Complete Python code¶

#!/usr/bin/env amspython
# coding: utf-8

# ## Initial Imports

from scm.plams import read_molecules, Settings, AMSJob, init, config, JobRunner


# this line is not required in AMS2025+
init()


# ## Summary Text File

# Set up a results file, `summary.txt`, which will hold a table with reaction energies.

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")


# ## Benchmark Calculation Setup

# The molecules used in the benchmark calculations are loaded, and the settings for each engine created.

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` below 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()


# ## Running Benchmark Calculations

# Benchmark calculations are configured to run in parallel with one core per job.

import multiprocessing

maxjobs = multiprocessing.cpu_count()
config.default_jobrunner = JobRunner(parallel=True, maxjobs=maxjobs)
config.job.runscript.nproc = 1

print(f"Running up to {maxjobs} jobs in parallel")


# Note: calculations will take some time to run, around 1-2 hours on a modern laptop.

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)


# ## Results

# Results can be loaded from the summary file and displayed using pandas. The pandas package is installable with `amspackages`.

with open(summary_fname) as summary_file:
    try:
        import pandas as pd
        from IPython.display import display, Markdown
        import sys

        data = pd.read_csv(summary_file, delim_whitespace=True).iloc[:, :-1]

        # Pretty-print if in notebook
        if "ipykernel" in sys.modules:
            display(Markdown(data.to_markdown()))
        else:
            print(data.to_markdown())

    except ImportError:
        data = summary_file.read()
        print(data)