def make_rotors(self, species, norot=None):
rotors = []
if self.par['rotor_scan']:
for i, rot in enumerate(species.dihed):
if norot is not None:
if frequencies.skip_rotor(norot, rot) == 1:
continue
rotorpot, rotortype = self.make_rotorpot(species, i, rot)
if rotortype == 'hindered':
rotors.append(
self.hinderedrotortpl.format(
group=' '.join([
str(pi + 1) for pi in frequencies.partition(
species, rot, species.natom)[0][1:]
]),
axis='{} {}'.format(str(rot[1] + 1),
str(rot[2] + 1)),
rotorsymm=self.rotorsymm(species, rot),
nrotorpot=self.nrotorpot(species, rot),
rotorpot=rotorpot))
elif rotortype == 'free':
rotors.append(
self.freerotortpl.format(
geom=self.make_geom(species),
natom=species.natom,
group=' '.join([
str(pi + 1) for pi in frequencies.partition(
species, rot, species.natom)[0][1:]
]),
axis='{} {}'.format(str(rot[1] + 1),
str(rot[2] + 1)),
))
rotors = '\n'.join(rotors)
return rotors
def write_well(self, species):
"""
Create the block for MESS for a well.
well0: reactant on this PES (zero-energy reference)
"""
# open the templates
well_file = pkg_resources.resource_filename('tpl', 'mess_well.tpl')
with open(well_file) as f:
tpl = f.read()
hir_file = pkg_resources.resource_filename('tpl', 'mess_hinderedrotor.tpl')
with open(hir_file) as f:
rotor_tpl = f.read()
rotors = []
if self.par.par['rotor_scan']:
for i, rot in enumerate(species.dihed):
group = ' '.join([str(pi+1) for pi in frequencies.partition(species, rot, species.natom)[0][1:]])
axis = '{} {}'.format(str(rot[1]+1), str(rot[2]+1))
rotorsymm = species.sigma_int[rot[1]][rot[2]]
nrotorpot = species.hir.nrotation // rotorsymm
ens = species.hir.hir_energies[i]
rotorpot = [(ei - ens[0])*constants.AUtoKCAL for ei in ens]
rotorpot = ' '.join(['{:.2f}'.format(ei) for ei in rotorpot[:species.hir.nrotation // rotorsymm]])
rotors.append(rotor_tpl.format(group=group,
axis=axis,
rotorsymm=rotorsymm,
nrotorpot=nrotorpot,
rotorpot=rotorpot))
rotors = '\n'.join(rotors)
freq = ''
#reduced freqs used for mess input to make more accurate with HIR corrections
for i, fr in enumerate(species.reduced_freqs):
if i == 0:
freq += '{:.4f}'.format(fr)
elif i > 0 and i % 3 == 0:
freq += '\n {:.4f}'.format(fr)
else:
freq += ' {:.4f}'.format(fr)
geom = ''
for i, at in enumerate(species.atom):
if i > 0:
geom += ' '
x, y, z = species.geom[i]
geom += '{} {:.6f} {:.6f} {:.6f}\n'.format(at, x, y, z)
if self.par.par['pes']:
name = '{name}'
energy = '{zeroenergy}'
else:
name = self.well_names[species.chemid] + ' ! ' + str(species.chemid)
energy = ((species.energy + species.zpe) - (self.species.energy + self.species.zpe)) * constants.AUtoKCAL
mess_well = tpl.format(chemid=name,
natom=species.natom,
geom=geom,
symm=float(species.sigma_ext) / float(species.nopt),
nfreq=len(species.reduced_freqs),
freq=freq,
hinderedrotor=rotors,
nelec=1,
charge=species.charge,
mult=species.mult,
zeroenergy=energy)
f = open(str(species.chemid) + '.mess', 'w')
f.write(mess_well)
f.close()
return mess_well
def write_barrier(self, reaction):
"""
Create the block for a MESS barrier.
"""
# open the templates
ts_file = pkg_resources.resource_filename('tpl', 'mess_ts.tpl')
with open(ts_file) as f:
tpl = f.read()
hir_file = pkg_resources.resource_filename('tpl', 'mess_hinderedrotor.tpl')
with open(hir_file) as f:
rotor_tpl = f.read()
tunn_file = pkg_resources.resource_filename('tpl', 'mess_tunneling.tpl')
with open(tunn_file) as f:
tun_tpl = f.read()
rotors = []
if self.par.par['rotor_scan']:
for i, rot in enumerate(reaction.ts.dihed):
group = ' '.join([str(pi+1) for pi in frequencies.partition(reaction.ts, rot, reaction.ts.natom)[0][1:]])
axis = '{} {}'.format(str(rot[1]+1), str(rot[2]+1))
rotorsymm = reaction.ts.sigma_int[rot[1]][rot[2]]
nrotorpot = reaction.ts.hir.nrotation // rotorsymm
ens = reaction.ts.hir.hir_energies[i]
rotorpot = [(ei - ens[0])*constants.AUtoKCAL for ei in ens]
rotorpot = ' '.join(['{:.2f}'.format(ei) for ei in rotorpot[:reaction.ts.hir.nrotation // rotorsymm]])
rotors.append(rotor_tpl.format(group=group,
axis=axis,
rotorsymm=rotorsymm,
nrotorpot=nrotorpot,
rotorpot=rotorpot))
rotors = '\n'.join(rotors)
freq = ''
#reduced freqs used for better accuracy of mess input files
for i, fr in enumerate(reaction.ts.reduced_freqs[1:]):
if i == 0:
freq += '{:.4f}'.format(fr)
elif i > 0 and i % 3 == 0:
freq += '\n {:.4f}'.format(fr)
else:
freq += ' {:.4f}'.format(fr)
geom = ''
for i, at in enumerate(reaction.ts.atom):
if i > 0:
geom += ' '
x, y, z = reaction.ts.geom[i]
geom += '{} {:.6f} {:.6f} {:.6f}\n'.format(at, x, y, z)
barriers = [
((reaction.ts.energy + reaction.ts.zpe) - (self.species.energy + self.species.zpe)) * constants.AUtoKCAL,
((reaction.ts.energy + reaction.ts.zpe) - sum([(opt.species.energy + opt.species.zpe) for opt in reaction.prod_opt])) * constants.AUtoKCAL,
]
if any([bi < 0 for bi in barriers]):
tun = ''
else:
tun = tun_tpl.format(cutoff=min(barriers),
imfreq=-reaction.ts.reduced_freqs[0],
welldepth1=barriers[0],
welldepth2=barriers[1])
if len(reaction.products) == 1:
prod_name = self.well_names[reaction.products[0].chemid]
elif len(reaction.products) == 2:
long_name = '_'.join(sorted([str(pi.chemid) for pi in reaction.products]))
prod_name = self.bimolec_names[long_name]
else:
long_name = '_'.join(sorted([str(pi.chemid) for pi in reaction.products]))
prod_name = self.termolec_names[long_name]
if self.par.par['pes']:
name = '{name}'
chemid_reac = ''
chemid_prod = ''
long_rxn_name = ''
energy = '{zeroenergy}'
else:
name = self.ts_names[reaction.instance_name]
chemid_reac = self.well_names[self.species.chemid]
chemid_prod = prod_name
long_rxn_name = reaction.instance_name
energy = ((reaction.ts.energy + reaction.ts.zpe) - (self.species.energy + self.species.zpe)) * constants.AUtoKCAL
mess_ts = tpl.format(rxn_name=name,
chemid_reac=chemid_reac,
chemid_prod=chemid_prod,
long_rxn_name=long_rxn_name,
natom=reaction.ts.natom,
geom=geom,
symm=float(reaction.ts.sigma_ext) / float(reaction.ts.nopt),
nfreq=len(reaction.ts.reduced_freqs) - 1,
freq=freq,
hinderedrotor=rotors,
tunneling=tun,
nelec=1,
charge=reaction.ts.charge,
mult=reaction.ts.mult,
zeroenergy=energy)
f = open(reaction.instance_name + '.mess', 'w')
f.write(mess_ts)
f.close()
return mess_ts
def write_bimol(self, species_list, bar):
"""
Create the block for MESS for a bimolecular product.
well0: reactant on this PES (zero-energy reference)
"""
bar=bar #0=barrier, 1=barrierless
# open the templates
if bar == 0:
bimol_file = pkg_resources.resource_filename('tpl', 'mess_bimol.tpl')
elif bar == 1:
bimol_file = pkg_resources.resource_filename('tpl', 'mess_barrierless.tpl')
with open(bimol_file) as f:
tpl = f.read()
fragment_file = pkg_resources.resource_filename('tpl', 'mess_fragment.tpl')
with open(fragment_file) as f:
fragment_tpl = f.read()
hir_file = pkg_resources.resource_filename('tpl', 'mess_hinderedrotor.tpl')
with open(hir_file) as f:
rotor_tpl = f.read()
atom_file = pkg_resources.resource_filename('tpl', 'mess_atom.tpl')
with open(atom_file) as f:
atom_tpl = f.read()
fragments=''
for species in species_list:
if species.natom > 1:
rotors = []
if self.par.par['rotor_scan']:
for i, rot in enumerate(species.dihed):
group = ' '.join([str(pi+1) for pi in frequencies.partition(species, rot, species.natom)[0][1:]])
axis = '{} {}'.format(str(rot[1]+1), str(rot[2]+1))
rotorsymm = species.sigma_int[rot[1]][rot[2]]
nrotorpot = species.hir.nrotation // rotorsymm
ens = species.hir.hir_energies[i]
rotorpot = [(ei - ens[0])*constants.AUtoKCAL for ei in ens]
rotorpot = ' '.join(['{:.2f}'.format(ei) for ei in rotorpot[:species.hir.nrotation // rotorsymm]])
rotors.append(rotor_tpl.format(group=group,
axis=axis,
rotorsymm=rotorsymm,
nrotorpot=nrotorpot,
rotorpot=rotorpot))
rotors = '\n'.join(rotors)
freq = ''
#reduced freqs used always bc HIR creates more accurate mess input
for i, fr in enumerate(species.reduced_freqs):
if i == 0:
freq += '{:.4f}'.format(fr)
elif i > 0 and i % 3 == 0:
freq += '\n {:.4f}'.format(fr)
else:
freq += ' {:.4f}'.format(fr)
geom = ''
for i, at in enumerate(species.atom):
if i > 0:
geom += ' '
x, y, z = species.geom[i]
geom += '{} {:.6f} {:.6f} {:.6f}\n'.format(at, x, y, z)
energy = ((species.energy + species.zpe) - (self.species.energy + self.species.zpe)) * constants.AUtoKCAL
if self.par.par['pes']:
name = 'fr_name_{}'.format(species.chemid)
name = '{' + name + '}'
else:
name = self.fragment_names[species.chemid] + ' ! ' + str(species.chemid)
fragments += fragment_tpl.format(chemid=name,
natom=species.natom,
geom=geom,
symm=float(species.sigma_ext) / float(species.nopt),
nfreq=len(species.reduced_freqs),
freq=freq,
hinderedrotor=rotors,
nelec=1,
charge=species.charge,
mult=species.mult)
fragments += '\n'
else:
if self.par.par['pes']:
name = 'fr_name_{}'.format(species.chemid)
name = '{' + name + '}'
else:
name = self.fragment_names[species.chemid] + ' ! ' + str(species.chemid)
# atom template
fragments += atom_tpl.format(chemid=name,
element=species.atom[0],
nelec=1,
charge=species.charge,
mult=species.mult)
fragments += '\n'
pr_name = '_'.join(sorted([str(species.chemid) for species in species_list]))
if self.par.par['pes']:
name = '{name}'
energy = '{ground_energy}'
else:
if bar == 0:
name = self.bimolec_names[pr_name] + ' ! ' + pr_name
elif bar == 1:
name = self.barrierless_names[pr_name]
energy = (sum([sp.energy for sp in species_list]) + sum([sp.zpe for sp in species_list]) -
(self.species.energy + self.species.zpe)) * constants.AUtoKCAL
if bar == 0:
bimol = tpl.format(chemids=name,
fragments=fragments,
ground_energy=energy)
elif bar == 1:
bimol = tpl.format(barrier='nobar',
reactant=name,
dummy='',
chemids='',
fragments=fragments,
ground_energy=energy)
f = open(pr_name + '.mess', 'w')
f.write(bimol)
f.close()
return bimol