def run():
log = "logs/05_dmso_hf_orca_freq.out"
qc = QCData(log, point_group="c1")
T = 298.15
thermo = thermochemistry(qc, T)
print_thermo_results(thermo)
log = "logs/04_dmso_hf_freq.log"
qc = QCData(log, point_group="c1")
T = 298.15
thermo = thermochemistry(qc, T)
print_thermo_results(thermo)
def run():
args = parse_args(sys.argv[1:])
inp_fn = args.inp_fn
T = args.temp
pressure = args.pressure
point_group = args.pg
scale = args.scale
vib_kind = args.vibs
print(f"Using {vib_kind.upper()}-approach for vibrational entropies.")
qc = QCData(inp_fn, point_group=point_group, scale_factor=scale)
if args.temps:
temps = np.linspace(*args.temps)
else:
temps = [
T,
]
thermos = [
thermochemistry(qc, T, pressure=pressure, kind=vib_kind) for T in temps
]
print_thermos(thermos)
dump_thermos(inp_fn, thermos)
def test_thermoanalysis(this_dir):
hess_fn = this_dir / "h2o_hessian.h5"
with h5py.File(hess_fn, "r") as handle:
masses = handle["masses"][:]
vibfreqs = handle["vibfreqs"][:]
coords3d = handle["coords3d"][:]
energy = handle.attrs["energy"]
mult = handle.attrs["mult"]
thermo_dict = {
"masses": masses,
"vibfreqs": vibfreqs,
"coords3d": coords3d,
"energy": energy,
"mult": mult,
}
from thermoanalysis.QCData import QCData
from thermoanalysis.thermo import thermochemistry
qcd = QCData(thermo_dict)
thermo = thermochemistry(qcd, temperature=298.15)
assert thermo.M == pytest.approx(18.01528)
assert thermo.dG == pytest.approx(0.002267160)
def calculate_potential(result_1, result_2, T=298.15):
qcd_1 = redox_result_to_qcdata(result_1)
qcd_2 = redox_result_to_qcdata(result_2)
thermo_1 = thermochemistry(qcd_1, temperature=T)
thermo_2 = thermochemistry(qcd_2, temperature=T)
DG_solv_neut = result_1.dG_solv
DG_solv_oxd = result_2.dG_solv
print(f"ΔG_solv_neut = {DG_solv_neut: >8.6f} E_h")
print(f"ΔG_solv_oxd = {DG_solv_oxd: >8.6f} E_h")
DG_ox_g = thermo_2.G - thermo_1.G
print(f"ΔG_oxd_gas = {DG_ox_g: >8.6f} E_h")
DG_ox_solv = DG_ox_g + DG_solv_oxd - DG_solv_neut
print(f"ΔG_oxd_solv = {DG_ox_solv: >8.6f} E_h")
n = abs(result_1.charge - result_2.charge)
print(f"Δelectron(s) = {n}")
# To Joule mol⁻¹
redox_pot = DG_ox_solv * AU2J * NA / (n * F)
print(f"E^0/+ = {redox_pot:.2f} V")
return redox_pot
def test_orca_thermochemistry():
log = str(THIS_DIR / "logs/05_dmso_hf_orca_freq.out")
qc = QCData(log, point_group="c1")
T = 298.15
thermo = thermochemistry(qc, T, kind="qrrho")
zpe_ref = 0.08393782
assert thermo.ZPE == approx(zpe_ref)
u_trans_ref = 0.00141627
assert thermo.U_trans == approx(u_trans_ref, rel=1e-5)
u_rot_ref = 0.00141627
assert thermo.U_rot == approx(u_rot_ref, rel=1e-5)
s_el_ref = 0.
assert thermo.S_el == approx(s_el_ref)
s_trans_ref = 0.01852169
assert (thermo.S_trans*T) == approx(s_trans_ref, rel=1e-3)
s_rot_ref = 0.01092172
assert (thermo.S_rot*T) == approx(s_rot_ref, rel=1e-1)
s_vib_ref = 0.00546508
assert (thermo.S_vib*T) == approx(s_vib_ref, rel=1e-4)
def test_g16_thermochemistry():
log = str(THIS_DIR / "logs/04_dmso_hf_freq.log")
qc = QCData(log, point_group="c1")
T = 298.15
thermo = thermochemistry(qc, T, kind="rrho")
zpe_ref = 0.083950
assert thermo.ZPE == approx(zpe_ref)
u_trans_ref = 0.889 * KCAL_MOL2AU
assert thermo.U_trans == approx(u_trans_ref, rel=1e-3)
u_rot_ref = 0.889 * KCAL_MOL2AU
assert thermo.U_rot == approx(u_rot_ref, rel=1e-3)
u_vib_ref = 54.676 * KCAL_MOL2AU
assert thermo.U_vib == approx(u_vib_ref, rel=1e-1)
s_el_ref = 0. * CAL_MOL2AU
assert thermo.S_el == approx(s_el_ref)
s_trans_ref = 38.978 * CAL_MOL2AU
assert (thermo.S_trans) == approx(s_trans_ref)
s_rot_ref = 25.168 * CAL_MOL2AU
assert (thermo.S_rot) == approx(s_rot_ref, rel=1e-3)
s_vib_ref = 11.519 * CAL_MOL2AU
assert (thermo.S_vib) == approx(s_vib_ref, rel=1e-3)
def run():
args = parse_args(sys.argv[1:])
no_alt = args.no_alt
show_rxs = not args.norxs
show_paths = not args.nopaths
temperature = args.T
if args.quick:
show_paths = False
educts, ts, products = [
reactants.split(",") for reactants in args.quick.split(";")
]
assert len(ts) == 1
ed_keys = [f"ed{i}" for i in range(len(educts))]
prod_keys = [f"prod{i}" for i in range(len(products))]
inp_dict = {
"molecules": dict(),
"program": "orca",
}
def add_mols(keys, fns):
for key, fn in zip(keys, fns):
inp_dict["molecules"][key] = {
"freq": fn,
}
add_mols(ed_keys, educts)
add_mols([
"ts",
], ts)
add_mols(prod_keys, products)
# Dummy reaction
inp_dict["reactions"] = {
"quick": {
"educts": ed_keys,
"ts": "ts",
"products": prod_keys,
}
}
elif args.yaml:
with open(args.yaml) as handle:
inp_dict = yaml.load(handle)
else:
print(
"Specify either a YAML file or use --quick! See also 'plotprofile --help'"
)
sys.exit()
reactions = inp_dict["reactions"]
if args.interactive:
rx_keys = list(reactions.keys())
for i, rx in enumerate(rx_keys):
print(f"{i:02d}: {rx}")
ind = int(input("Show reaction: ", ))
rx_key = rx_keys[ind]
reaction = reactions[rx_key]
reactions = {
rx_key: reaction,
}
# Modify molecules so only the ones actually needed are loaded
rx_molecules = list(
it.chain(*[to_list(mols) for mols in reaction.values()]))
inp_dict["molecules"] = {
key: val
for key, val in inp_dict["molecules"].items()
if key in rx_molecules
}
molecules = inp_dict["molecules"]
thermos = load_thermos(molecules, inp_dict["program"])
mol_energies = load_molecule_energies(thermos, no_alt=no_alt)
rx_strs = {rx_name: rx_to_string(rx) for rx_name, rx in reactions.items()}
if args.parsedash:
freq_logs = {k: v["freq"] for k, v in inp_dict["molecules"].items()}
qc_datas = {k: QCData(v) for k, v in freq_logs.items()}
temps = np.arange(298.00, 373.00, 5)
rows = list()
for mol_name, temp in it.product(qc_datas, temps):
qc = qc_datas[mol_name]
tc = thermochemistry(qc, temp)
row = [
mol_name,
] + list(tc)
rows.append(row)
cols = [
"name",
] + list(tc._fields)
df = pd.DataFrame(rows, columns=cols)
df.to_pickle("thermochem_data")
thermochem_df = pd.read_pickle("thermochem_data")
df = make_dash_data(inp_dict["reactions"], thermos, thermochem_df)
df.to_pickle("dash_data")
print()
print("Using these G-values:")
for key, val in mol_energies.items():
print(key)
pprint(val._asdict())
print()
rx_energies = make_reactions(reactions, mol_energies)
paths = inp_dict.get("paths", None)
if paths is None:
print("Found no defined paths in .yaml file. Using all defined "
"reactions instead.")
paths = {"autogenerated": list(reactions.keys())}
if args.interactive:
paths = dict()
print_path_rx_energies(paths, rx_energies, rx_strs, temperature)
dump_energies(rx_energies)
mol_labels = {
# Use molecule key as fallback if no label is defined
mol: values.get("label", mol)
for mol, values in molecules.items()
}
rx_labels = {}
rx_titles = {}
# Create label strings for plotting
for rx_name in reactions:
labels = [
v for k, v in reactions[rx_name].items()
if k in ("educts", "ts", "products")
]
pretty_labels = list()
for lbl in labels:
if isinstance(lbl, str):
lbl = [
lbl,
]
# Replace with pretty labels
lbl = [mol_labels[mol] for mol in lbl]
lbl = ",\n".join(lbl)
pretty_labels.append(lbl)
rx_labels[rx_name] = pretty_labels
rx_title = reactions[rx_name].get("label", rx_name)
rx_titles[rx_name] = rx_title
# Try to use the 'best' energies for plotting. That is with alternative
# single point and solvation.
best_rx_energies = {
rx_name: rx_energies[rx_name]["G_solv_alt"]
for rx_name in rx_labels
}
if show_rxs:
plot_reactions(best_rx_energies, rx_labels, rx_titles, temperature)
else:
print("Skipped plotting of reactions!")
if show_paths and not args.interactive and (len(best_rx_energies) > 1):
plot_paths(best_rx_energies, paths, rx_labels, rx_titles)
else:
print("Skipped plotting of reaction paths!")
path_reactions = set(list(it.chain(*paths.values())))
all_reactions = set(list(reactions.keys()))
remainder = all_reactions - path_reactions
if len(remainder) > 0:
print()
print("Warning!".upper())
print("Not all defined reactions appeared in (defined) paths!")
for i, rx in enumerate(remainder):
print(f"\t{i:02d}: {rx}")
print("Warning!".upper())
print()
remainder_path = {
"remainder": remainder,
}
print_path_rx_energies(remainder_path, rx_energies, rx_strs,
temperature)
to_compare = inp_dict.get("compare", dict())
compare_molecules(to_compare, mol_energies)
# compare_molecules(to_compare, mol_energies, attr="G_gas_alt")
# Kinetics
if "kinetics" in inp_dict:
kin_dict = inp_dict["kinetics"]
kin_reactions = kin_dict.get("only", reactions.keys())
reaction_objs = list()
for rx_name in kin_reactions:
reactants = reactions[rx_name]
educts = reactants["educts"]
ts = reactants["ts"]
products = reactants["products"]
energies = rx_energies[rx_name]
frx = Reaction(rx_name, educts, ts, products, energies)
brx = frx.get_back_reaction()
reaction_objs.extend((frx, brx))
c0s = kin_dict["c0s"]
t_span = kin_dict["t_span"]
mols, res = kinetics(reaction_objs, c0s, t_span=t_span)
plot_kinetics(mols, res)