Reaction energies with many different engines¶

#!/usr/bin/env plams
"""
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
"""
import os

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