Worked Example¶
Initialization¶
import numpy as np
import multiprocessing
from scm.plams.recipes.numgrad import NumGradJob
from scm.plams import config, JobRunner, AMSJob, Settings, AMSResults, Units, init
# this line is not required in AMS2025+
init()
PLAMS working folder: /path/plams/NumGrad/plams_workdir.003
Parallelization¶
config.default_jobrunner = JobRunner(parallel=True, maxjobs=multiprocessing.cpu_count())
Define molecule¶
mol = AMSJob.from_input(
"""
System
Atoms
C 0.000000000000 0.138569980000 0.355570700000
O 0.000000000000 0.187935770000 -1.074466460000
H 0.882876920000 -0.383123830000 0.697839450000
H -0.882876940000 -0.383123830000 0.697839450000
H 0.000000000000 1.145042790000 0.750208830000
End
End
"""
).molecule[""]
Setup and run jobs¶
s = Settings()
s.input.AMS.Task = "SinglePoint"
s.input.ForceField.Type = "UFF"
s.runscript.nproc = 1
j = NumGradJob(name="numgrad", molecule=mol, settings=s, jobtype=AMSJob)
r = j.run()
r.wait()
s_analytical = s.copy()
s_analytical.input.AMS.Properties.Gradients = "Yes"
analytical_job = AMSJob(name="analytical", molecule=mol, settings=s_analytical)
analytical_job.run()
[05.03|16:16:05] JOB numgrad STARTED
[05.03|16:16:05] Waiting for job numgrad to finish
[05.03|16:16:05] JOB numgrad RUNNING
[05.03|16:16:05] JOB numgrad/1_x_-1 STARTED
[05.03|16:16:05] JOB numgrad/1_x_1 STARTED
[05.03|16:16:05] JOB numgrad/1_y_-1 STARTED
[05.03|16:16:05] JOB numgrad/1_y_1 STARTED
[05.03|16:16:05] JOB numgrad/1_z_-1 STARTED
[05.03|16:16:05] JOB numgrad/1_z_1 STARTED
[05.03|16:16:05] JOB numgrad/2_x_-1 STARTED
[05.03|16:16:05] JOB numgrad/2_x_1 STARTED
... (PLAMS log lines truncated) ...
<scm.plams.interfaces.adfsuite.ams.AMSResults at 0x77d85d1da100>
[05.03|16:16:11] JOB analytical RUNNING
[05.03|16:16:11] JOB analytical FINISHED
[05.03|16:16:11] JOB analytical SUCCESSFUL
Print results¶
numerical_gradients = np.array(r.get_gradient(AMSResults.get_energy)).reshape(-1, 3)
analytical_gradients = np.array(analytical_job.results.get_gradients()).reshape(-1, 3) * Units.convert(
1.0, "bohr^-1", "angstrom^-1"
)
print("Numerical Gradients (NumGradJob), hartree/angstrom:")
print(numerical_gradients)
print("Analytical Gradients, hartree/angstrom:")
print(analytical_gradients)
print("Error Gradients, hartree/angstrom:")
print(numerical_gradients - analytical_gradients)
Numerical Gradients (NumGradJob), hartree/angstrom:
[[ 1.60868100e-08 -1.69669118e-02 4.89757712e-01]
[-1.04939876e-09 1.59476070e-02 -4.59496019e-01]
[-2.43299529e-02 1.43887838e-02 -9.57760819e-03]
[ 2.43299384e-02 1.43887756e-02 -9.57760381e-03]
[-5.15117463e-10 -2.77353210e-02 -1.11275734e-02]]
Analytical Gradients, hartree/angstrom:
[[ 1.60879471e-08 -1.70121112e-02 4.89788974e-01]
[-1.04943735e-09 1.59456436e-02 -4.59495951e-01]
[-2.43388668e-02 1.44021876e-02 -9.58077129e-03]
[ 2.43388522e-02 1.44021793e-02 -9.58076691e-03]
[-5.15150510e-10 -2.77378992e-02 -1.11314841e-02]]
Error Gradients, hartree/angstrom:
[[-1.13706585e-12 4.51994875e-05 -3.12614668e-05]
[ 3.85875469e-14 1.96343429e-06 -6.77586056e-08]
[ 8.91382542e-06 -1.34037122e-05 3.16309721e-06]
[-8.91382498e-06 -1.34037118e-05 3.16309724e-06]
[ 3.30475429e-14 2.57812910e-06 3.91074449e-06]]