Worked Example¶
Initialization¶
from scm.plams import *
# this line is not required in AMS2025+
init()
PLAMS working folder: /path/plams/examples/NumHess/plams_workdir
Define molecule¶
Normally you would read the molecule from an xyz file
# mol = Molecule('methanol.xyz')
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 job¶
Here we use the fast DFTB engine, for ADF it is recommended to disable symmetry
s = Settings()
s.input.ams.task = "SinglePoint"
s.input.ams.Properties.Gradients = "Yes"
# s.input.adf.basis.type = 'DZP'
# s.input.adf.symmetry = 'NOSYM'
# s.input.adf.xc.gga = 'PW91'
s.input.DFTB.Model = "GFN1-xTB"
s.runscript.nproc = 1
j = NumHessJob(name="test", molecule=mol, settings=s, jobtype=AMSJob, gradient=lambda x: x.get_gradients().reshape(-1))
r = j.run(jobrunner=JobRunner(parallel=True, maxjobs=8))
[06.03|13:55:22] JOB test STARTED
[06.03|13:55:22] JOB test RUNNING
[06.03|13:55:22] JOB test/1_0_-1 STARTED
[06.03|13:55:22] JOB test/1_0_1 STARTED
Print results¶
print(r.get_hessian(mass_weighted=True))
[06.03|13:55:22] JOB test/1_1_-1 STARTED
[06.03|13:55:22] Waiting for job test to finish
[06.03|13:55:22] JOB test/1_1_1 STARTED
[06.03|13:55:22] JOB test/1_2_-1 STARTED
[06.03|13:55:22] JOB test/1_2_1 STARTED
[06.03|13:55:22] JOB test/1_0_-1 RUNNING
[06.03|13:55:22] JOB test/2_0_-1 STARTED
[06.03|13:55:22] JOB test/2_0_1 STARTED
[06.03|13:55:22] JOB test/2_1_-1 STARTED
[06.03|13:55:22] JOB test/2_1_1 STARTED
[06.03|13:55:22] JOB test/2_2_-1 STARTED
... (PLAMS log lines truncated) ...
[[ 2.43775999e-03 -1.24945968e-10 8.35714013e-11 -2.16941328e-05
5.02435569e-12 -7.14677254e-12 -1.60687481e-02 1.15383294e-02
-7.21385604e-03 -1.60687464e-02 -1.15383280e-02 7.21385522e-03
3.47625119e-03 3.62021265e-11 -5.46656826e-11]
[-1.24945968e-10 2.43617119e-03 1.02498360e-05 4.74486821e-12
-2.19212819e-05 2.94502688e-05 1.14532498e-02 -3.28822540e-03
4.41476048e-03 -1.14532483e-02 -3.28822472e-03 4.41475997e-03
-8.03126599e-11 -2.20627127e-02 -9.41894828e-03]
[ 8.35714013e-11 1.02498360e-05 2.14233490e-03 7.19072217e-13
2.90465272e-05 -8.63468227e-04 -4.79807048e-03 3.01867574e-03
-3.68101848e-03 4.79806931e-03 3.01867515e-03 -3.68101833e-03
-4.67601951e-11 -6.61690618e-03 -4.46017458e-03]
[-2.16941328e-05 4.74486821e-12 7.19072217e-13 1.49619173e-04
-2.14387656e-12 8.46463904e-13 -3.85034451e-04 -5.25094480e-04
-1.04652467e-03 -3.85034464e-04 5.25094462e-04 1.04652463e-03
-1.35573946e-03 -4.86485419e-12 2.14361038e-11]
[ 5.02435569e-12 -2.19212819e-05 2.90465272e-05 -2.14387656e-12
1.50336369e-04 -3.08725780e-05 -5.36109667e-04 -1.06913031e-03
6.27011593e-04 5.36109618e-04 -1.06913034e-03 6.27011524e-04
1.40055968e-11 3.87414930e-06 -1.11023668e-03]
[-7.14677254e-12 2.94502688e-05 -8.63468227e-04 8.46463904e-13
-3.08725780e-05 1.04165349e-03 -7.28706894e-04 4.42296851e-04
-2.04725210e-03 7.28706950e-04 4.42296845e-04 -2.04725207e-03
1.96785022e-11 -7.46717101e-04 -2.14861643e-03]
[-1.60687481e-02 1.14532498e-02 -4.79807048e-03 -3.85034451e-04
-5.36109667e-04 -7.28706894e-04 2.30394724e-01 -1.34285111e-01
7.67026070e-02 -2.16065892e-02 5.58885425e-03 -1.11180652e-02
-1.12833086e-02 6.64824977e-04 3.15373514e-03]
[ 1.15383294e-02 -3.28822540e-03 3.01867574e-03 -5.25094480e-04
-1.06913031e-03 4.42296851e-04 -1.34285111e-01 8.15853116e-02
-4.64977897e-02 -5.58885505e-03 -7.11299026e-03 -1.05553100e-02
1.06516082e-02 -1.84750271e-02 1.40635538e-02]
[-7.21385604e-03 4.41476048e-03 -3.68101848e-03 -1.04652467e-03
6.27011593e-04 -2.04725210e-03 7.67026070e-02 -4.64977897e-02
6.64040738e-02 1.11180655e-02 -1.05553100e-02 4.44753112e-03
1.47911831e-02 -5.53928405e-03 5.49673857e-03]
[-1.60687464e-02 -1.14532483e-02 4.79806931e-03 -3.85034464e-04
5.36109618e-04 7.28706950e-04 -2.16065892e-02 -5.58885505e-03
1.11180655e-02 2.30394703e-01 1.34285094e-01 -7.67025954e-02
-1.12833089e-02 -6.64823699e-04 -3.15373388e-03]
[-1.15383280e-02 -3.28822472e-03 3.01867515e-03 5.25094462e-04
-1.06913034e-03 4.42296845e-04 5.58885425e-03 -7.11299026e-03
-1.05553100e-02 1.34285094e-01 8.15853035e-02 -4.64977824e-02
-1.06516072e-02 -1.84750267e-02 1.40635536e-02]
[ 7.21385522e-03 4.41475997e-03 -3.68101833e-03 1.04652463e-03
6.27011524e-04 -2.04725207e-03 -1.11180652e-02 -1.05553100e-02
4.44753112e-03 -7.67025954e-02 -4.64977824e-02 6.64040713e-02
-1.47911830e-02 -5.53928397e-03 5.49673857e-03]
[ 3.47625119e-03 -8.03126599e-11 -4.67601951e-11 -1.35573946e-03
1.40055968e-11 1.96785022e-11 -1.12833086e-02 1.06516082e-02
1.47911831e-02 -1.12833089e-02 -1.06516072e-02 -1.47911830e-02
2.46727294e-03 -2.63269039e-10 2.12920387e-11]
[ 3.62021265e-11 -2.20627127e-02 -6.61690618e-03 -4.86485419e-12
3.87414930e-06 -7.46717101e-04 6.64824977e-04 -1.84750271e-02
-5.53928405e-03 -6.64823699e-04 -1.84750267e-02 -5.53928397e-03
-2.63269039e-10 2.99742684e-01 1.01775207e-01]
[-5.46656826e-11 -9.41894828e-03 -4.46017458e-03 2.14361038e-11
-1.11023668e-03 -2.14861643e-03 3.15373514e-03 1.40635538e-02
5.49673857e-03 -3.15373388e-03 1.40635536e-02 5.49673857e-03
2.12920387e-11 1.01775207e-01 7.62490469e-02]]