5.1.1. Charge transfer integrals with ADFΒΆ

Calculating charge transfer integrals with ADF requires running a standard two-fragment analysis: two calculations for fragments and one for the full system. The additional TRANSFERINTEGRALS key should be used in the full system calculation. Please refer to the ADF manual for more information about charge transfer integrals.

Performing such a 3 step calculation with PLAMS is a straightforward application of ADF fragment job recipe:

# Add new results extraction method
def get_transfer_integrals(self):
    return self.job.full.results._kf.read_section('TransferIntegrals')

# Common settings for all 3 jobs
common = Settings()
common.input.basis.type = 'TZP'
common.input.basis.core = 'None'
common.input.basis.createoutput = 'None'
common.input.xc.gga = 'PW91'
common.input.symmetry = 'Nosym'
common.input.noprint = 'Logfile'

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

# Load XYZ file and separate it into 2 fragments
mol = Molecule('full_system.xyz')
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)
    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 TAPE21
TI = results.get_transfer_integrals()
for key in TI:
    print(key, TI[key])

In the code above you can see the usage of Binding decorators to enrich ADFFragmentResults with a method extracting transfer integrals. Another feature worth noting is automatic separation of a molecular system into two fragments.