Reaction energies with many different engines¶

#!/usr/bin/env amspython
from scm.plams import read_molecules, Settings, AMSJob

"""
Script for evaluating the HC7-11 and ISOL6 benchmark sets with different computational methods.

Modify the s_engine_dict variable below to specify which settings will be used.

A table with reaction energies will be printed to summary.txt
"""

summary_fname = "summary.txt"
with open(summary_fname, "w", buffering=1) as summary_file:
    summary_file.write(
        "#Method HC7_1 HC7_2 HC7_3 HC7_4 HC7_5 HC7_6 HC7_7 ISOL6_1 ISOL6_2 ISOL6_3 ISOL6_4 ISOL6_5 (kcal/mol)\n"
    )
    summary_file.write("Truhlar_ref 14.34 25.02 1.90 9.81 14.84 193.99 127.22 9.77 21.76 6.82 33.52 5.30\n")
    summary_file.write("Smith_wB97X_ref 28.77 41.09 1.75 6.26 9.30 238.83 157.65 9.32 20.80 1.03 26.43 0.40\n")

mol_dict = read_molecules("HC7-11")
mol_dict.update(read_molecules("ISOL6"))

s_reaxff = Settings()
s_reaxff.input.ReaxFF.ForceField = "CHON-2019.ff"

s_ani2x = Settings()
s_ani2x.input.MLPotential.Backend = "TorchANI"
s_ani2x.input.MLPotential.Model = "ANI-2x"

s_ani1ccx = Settings()
s_ani1ccx.input.MLPotential.Backend = "TorchANI"
s_ani1ccx.input.MLPotential.Model = "ANI-1ccx"

s_dftb = Settings()
s_dftb.input.DFTB.Model = "SCC-DFTB"
s_dftb.input.DFTB.ResourcesDir = "DFTB.org/mio-1-1"

s_band = Settings()
s_band.input.BAND.XC.libxc = "wb97x"
s_band.input.BAND.Basis.Type = "TZP"
s_band.input.BAND.Basis.Core = "None"

s_adf = Settings()
s_adf.input.ADF.Basis.Type = "TZP"
s_adf.input.ADF.Basis.Core = "None"
s_adf.input.ADF.XC.libxc = "WB97X"

s_mp2 = Settings()
s_mp2.input.ADF.Basis.Type = "TZ2P"
s_mp2.input.ADF.Basis.Core = "None"
s_mp2.input.ADF.XC.MP2 = ""

# The engines in s_engine_dict will be used for the calculation
# You can remove the engines that you would not like to run (for example, if you do not have the necessary license)
s_engine_dict = {
    "ANI-1ccx": s_ani1ccx,
    "ANI-2x": s_ani2x,
    "DFTB": s_dftb,
    "ReaxFF": s_reaxff,
    "ADF": s_adf,
    "MP2": s_mp2,
    "BAND": s_band,
}

s_ams = Settings()
s_ams.input.ams.Task = "SinglePoint"
# s_ams.input.ams.Task = 'GeometryOptimization'
# s_ams.input.ams.GeometryOptimization.CoordinateType = 'Cartesian'

jobs = dict()

with open(summary_fname, "a", buffering=1) as summary_file:
    for engine_name, s_engine in s_engine_dict.items():
        s = s_ams.copy() + s_engine.copy()
        jobs[engine_name] = dict()

        # call .run() for *all* jobs *before* accessing job.results.get_energy() for *any* job
        for mol_name, mol in mol_dict.items():
            jobs[engine_name][mol_name] = AMSJob(settings=s, molecule=mol, name=engine_name + "_" + mol_name)
            jobs[engine_name][mol_name].run()

    for engine_name in s_engine_dict:
        # for each engine, calculate reaction energies
        E = dict()
        for mol_name, job in jobs[engine_name].items():
            E[mol_name] = job.results.get_energy(unit="kcal/mol")
        deltaE_list = [
            ##### HC7/11 ######
            E["22"] - E["1"],
            E["31"] - E["1"],
            E["octane"] - E["2233tetramethylbutane"],
            5 * E["ethane"] - E["hexane"] - 4 * E["methane"],
            7 * E["ethane"] - E["octane"] - 6 * E["methane"],
            3 * E["ethylene"] + 2 * E["ethyne"] - E["adamantane"],
            3 * E["ethylene"] + 1 * E["ethyne"] - E["bicyclo222octane"],
            ###### start ISOL6 ######
            E["p_3"] - E["e_3"],
            E["p_9"] - E["e_9"],
            E["p_10"] - E["e_10"],
            E["p_13"] - E["e_13"],
            E["p_14"] - E["e_14"],
        ]

        out_str = engine_name
        for deltaE in deltaE_list:
            out_str += " {:.1f}".format(deltaE)
        out_str += "\n"

        print(out_str)
        summary_file.write(out_str)


# summary.txt will contain a table similar to the below
##Method          HC7_1   HC7_2  HC7_3  HC7_4  HC7_5   HC7_6   HC7_7 ISOL6_1 ISOL6_2 ISOL6_3 ISOL6_4 ISOL6_5 (kcal/mol)
# Truhlar_ref      14.34   25.02   1.90   9.81  14.84  193.99  127.22    9.77   21.76    6.82   33.52    5.30
# Smith_wB97X_ref  28.77   41.09   1.75   6.26   9.30  238.83  157.65    9.32   20.80    1.03   26.43    0.40
# ANI-1ccx         15.8    30.7   -0.2    7.7   11.7   196.5   127.9     9.2    21.5     3.8    35.4     6.9
# ANI-2x           42.4    48.1   -1.9    5.4    8.0   238.4   156.9     7.9    20.8    -1.5    26.7     0.5
# DFTB              7.1    19.0    0.2    3.6    5.4   223.5   150.8    11.7    22.6     7.9    35.2     8.6
# ReaxFF           34.3    23.0   13.4    2.6    5.5   289.2   168.3    -9.2    24.2    70.7    30.9    89.3
# ADF              20.8    31.4   -1.9    6.7    9.9   214.5   139.7     9.5    20.5     4.7    31.0     4.8
# MP2              20.5    27.1    5.4    9.9   15.0   214.8   141.3    11.0    24.6     8.4    36.8     6.2
# BAND             19.2    30.2   -2.7    7.3   11.0   218.5   141.3     9.9    18.5     5.3    31.7     4.7