def main():
# Get user input.
args = parse_user_input()
# Start timer.
click()
# Run Q-Chem geometry optimization.
M = QCOptIC(args.initial, args.charge, args.mult, args.method, args.basis, cycles=args.cycles)
# Select frames where the energy is monotonically decreasing.
M = M[monotonic_decreasing(M.qm_energies)]
# Write optimization results to file.
M.write('optimize.xyz')
# Write Mulliken charge and spin populations to file.
QS = M.get_populations()
QS.write('optimize.pop', ftype='xyz')
# Archive and exit.
tarexit()
def main():
# Get user input.
args = parse_user_input()
# Start timer.
click()
subxyz = []
subna = []
subchg = []
submult = []
subvalid = []
subefstart = []
subeffinal = []
SumFrags = []
fragfiles = []
# Pick out the files in the tarfile that have the structure "example*.sub_*.xyz"
idhome = os.path.abspath('..')
tar = tarfile.open(os.path.join(idhome, 'fragmentid.tar.bz2'), 'r')
for tarinfo in tar:
splitlist = tarinfo.name.split(".")
if len(splitlist) > 2:
if splitlist[2] == "xyz":
subxyz.append(tarinfo.name)
fragfiles.append(tarinfo)
# Extract these files from the tarfile
tar.extractall(members=fragfiles)
tar.close()
# Load files as molecules
for frag in subxyz:
M = Molecule(frag)
M.read_comm_charge_mult()
subchg.append(M.charge)
submult.append(M.mult)
subna.append(M.na)
efstart = re.search('(?<=Molecular formula )\w+', M.comms[0]).group(0)
subefstart.append(efstart)
print("Running individual optimizations.")
# Run individual geometry optimizations.
FragE = 0.0
FragZPE = 0.0
FragEntr = 0.0
FragEnth = 0.0
for i in range(len(subxyz)):
if subna[i] > 1:
M = QCOptIC(subxyz[i],
subchg[i],
submult[i],
args.method,
args.basis,
cycles=args.cycles,
qcin='%s.opt.in' % os.path.splitext(subxyz[i])[0])
# Select frames where the energy is monotonically decreasing.
M = M[monotonic_decreasing(M.qm_energies)]
else:
# Special case of a single atom
QCSP = QChem(subxyz[i],
charge=subchg[i],
mult=submult[i],
method=args.method,
basis=args.basis,
qcin='%s.sp.in' % os.path.splitext(subxyz[i])[0])
QCSP.make_stable()
QCSP.jobtype = 'sp'
QCSP.calculate()
M = QCSP.load_qcout()
# Write optimization final result to file.
M = M[-1]
fragoptfile = os.path.splitext(subxyz[i])[0] + ".opt.xyz"
M.write(fragoptfile)
QCFR = QChem(fragoptfile,
charge=subchg[i],
mult=submult[i],
method=args.method,
basis=args.basis,
qcin='%s.freq.in' % os.path.splitext(fragoptfile)[0])
QCFR.freq()
M = QCFR.load_qcout()
# Print out new molecular formulas.
# This time we should be able to use covalent radii.
M.build_topology(force_bonds=True)
optformula = ' '.join([m.ef() for m in M.molecules])
subeffinal.append(optformula)
print(("%s.opt.xyz : formula %s; charge %i; mult %i; energy %f Ha;"
"ZPE %f kcal/mol; entropy %f cal/mol.K; enthalpy %f kcal/mol" %
(os.path.splitext(subxyz[i])[0], optformula, subchg[i],
submult[i], M.qm_energies[0], M.qm_zpe[0], M.qm_entropy[0],
M.qm_enthalpy[0])))
FragE += M.qm_energies[0]
FragZPE += M.qm_zpe[0]
FragEntr += M.qm_entropy[0]
FragEnth += M.qm_enthalpy[0]
SumFrags.append(M[0])
for fragment in SumFrags:
fragment.write('fragmentopt.xyz', append=True)
if subefstart != subeffinal:
print("Fragments changed during optimization, calculation invalid")
print("Final electronic energy (Ha) of optimized frags: % 18.10f" % FragE)
print("Final ZPE (kcal/mol) of optimized frags: % 18.10f" % FragZPE)
print("Final entropy (cal/mol.K) of optimized frags: % 18.10f" % FragEntr)
print("Final enthalpy (kcal/mol) of optimized frags: % 18.10f" % FragEnth)
nrg = open('fragmentopt.nrg', 'w')
for subef in subeffinal:
nrg.write(subef + " ")
nrg.write("\nTotal electronic energy: %f Ha\n" % FragE)
nrg.write("Total ZPE: %f kcal/mol\n" % FragZPE)
nrg.write("Total entropy (STP): %f cal/mol.K\n" % FragEntr)
nrg.write("Total enthalpy (STP): %f kcal/mol\n" % FragEnth)
if subefstart != subeffinal: nrg.write("invalid")
nrg.close()
# Archive and exit.
tarexit()
M = M[::-1]
iTS = len(M) - iTS
# Energies in kcal/mol.
E = M.qm_energies
E -= E[0]
E *= 627.51
# Write IRC energies to comments.
M.comms = [
"Intrinsic Reaction Coordinate: Energy = % .4f kcal/mol" % i for i in E
]
M.comms[iTS] += " (Transition State)"
# Eliminate geometry optimization frames that go up in energy.
selct = np.concatenate((monotonic_decreasing(E, iTS, 0, verbose=True)[::-1],
monotonic_decreasing(E, iTS, len(M),
verbose=True)[1:]))
M = M[selct]
E = E[selct]
# Save the IRC energy as a function of arc length.
ArcMol = arc(M, RMSD=True)
ArcMolCumul = np.insert(np.cumsum(ArcMol), 0, 0.0)
np.savetxt("irc.nrg",
np.hstack((ArcMolCumul.reshape(-1, 1), E.reshape(-1, 1))),
fmt="% 14.6f",
header="Arclength(Ang) Energy(kcal/mol)")
MOld = Molecule("irc.xyz")
ArcOld = arc(MOld, RMSD=True)