[3], restartts)
zmat = tstype[k] + '.dat'
io.write_file(zmatstring, zmat)
else:
params = ('1', args.abcd, nodes, args.interval,
args.nsteps, 'False', 'start', 'MdTau'
in args.jobs)
TS = build.MOL(params, 'ts')
TS.charge = TSprops[0]
TS.mult = int(2. * TSprops[1] + 1)
TS.symnum = ' 1'
zmatstring = TS.build(tstype[k], args.reactype, args.jobs,
False, TSprops[2])
zmat = tstype[k] + '.dat'
io.write_file(zmatstring, zmat)
msg = 'Completed'
log.info(msg)
mol = reac[0]
#Builds me_head.dat
if args.reactype:
msg = 'Building me_head.dat'
log.debug(msg)
if args.mehead:
if io.check_file('../' + args.mehead):
headstring = io.read_file('../' + args.mehead)
elif io.check_file(args.me_head):
headstring = io.read_file(args.mehead)
else:
headstring = build.build_mehead()
else:
headstring = build.build_mehead()
io.write_file(headstring, 'me_head.dat')
msg = 'Completed'
log.info(msg)
#Builds theory.dat
msg = 'Building theory.dat'
log.debug(msg)
theostring = build.build_theory(args.meths, tss, args.zedoptions,
args.oneoptions, args.adiabatic)
io.write_file(theostring, 'theory.dat')
msg = 'Completed'
log.info(msg)
#Builds estoktp.dat to restart at any step
msg = 'Building estoktp.dat'
log.debug(msg)
jobs = update_jobs(args.jobs, args.restart)
params = (stoichs, args.reactype, args.coresh, args.coresl, args.meml,
args.memh, args.esoptions)
eststring = build.build_estoktp(params, jobs, i, j, tss, args.xyzstart,
foundlist, ists)
io.write_file(eststring, 'estoktp.dat')
msg = 'Completed'
log.info(msg)
os.chdir('..')
return stoichs, symnums
def main(inputfile, outputfile, configfile=''):
torspath = os.path.dirname(os.path.realpath(sys.argv[0]))
if configfile == '':
configfile = torspath + os.path.sep + 'rcd/configfile.txt'
Config = config.CONFIG(configfile, outputfile)
args = config.ARGS(inputfile)
paths = {}
paths['g09'] = args.g09
paths['torsscan'] = torspath
sys.path.insert(0, es.get_paths(paths, 'torsscan'))
log.info(random_cute_animal())
##### Build and Run EStokTP ######
####################################
import shutil
symnums = []
samps = None
if args.restart < 8:
index = 0
if "Opt" in args.jobs and args.restart < 1:
alljobs = args.jobs
args.jobs = ["Opt"]
es.run_level0(args, paths)
args.restart = 1
args.jobs = alljobs
if "1dTau" in args.jobs and args.restart < 4:
logging.info("========\nBEGIN LEVEL 1 and 1DHR\n========\n")
alljobs = args.jobs
negvals = True
attempt = 0
while (negvals and attempt < 3):
attempt += 1
args.jobs = ["Opt_1", "1dTau"]
negvals = False
if attempt == 1 and args.restart == 3:
pass
else:
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if io.check_file('output/estoktp.out'):
shutil.copy('output/estoktp.out', 'output/estoktp_l1.out')
args.restart = 3
for i in range(len(args.reacs)):
lowene = 0.0
lowenefile = None
if io.check_file('me_files/reac' + str(i + 1) + '_hr.me'):
hr = io.read_file('me_files/reac' + str(i + 1) +
'_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp' + str(
i + 1).zfill(2) + '_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
logging.info(xyz)
slabel = ob.get_slabel(ob.get_mol(xyz))
if slabel.split('_m')[0] == ob.get_slabel(
args.reacs[i]).split('_m')[0]:
negvals = True
if io.check_file('data/ts.dat') and i == 0:
if 'isomerization' in args.reactype.lower():
tsfile = io.read_file('data/ts.dat')
ijk = tsfile.split('ji ki')[1].split()[:3]
ijk.append(
tsfile.split('ireact2')[1].split('\n')
[1].split()[-1])
xyz = xyz.splitlines()
xyz[int(ijk[0]) +
1] = '2 ' + xyz[int(ijk[0]) + 1]
xyz[int(ijk[1]) +
1] = '3 ' + xyz[int(ijk[1]) + 1]
xyz[int(ijk[2]) +
1] = '4 ' + xyz[int(ijk[2]) + 1]
xyz[int(ijk[3]) +
1] = '1 ' + xyz[int(ijk[3]) + 1]
xyz = '\n'.join(xyz)
else:
ijk = io.read_file('data/ts.dat').split(
'ksite')[1].split()[:3]
xyz = xyz.splitlines()
xyz[int(ijk[0]) +
1] = '2 ' + xyz[int(ijk[0]) + 1]
xyz[int(ijk[1]) +
1] = '1 ' + xyz[int(ijk[1]) + 1]
xyz[int(ijk[2]) +
1] = '3 ' + xyz[int(ijk[2]) + 1]
xyz = '\n'.join(xyz)
slabel = ob.get_smiles_filename(
ob.get_slabel(args.reacs[i]))
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/' + slabel + '.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to {}'
.format(slabel + '.xyz'))
else:
log.warning(
'Lower configuration found in 1dTau. But has different smiles: {} vs. {}'
.format(slabel, ob.get_slabel(args.reacs[i])))
for l in range(len(args.prods)):
lowene = 0.
lowenefile = None
if io.check_file('me_files/prod' + str(l + 1) + '_hr.me'):
hr = io.read_file('me_files/prod' + str(l + 1) +
'_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp' + str(
i + l + 2).zfill(2) + '_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
slabel = ob.get_slabel(ob.get_mol(xyz))
if slabel.split('_m')[0] == ob.get_slabel(
args.prods[l]).split('_m')[0]:
negvals = True
slabel = ob.get_smiles_filename(
ob.get_slabel(args.prods[l]))
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/' + slabel + '.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to {}'
.format(slabel + '.xyz'))
else:
log.warning(
'Lower configuration found in 1dTau. But has different smiles: {} vs. {}'
.format(slabel, ob.get_slabel(args.prods[l])))
if args.reactype.lower() in [
'addition', 'abstraction', 'isomerization',
'addition_well', 'isomerization_well'
]:
lowene = 0.
lowenefile = None
if io.check_file('me_files/ts_hr.me'):
hr = io.read_file('me_files/ts_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp00_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
negvals = True
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/ts.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to ts.xyz'
)
if args.wellp and args.wellp.lower() != 'false':
lowene = 0.
lowenefile = None
if io.check_file('me_files/wellp_hr.me'):
hr = io.read_file('me_files/wellp_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp06_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
negvals = True
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/wellp.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to wellp.xyz'
)
if args.wellr and args.wellr.lower() != 'false':
lowene = 0.
lowenefile = None
if io.check_file('me_files/wellr_hr.me'):
hr = io.read_file('me_files/wellr_hr.me')
hr = hr.split('Rotor')
startkey = 'Potential'
for j, rotor in enumerate(hr[1:]):
pot = rotor.split(startkey)[1]
pot = pot.splitlines()[1]
for k, ene in enumerate(pot.split()):
if float(ene) - lowene < -0.1:
lowene = float(ene)
lowenefile = 'hr_geoms/geom_isp05_hr' + str(
j + 1).zfill(2) + '_hpt' + str(
k + 1).zfill(2) + '.xyz'
if lowenefile:
xyz = io.read_file(lowenefile)
negvals = True
io.mkdir('geomdir')
io.write_file(xyz, 'geomdir/wellr.xyz')
args.restart = 1
args.XYZ = 'geomdir'
args.xyzstart = '0'
log.warning(
'Lower configuration found in 1dTau. Restarting at Level1. Saved geometry to wellr.xyz'
)
args.jobs = alljobs
elif "Opt_1" in args.jobs and args.restart < 2:
log.info("========\nBEGIN LEVEL 1\n========\n")
alljobs = args.jobs
args.jobs = ["Opt_1"]
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if io.check_file('output/estoktp.out'):
shutil.copy('output/estoktp.out', 'output/estoktp_l1.out')
args.jobs = alljobs
args.restart = 2
if args.anharm.lower() != 'false' and 'd' not in args.nodes[0]:
from rcd import thermo
log.info("========\nBEGIN VPT2\n========\n")
optlevel, anlevel = thermo.get_anlevel(args.anharm, args.meths)
for n, reac in enumerate(args.reacs):
typ = 'reac'
natom = ob.get_natom(reac)
if natom > 1:
mult = ob.get_mult(reac)
if io.check_file('me_files/' + typ + str(n + 1) +
'_fr.me'):
mefreqs = io.read_file('me_files/' + typ + str(n + 1) +
'_fr.me')
if not 'Anh' in mefreqs:
anfr, fr1, anx, fr2, fr3, _ = thermo.get_anharm(
typ, str(n + 1), natom, args.nodes[0],
anlevel, args.anovrwrt, reac,
optlevel.split('/'), paths)
io.write_file(
mefreqs,
'me_files/' + typ + str(n + 1) + '_harm.me')
lines, mefreqs = mefreqs.split('ZeroEnergy')
lines = fr1 + fr2.split(
'End')[0] + '\n ZeroEnergy' + mefreqs
io.write_file(
lines,
'me_files/' + typ + str(n + 1) + '_fr.me')
for n, prod in enumerate(args.prods):
typ = 'prod'
natom = ob.get_natom(prod)
if natom > 1:
mult = ob.get_mult(prod)
if io.check_file('me_files/' + typ + str(n + 1) +
'_fr.me'):
mefreqs = io.read_file('me_files/' + typ + str(n + 1) +
'_fr.me')
if not 'Anh' in mefreqs:
anfr, fr1, anx, fr2, fr3, _ = thermo.get_anharm(
typ, str(n + 1), natom, args.nodes[0],
anlevel, args.anovrwrt, prod,
optlevel.split('/'), paths)
io.write_file(
mefreqs,
'me_files/' + typ + str(n + 1) + '_harm.me')
lines, mefreqs = mefreqs.split('ZeroEnergy')
lines = fr1 + fr2.split(
'End')[0] + '\n ZeroEnergy' + mefreqs
io.write_file(
lines,
'me_files/' + typ + str(n + 1) + '_fr.me')
if args.reactype and io.check_file('geoms/tsgta_l1.xyz'):
typ = 'ts'
mol = io.read_file('geoms/tsgta_l1.xyz')
ts = ob.get_mol(mol)
natom = ob.get_natom(ts)
mult = ob.get_mult(ts)
if io.check_file('me_files/ts_fr.me'):
mefreqs = io.read_file('me_files/ts_fr.me')
if not 'Anh' in mefreqs:
anfr, fr1, anx, fr2, fr3, _ = thermo.get_anharm(
typ, str(n + 1), natom, args.nodes[0], anlevel,
args.anovrwrt, 'ts', optlevel.split('/'), paths)
io.write_file(mefreqs, 'me_files/' + typ + '_harm.me')
lines, mefreqs = mefreqs.split('ZeroEnergy')
imag = fr3.split('WellDepth')[0].split(
'ImaginaryFrequency[1/cm]')[1].replace('\t',
'').strip()
mefreqs = mefreqs.splitlines()
for i, line in enumerate(mefreqs):
if 'Imaginary' in line:
mefreqs[
i] = ' ImaginaryFrequency[1/cm] {}'.format(
imag)
mefreqs = '\n'.join(mefreqs)
lines = fr1 + fr2.split(
'End')[0] + '\n ZeroEnergy' + mefreqs
io.write_file(lines, 'me_files/' + typ + '_fr.me')
log.info("========\nBEGIN MDHR, HL\n========\n")
if 'kTP' in args.jobs:
alljobs = args.jobs
args.jobs = []
for job in alljobs:
if job != 'kTP':
args.jobs.append(job)
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if io.check_file('me_files/ts_en.me'):
tsen = float(io.read_file('me_files/ts_en.me'))
tsen += float(io.read_file('me_files/ts_zpe.me'))
reacen = 0
proden = 0
for i, reac in enumerate(args.reacs):
if io.check_file('me_files/reac{}_en.me'.format(i + 1)):
reacen += float(
io.read_file('me_files/reac{}_en.me'.format(i +
1)))
reacen += float(
io.read_file('me_files/reac{}_zpe.me'.format(i +
1)))
if args.reactype.lower(
) == 'addition_well' or args.reactype.lower(
) == 'isomerization_well':
if io.check_file('me_files/wellp_en.me'):
proden += float(io.read_file('me_files/wellp_en.me'))
proden += float(io.read_file('me_files/wellp_zpe.me'))
else:
for i, prod in enumerate(args.prods):
if io.check_file('me_files/prod{}_en.me'.format(i +
1)):
proden += float(
io.read_file(
'me_files/prod{}_en.me'.format(i + 1)))
proden += float(
io.read_file(
'me_files/prod{}_zpe.me'.format(i + 1)))
if tsen <= reacen or tsen <= proden:
log.info('Well Depth is negative. NoTunnel is turned on')
if args.esoptions:
args.esoptions += ',NoTunnel'
else:
args.esoptions = 'NoTunnel'
log.info("========\nBEGIN kTP\n========\n")
args.jobs = alljobs
restart = 7
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
else:
stoichs, symnums = es.build_files(args, paths)
es.execute(paths, args.nodes[0])
if ("1dTau" in args.jobs or 'MdTau' in args.jobs):
for i in range(len(args.reacs)):
es.check_hrs(i + 1, 'reac')
for i in range(len(args.prods)):
es.check_hrs(i + 1, 'prod')
es.me_file_abs_path()
if args.restart == 10:
io.execute(['mess', 'me_ktp.inp'])
if args.reactype and io.check_file('rate.out'):
import me_parser
#initialize the class in which to store the results
data = me_parser.paper()
data.reactions = []
# set some constants, depending upon whether the rate coefficients are to be used for CHEMKIN or something else.
data.T0 = 1.0
data.R = 1.987 # cal/mol-K. Note that PLOG formalism requires Ea in cal/mol-K!
data.N_avo = 6.0221415E23 #convert bimolecular rate coefficients from cm^3/sec to cm^3/mol/s
# set the minimum and maximum temperature
#data.Tmin = 600.0
#data.Tmax = 1200.0
# read me.out file from the command line
me_dot_out = 'rate.out'
if io.check_file(me_dot_out):
lines = io.read_file(me_dot_out, True)
if len(lines) < 2:
log.info('rate.out is empty')
## copy new plog executable to the path of the source file
#path = os.path.abspath(os.path.dirname(me_dot_out))
#
#command = 'cp /home/elliott/bin/dsarrfit.x_cfg ' + path
#log.info( command)
#os.system(command)
# parse results for the temperature, pressure, and names of channels
me_parser.get_temp_pres(data, lines)
# parse results for the pdep rate constants
me_parser.get_pdep_k(data, lines)
# fit the results to PLOG expressions
me_parser.fit_pdep(
data, nonlin_fit=False
) #replace <True> with <False> if you don't want to use the nonlinear solver (not recommended)
# print the resulting PLOG expressions to file
me_parser.print_plog(data, me_dot_out)
# plot the results: dashed line = single PLOG, solid line = double PLOG
#me_parser.plot_reactant(data, me_dot_out, show_plot=False, save_plot=True)
####### Parse results #########
########################################
from rcd import results
rs = results.RESULTS(args, paths)
args.hlen = rs.get_hlen()
args.optlevel = rs.optlevel
args.enlevel = rs.enlevel
args.taulevel = rs.taulevel
if args.parseall.lower() == 'true' or args.alltherm.lower() == 'true':
rs.get_results()
####### Build and run thermo #########
########################################
from rcd import thermo
rs.thermo = False
if args.alltherm.lower() == 'true':
rs.thermo = True
args.symnums = symnums
rs.dH0, rs.dH298, rs.hfbases, rs.anfreqs, rs.anxmat = thermo.run(
args, paths, rs.d)
if args.parseall.lower() == 'true':
rs.get_thermo_results()
return