Charge transfer integrals with ADFΒΆ

#!/usr/bin/env plams
# Add new results extraction method
@add_to_class(ADFFragmentResults)
def get_transfer_integrals(self):
    return self.job.full.results.read_rkf_section("TransferIntegrals", file="adf")


# Common settings for all 3 jobs
# In the interest of computational speed we use a minimal basis
# set. For more quantitatively meaningful results, you should use
# a larger basis.
common = Settings()
common.input.ams.Task = "SinglePoint"
common.input.adf.Basis.Type = "SZ"
common.input.adf.Basis.Core = "None"
common.input.adf.Symmetry = "NoSym"

# Specific settings for full system job
full = Settings()
full.input.adf.transferintegrals = True

# Load XYZ file and separate it into 2 fragments
mol = Molecule("BenzeneDimer.xyz")
mol.guess_bonds()
fragments = mol.separate()
if len(fragments) != 2:
    log("ERROR: Molecule {} was split into {} fragments".format(mol.properties.name, len(fragments)))
    import sys

    sys.exit(1)
else:
    mol1, mol2 = fragments

# Alternatively one could simply load fragments from separate xyz files:
# mol1 = Molecule('fragment1.xyz')
# mol2 = Molecule('fragment2.xyz')

job = ADFFragmentJob(name="ADFTI", fragment1=mol1, fragment2=mol2, settings=common, full_settings=full)
results = job.run()

# TI is a dictionary with the whole TransferIntegrals section from adf.rkf
print("== Results ==")
TI = results.get_transfer_integrals()
for key, value in sorted(TI.items()):
    print("{:<28}: {:>12.6f}".format(key, value))

Note

To execute this PLAMS script:

Output

[10:20:01] PLAMS working folder: /scratch/rundir.plams.ChargeTransferIntegralsADF/plams_workdir
[10:20:01] JOB ADFTI STARTED
[10:20:01] JOB ADFTI RUNNING
[10:20:01] JOB ADFTI/frag1 STARTED
[10:20:01] JOB ADFTI/frag1 RUNNING
[10:20:07] JOB ADFTI/frag1 FINISHED
[10:20:07] JOB ADFTI/frag1 SUCCESSFUL
[10:20:07] JOB ADFTI/frag2 STARTED
[10:20:07] JOB ADFTI/frag2 RUNNING
[10:20:10] JOB ADFTI/frag2 FINISHED
[10:20:10] JOB ADFTI/frag2 SUCCESSFUL
[10:20:10] JOB ADFTI/full STARTED
[10:20:10] JOB ADFTI/full RUNNING
[10:20:22] JOB ADFTI/full FINISHED
[10:20:22] JOB ADFTI/full SUCCESSFUL
[10:20:22] JOB ADFTI FINISHED
[10:20:22] JOB ADFTI SUCCESSFUL
== Results ==
J(charge recombination 12)  :    -0.010748
J(charge recombination 21)  :    -0.010747
J(electron)                 :    -0.012049
J(hole)                     :     0.034996
S(charge recombination 12)  :     0.016227
S(charge recombination 21)  :     0.016226
S(electron)                 :     0.018761
S(hole)                     :    -0.049852
V(charge recombination 12)  :    -0.009868
V(charge recombination 21)  :    -0.009868
V(electron)                 :    -0.013127
V(hole)                     :     0.026792
Vtot(charge recombination 12):     0.013197
Vtot(charge recombination 21):     0.013197
Vtot(electron)              :     0.021460
Vtot(hole)                  :     0.034181
e1(electron)                :     0.057207
e1(hole)                    :    -0.165894
e2(electron)                :     0.057209
e2(hole)                    :    -0.165896
[10:20:22] PLAMS run finished. Goodbye
Test duration in seconds: 22