Benchmark accuracy of basis setsΒΆ
import multiprocessing
# Run jobs as many jobs as possible in parallel:
config.default_jobrunner = JobRunner(parallel=True, maxjobs=multiprocessing.cpu_count())
config.job.runscript.nproc = 1
# The molecules we want to use in our benchmark:
mol_smiles = {'Methane' : 'C',
'Ethane' : 'C-C',
'Ethylene' : 'C=C',
'Acetylene': 'C#C'}
molecules = {}
for name, smiles in mol_smiles.items():
# Compute 10 conformers, optimize with UFF and pick the lowest in energy.
molecules[name] = from_smiles(smiles, nconfs=10, forcefield='uff')[0]
print(name, molecules[name])
# Initialize the common settings:
common_settings = Settings()
common_settings.input.ams.Task = 'SinglePoint'
common_settings.input.ams.System.Symmetrize = 'Yes'
common_settings.input.adf.Basis.Core = 'None'
basis = ['QZ4P', 'TZ2P', 'TZP', 'DZP', 'DZ', 'SZ']
reference_basis = 'QZ4P'
# Set up and run the calculations:
results = {}
for bas in basis:
for name, molecule in molecules.items():
settings = common_settings.copy()
settings.input.adf.Basis.Type = bas
job = AMSJob(name=name+'_'+bas, molecule=molecule, settings=settings)
results[(name,bas)] = job.run()
# Calculate the average absolute error in bond energy per atom for each basis set:
average_errors = {}
for bas in basis:
if bas != reference_basis:
errors = []
for name, molecule in molecules.items():
reference_energy = results[(name,reference_basis)].get_energy(unit='kcal/mol')
energy = results[(name,bas)].get_energy(unit='kcal/mol')
errors.append(abs(energy - reference_energy)/len(molecule))
print('Energy for {} using {} basis set: {} [kcal/mol]'.format(name,bas,energy))
average_errors[bas] = sum(errors)/len(errors)
print('== Results ==')
print('Average absolute error in bond energy per atom')
for bas in basis:
if bas != reference_basis:
print('Error for basis set {:<4}: {:>10.3f} [kcal/mol]'.format(bas, average_errors[bas]))
Output
[21:51:53] PLAMS working folder: /home/mirko/scratch/test.plams/rundir.plams.BasisSetBenchmark/plams_workdir
Methane Atoms:
1 C 0.000000 0.000000 0.000000
2 H 0.538912 0.762358 -0.599295
3 H 0.731244 -0.596616 0.583182
4 H -0.567129 -0.670302 -0.678108
5 H -0.703028 0.504560 0.694220
Bonds:
(1)--1.0--(2)
(1)--1.0--(3)
(1)--1.0--(4)
(1)--1.0--(5)
Ethane Atoms:
1 C -0.757196 -0.040522 0.044605
2 C 0.757196 0.040522 -0.044605
3 H -1.205222 0.185290 -0.945970
4 H -1.130281 0.694397 0.788688
5 H -1.061719 -1.061491 0.357407
6 H 1.205222 -0.185290 0.945971
7 H 1.130281 -0.694396 -0.788689
8 H 1.061719 1.061491 -0.357406
Bonds:
(1)--1.0--(2)
(1)--1.0--(3)
(1)--1.0--(4)
(1)--1.0--(5)
(2)--1.0--(6)
(2)--1.0--(7)
(2)--1.0--(8)
Ethylene Atoms:
1 C 0.664485 0.027988 -0.023685
2 C -0.664485 -0.027988 0.023685
3 H 1.253433 -0.878614 0.070299
4 H 1.167038 0.980564 -0.156575
5 H -1.253433 0.878614 -0.070299
6 H -1.167038 -0.980564 0.156575
Bonds:
(1)--2.0--(2)
(1)--1.0--(3)
(1)--1.0--(4)
(2)--1.0--(5)
(2)--1.0--(6)
Acetylene Atoms:
1 C -0.587409 0.175060 -0.002211
2 C 0.587409 -0.094463 0.002211
3 H -1.618985 0.411721 -0.006095
4 H 1.618985 -0.331124 0.006094
Bonds:
(1)--3.0--(2)
(1)--1.0--(3)
(2)--1.0--(4)
[21:51:53] JOB Methane_QZ4P STARTED
[21:51:53] JOB Ethane_QZ4P STARTED
[21:51:53] JOB Ethylene_QZ4P STARTED
[21:51:53] JOB Acetylene_QZ4P STARTED
[21:51:53] JOB Methane_QZ4P RUNNING
[21:51:53] JOB Methane_TZ2P STARTED
[21:51:53] JOB Ethane_QZ4P RUNNING
[21:51:53] JOB Ethylene_QZ4P RUNNING
[21:51:53] JOB Ethane_TZ2P STARTED
[21:51:53] JOB Ethylene_TZ2P STARTED
[21:51:53] JOB Acetylene_QZ4P RUNNING
[21:51:53] JOB Acetylene_TZ2P STARTED
[21:51:53] JOB Methane_TZ2P RUNNING
[21:51:53] JOB Methane_TZP STARTED
[21:51:53] JOB Ethane_TZ2P RUNNING
[21:51:53] JOB Ethane_TZP STARTED
[21:51:53] JOB Ethylene_TZ2P RUNNING
[21:51:53] JOB Acetylene_TZ2P RUNNING
[21:51:53] JOB Ethylene_TZP STARTED
[21:51:53] JOB Methane_TZP RUNNING
[21:51:53] JOB Acetylene_TZP STARTED
[21:51:53] JOB Ethane_TZP RUNNING
[21:51:53] JOB Methane_DZP STARTED
[21:51:53] JOB Ethane_DZP STARTED
[21:51:53] JOB Ethylene_TZP RUNNING
[21:51:53] JOB Ethylene_DZP STARTED
[21:51:53] JOB Acetylene_TZP RUNNING
[21:51:53] JOB Acetylene_DZP STARTED
[21:51:53] JOB Methane_DZP RUNNING
[21:51:53] JOB Methane_DZ STARTED
[21:51:53] JOB Ethane_DZP RUNNING
[21:51:53] JOB Ethylene_DZP RUNNING
[21:51:53] JOB Acetylene_DZP RUNNING
[21:51:53] JOB Ethane_DZ STARTED
[21:51:53] JOB Ethylene_DZ STARTED
[21:51:53] JOB Methane_DZ RUNNING
[21:51:53] JOB Ethane_DZ RUNNING
[21:51:53] JOB Acetylene_DZ STARTED
[21:51:53] JOB Ethylene_DZ RUNNING
[21:51:53] JOB Methane_SZ STARTED
[21:51:53] JOB Acetylene_DZ RUNNING
[21:51:53] JOB Ethane_SZ STARTED
[21:51:53] JOB Ethylene_SZ STARTED
[21:51:53] JOB Acetylene_SZ STARTED
[21:51:53] JOB Methane_SZ RUNNING
[21:51:53] JOB Ethane_SZ RUNNING
[21:51:53] Waiting for job Methane_QZ4P to finish
[21:51:53] JOB Ethylene_SZ RUNNING
[21:51:53] JOB Acetylene_SZ RUNNING
[21:51:56] JOB Methane_DZP FINISHED
[21:51:56] JOB Methane_DZP SUCCESSFUL
[21:51:57] JOB Methane_TZP FINISHED
[21:51:57] JOB Methane_TZP SUCCESSFUL
[21:51:57] JOB Methane_TZ2P FINISHED
[21:51:57] JOB Methane_TZ2P SUCCESSFUL
[21:51:58] JOB Ethylene_DZP FINISHED
[21:51:58] JOB Ethylene_DZP SUCCESSFUL
[21:51:58] JOB Acetylene_DZP FINISHED
[21:51:58] JOB Acetylene_DZP SUCCESSFUL
[21:51:58] JOB Acetylene_TZP FINISHED
[21:51:58] JOB Acetylene_TZP SUCCESSFUL
[21:51:58] JOB Methane_QZ4P FINISHED
[21:51:58] JOB Methane_QZ4P SUCCESSFUL
Energy for Methane using TZ2P basis set: -572.1101629292748 [kcal/mol]
[21:51:58] Waiting for job Ethane_QZ4P to finish
[21:51:58] JOB Ethylene_TZP FINISHED
[21:51:58] JOB Ethylene_TZP SUCCESSFUL
[21:51:59] JOB Methane_DZ FINISHED
[21:51:59] JOB Methane_DZ SUCCESSFUL
[21:51:59] JOB Ethane_DZP FINISHED
[21:51:59] JOB Ethane_DZP SUCCESSFUL
[21:52:00] JOB Ethylene_TZ2P FINISHED
[21:52:00] JOB Ethylene_TZ2P SUCCESSFUL
[21:52:00] JOB Acetylene_TZ2P FINISHED
[21:52:00] JOB Acetylene_TZ2P SUCCESSFUL
[21:52:00] JOB Methane_SZ FINISHED
[21:52:00] JOB Methane_SZ SUCCESSFUL
[21:52:00] JOB Ethylene_DZ FINISHED
[21:52:00] JOB Ethylene_DZ SUCCESSFUL
[21:52:00] JOB Ethane_TZP FINISHED
[21:52:00] JOB Ethane_TZP SUCCESSFUL
[21:52:01] JOB Acetylene_SZ FINISHED
[21:52:01] JOB Acetylene_SZ SUCCESSFUL
[21:52:01] JOB Acetylene_DZ FINISHED
[21:52:01] JOB Acetylene_DZ SUCCESSFUL
[21:52:01] JOB Ethylene_SZ FINISHED
[21:52:01] JOB Ethylene_SZ SUCCESSFUL
[21:52:01] JOB Ethane_DZ FINISHED
[21:52:01] JOB Ethane_DZ SUCCESSFUL
[21:52:02] JOB Ethylene_QZ4P FINISHED
[21:52:02] JOB Ethylene_QZ4P SUCCESSFUL
[21:52:02] JOB Ethane_SZ FINISHED
[21:52:02] JOB Ethane_SZ SUCCESSFUL
[21:52:02] JOB Acetylene_QZ4P FINISHED
[21:52:02] JOB Acetylene_QZ4P SUCCESSFUL
[21:52:03] JOB Ethane_TZ2P FINISHED
[21:52:03] JOB Ethane_TZ2P SUCCESSFUL
[21:52:08] JOB Ethane_QZ4P FINISHED
[21:52:08] JOB Ethane_QZ4P SUCCESSFUL
Energy for Ethane using TZ2P basis set: -971.882012717666 [kcal/mol]
Energy for Ethylene using TZ2P basis set: -769.43290265999 [kcal/mol]
Energy for Acetylene using TZ2P basis set: -555.6672866640299 [kcal/mol]
Energy for Methane using TZP basis set: -571.0449016648643 [kcal/mol]
Energy for Ethane using TZP basis set: -970.0758795895841 [kcal/mol]
Energy for Ethylene using TZP basis set: -767.3275161232395 [kcal/mol]
Energy for Acetylene using TZP basis set: -552.956282573915 [kcal/mol]
Energy for Methane using DZP basis set: -569.1190167665213 [kcal/mol]
Energy for Ethane using DZP basis set: -966.0916462896635 [kcal/mol]
Energy for Ethylene using DZP basis set: -764.4133003958359 [kcal/mol]
Energy for Acetylene using DZP basis set: -550.6461780402834 [kcal/mol]
Energy for Methane using DZ basis set: -560.9344371700147 [kcal/mol]
Energy for Ethane using DZ basis set: -951.1667072119619 [kcal/mol]
Energy for Ethylene using DZ basis set: -750.1745137243371 [kcal/mol]
Energy for Acetylene using DZ basis set: -537.1008064541019 [kcal/mol]
Energy for Methane using SZ basis set: -723.550125571837 [kcal/mol]
Energy for Ethane using SZ basis set: -1216.9142215158688 [kcal/mol]
Energy for Ethylene using SZ basis set: -934.6558219377758 [kcal/mol]
Energy for Acetylene using SZ basis set: -647.5029900541123 [kcal/mol]
== Results ==
Average absolute error in bond energy per atom
Error for basis set TZ2P: 0.170 [kcal/mol]
Error for basis set TZP : 0.537 [kcal/mol]
Error for basis set DZP : 1.024 [kcal/mol]
Error for basis set DZ : 3.339 [kcal/mol]
Error for basis set SZ : 27.683 [kcal/mol]
[21:52:08] PLAMS run finished. Goodbye
Test duration in seconds: 15