Worked Example

Initial Imports

Import PLAMS components and set up to run jobs in tandem.

from scm.plams import Settings, AMSJob, Molecule, Atom, FCFJob, config, JobRunner, init
from scm.plams.recipes.fcf_dos import FCFDOS

config.default_jobrunner.parallel = JobRunner(parallel=True, maxjobs=2)

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

PLAMS working folder: /path/plams/examples/ADFVibronicDOS/plams_workdir

Setup Molecules

Create the NO2 molecules using pre-optimized geometries (usually the geometry optimization step would come first).

no2_radical = Molecule()
no2_radical.add_atom(Atom(atnum=7, coords=(0.0, 0.0, -0.01857566)))
no2_radical.add_atom(Atom(atnum=8, coords=(0.0, 1.09915770, -0.49171967)))
no2_radical.add_atom(Atom(atnum=8, coords=(0.0, -1.09915770, -0.49171967)))

no2_anion = Molecule()
no2_anion.add_atom(Atom(atnum=7, coords=(0.0, 0.0, 0.12041)))
no2_anion.add_atom(Atom(atnum=8, coords=(0.0, 1.070642, -0.555172)))
no2_anion.add_atom(Atom(atnum=8, coords=(0.0, -1.070642, -0.555172)))

Calculate Vibrational Frequencies

Create the settings objects for the ADF donor/acceptor vibrational frequencies calculations. Run the calculations in parallel.

settings_freq = Settings()
settings_freq.input.adf.symmetry = "NoSym"
settings_freq.input.adf.basis.type = "DZP"
settings_freq.input.adf.basis.core = "None"
settings_freq.input.adf.xc.lda = "SCF VWN"
settings_freq.input.ams.Task = "SinglePoint"
settings_freq.input.ams.Properties.NormalModes = "Yes"
settings_freq.input.adf.title = "Vibrational frequencies"

settings_freq_radical = settings_freq.copy()
settings_freq_radical.input.ams.system.charge = 0
settings_freq_radical.input.adf.spinpolarization = 1
settings_freq_radical.input.adf.unrestricted = "Yes"

settings_freq_anion = settings_freq.copy()
settings_freq_anion.input.ams.system.charge = -1

freq_job_radical = AMSJob(molecule=no2_radical, settings=settings_freq_radical, name="fsradical")
freq_job_anion = AMSJob(molecule=no2_anion, settings=settings_freq_anion, name="fsanion")

freq_results = (freq_job_radical.run(), freq_job_anion.run())

[10.02|14:22:57] JOB fsradical STARTED
[10.02|14:22:57] JOB fsradical RUNNING
[10.02|14:23:08] JOB fsradical FINISHED
[10.02|14:23:08] JOB fsradical SUCCESSFUL
[10.02|14:23:08] JOB fsanion STARTED
[10.02|14:23:08] JOB fsanion RUNNING
[10.02|14:23:17] JOB fsanion FINISHED
[10.02|14:23:17] JOB fsanion SUCCESSFUL

Calculate Vibronic Spectra

Use Frank-Condon jobs to calculate the vibronic spectra.

def fcf_job(state1, state2, spctype, name):
    settings_fcf = Settings()
    settings_fcf.input.spectrum.type = spctype
    settings_fcf.input.state1 = state1
    settings_fcf.input.state2 = state2
    return FCFJob(inputjob1=state1, inputjob2=state2, settings=settings_fcf, name=name)


freq_radical = freq_results[0].rkfpath(file="adf")
freq_anion = freq_results[1].rkfpath(file="adf")

fc_abs = fcf_job(freq_radical, freq_anion, "absorption", "fcfabs")
fc_emi = fcf_job(freq_anion, freq_radical, "emission", "fcfemi")

fc_results = (fc_abs.run(), fc_emi.run())

[10.02|14:23:17] JOB fcfabs STARTED
[10.02|14:23:17] JOB fcfabs RUNNING
[10.02|14:23:19] JOB fcfabs FINISHED
[10.02|14:23:19] JOB fcfabs SUCCESSFUL
[10.02|14:23:19] JOB fcfemi STARTED
[10.02|14:23:19] JOB fcfemi RUNNING
[10.02|14:23:20] JOB fcfemi FINISHED
[10.02|14:23:20] JOB fcfemi SUCCESSFUL

Calculate Density of States

Calculate the DOS by computing the overlap of the absorption and emission FCF spectra.

job = FCFDOS(fc_results[0].kfpath(), fc_results[1].kfpath(), 10000.0, 10000.0)
dos = job.dos()

print(f"The density of states is {dos:.8e}")

The density of states is 1.30090295e-08