def create_interface(self):
"""
add params that you want to vary
"""
structure = self.input_structure.copy()
iface = Interface(structure,
hkl=self.system['hkl'],
ligand=Ligand.from_dict(self.system['ligand']),
from_ase=self.from_ase)
iface.sort()
sd = self.set_sd_flags(iface, n_layers=2)
# if there are other paramters that are being varied
# change the comment accordingly
comment = self.system['hkl'] + self.system['ligand']['name']
return Poscar(iface, comment=comment, selective_dynamics=sd)
def create_interface(self):
"""
add params that you want to vary
"""
structure = self.input_structure.copy()
iface = Interface(structure,
hkl=self.system['hkl'],
ligand = Ligand.from_dict(self.system['ligand']),
from_ase=self.from_ase)
iface.sort()
sd = self.set_sd_flags(iface, n_layers=2)
#if there are other paramters that are being varied
#change the comment accordingly
comment = self.system['hkl']+self.system['ligand']['name']
return Poscar(iface, comment=comment,
selective_dynamics=sd)
from pymatgen.io.vasp.inputs import Poscar
from mpinterfaces.interface import Interface, Ligand
if __name__ == '__main__':
# PbS 100 surface with single hydrazine as ligand
# strt=get_struct_from_mp("PbS",MAPI_KEY=MAPI_KEY)
# using smiles_to_xyz.py you can obtain molecule xyz
# using openbabel.
# example structure files are provided and set in dev_scripts
# bulk structure of slab
strt = Structure.from_file("dev_scripts/POSCAR_PbS")
# pre-relaxed Ligand in a box
mol_struct = Structure.from_file("dev_scripts/POSCAR_TCPO")
mol = Molecule(mol_struct.species, mol_struct.cart_coords)
hydrazine = Ligand([mol])
# intital supercell, this wont be the final supercell if
# surface coverage is specified
supercell = [1, 1, 1]
# miller index
hkl = [1, 0, 0]
# minimum slab thickness in Angstroms
min_thick = 19
# minimum vacuum thickness in Angstroms
# mind: the ligand will be placed in this vacuum, so the
# final effective vacuum space will be smaller than this
min_vac = 12
from pymatgen.io.vaspio.vasp_input import Incar, Poscar, Potcar, Kpoints
from pymatgen.core import Structure, Molecule
from mpinterfaces.interface import Interface, Ligand
#create ligand, interface and slab from the starting POSCARs
strt= Structure.from_file("POSCAR_PbS_bulk_with_vdw") #using POSCAR of vdW relaxed PbS
mol_struct= Structure.from_file("POSCAR_DMF") #using POSCAR of vdW relaxed PbS
mol= Molecule(mol_struct.species, mol_struct.cart_coords)
DMF= Ligand([mol]) #create Ligand DMF
supercell = [1,1,1]
# slab thickness and vacuum set manual for now to converged values, surface coverage fixed at 0.014 ligand/sq.Angstrom
#for consistency, best ligand spacing at the coverage
min_thick= 19
min_vac= 12
surface_coverage= 0.014
#hkl of facet to reproduce
hkl= [1,0,0]
# specify the species on slab to adsorb over
slab_species= 'Pb'
# specify the species onb ligand serving as the bridge atom
adatom_on_ligand= 'O'
#initial adsorption distance in angstrom
ads_distance = 3.0
# create the interface
##################### SECOND WORKFLOW: LIGAND ########################################
# pull structure of ligand
# firework 3 firetask1: cutoff convergence
# firework 4 firetask1: relaxation
mols = []
lig_firetasks = []
lig_fireworks = []
molecule = Structure.from_file(
"POSCAR_TCPO") #for testing purposes, can be constructed
#from smiles_to_poscar.py script
mols.append(molecule)
# create ligand from molecules
ligand = Ligand(mols,
cm_dist=[],
angle={},
link={},
remove=[],
charge=0,
spin_multiplicity=None,
validate_proximity=False)
#create firetasks for molecule cutoff convergence and relaxation
lig_firetasks.append(get_calibration_task(structure=ligand, \
turn_knobs={'ENCUT':[400,500,600]}, \
other_params={'job_dir': 'LigandConvergence'}))
lig_firetasks.append(get_calibration_task(structure=ligand, \
incar_params = {'NSW':100},\
other_params={'job_dir': 'LigandRelax'}))
#create firework for molecule cutoff convergence
lig_fireworks.append(
Firework(lig_firetasks[0], name='molecule_convergence'))