Vibronic Density of States with ADF

This example uses ADF to model the density of states involved in the charge transfer between two systems using the AH-FC method - in this case an NO2 radical and an NO2 anion.

To follow along, either

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

Complete Python code

#!/usr/bin/env amspython
# coding: utf-8

# ## 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()


# ## 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())


# ## 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())


# ## 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}")