def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = { 'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = { 'nnodes':1,
'nprocs':16,
'walltime':'48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {'hkl':slab_interface_params['hkl'],
'ligand':slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {'hkl':hkl,
'ligand':structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix':False,
'from_ase':True,
'Grid_type':'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = {
'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = {
'nnodes': 1,
'nprocs': 16,
'walltime': '48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {
'hkl': slab_interface_params['hkl'],
'ligand': slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {
'hkl': hkl,
'ligand': structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix': False,
'from_ase': True,
'Grid_type': 'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
