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)
# ligand displacement from the slab surface along the surface normal
# i.e adatom_on_lig will be displced by this amount from the
# adsorb_on_species atom
# on the slab
# in Angstrom
displacement = 3.0
# here we create the interface
iface = Interface(strt, hkl=hkl,
min_thick=min_thick, min_vac=min_vac,
supercell=supercell, surface_coverage=0.01,
ligand=hydrazine, displacement=displacement,
adatom_on_lig='N', adsorb_on_species='Pb',
primitive=False)
iface.create_interface()
iface.sort()
# extract bare slab
iface_slab = iface.slab
iface_slab.sort()
# set selective dynamics flags as required
true_site = [1, 1, 1]
false_site = [0, 0, 0]
sd_flag_iface = []
sd_flag_slab = []
# selective dynamics flags for the interface
for i in iface.sites:
sd_flag_iface.append(false_site)
# selective dynamics flags for the bare slab
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
interface_poscar = Poscar(iface, selective_dynamics=sd_flag_iface)
displacement = 3.0
# here we create the interface
iface = Interface(strt,
hkl=hkl,
min_thick=min_thick,
min_vac=min_vac,
supercell=supercell,
surface_coverage=0.01,
ligand=hydrazine,
displacement=displacement,
adatom_on_lig='N',
adsorb_on_species='Pb',
primitive=False)
iface.create_interface()
iface.sort()
# extract bare slab
iface_slab = iface.slab
iface_slab.sort()
# set selective dynamics flags as required
true_site = [1, 1, 1]
false_site = [0, 0, 0]
sd_flag_iface = []
sd_flag_slab = []
# selective dynamics flags for the interface
for i in iface.sites:
sd_flag_iface.append(false_site)
# selective dynamics flags for the bare slab
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
interface_poscar = Poscar(iface, selective_dynamics=sd_flag_iface)
def coloumb_configured_interface(iface, random=True,
translations=None,
rotations=None,
samples=10, lowest=5, ecut=None):
"""
Creates Ligand Slab interfaces of user specified translations
and rotations away from the initial guess of binding site
configuration, returns lowest energy structure according to
Coulomb model
Args:
Interface: Interface object: initial interface object
random: True for using Gaussian sampled random numbers for
rotations and translations
translations: list of [x,y,z] translations to be performed
rotation: list of [a,b,c] rotations to be performed w.r.t
Ligand axis
samples: number of interfaces to create
lowest: number of structures to return according to order of
minimum energies
Returns:
list of lowest energy interface objects
"""
ifaces = []
transform = []
for i in range(samples):
if random:
x = np.random.normal() # shift along x direction
y = np.random.normal() # shift along y direction
z = np.random.normal() # shift aling z direction
a = SymmOp.from_axis_angle_and_translation(axis=[1, 0, 0], \
angle=np.random.normal(0, 180))
b = SymmOp.from_axis_angle_and_translation(axis=[0, 1, 0], \
angle=np.random.normal(0, 180))
c = SymmOp.from_axis_angle_and_translation(axis=[0, 0, 1], \
angle=np.random.normal(0, 180))
ligand = iface.ligand
ligand.apply_operation(a)
ligand.apply_operation(b)
ligand.apply_operation(c)
# check if created interface maintains the ligand adsorbed
# over the surface
for j in iface.top_atoms:
if not iface.cart_coords[j][2] + iface.displacement > \
min(ligand.cart_coords[:, 2]):
transform.append(True)
if all(transform):
iface = Interface(iface.strt, hkl=iface.hkl,
min_thick=iface.min_thick,
min_vac=iface.min_vac,
supercell=iface.supercell,
surface_coverage=iface.surface_coverage,
ligand=iface.ligand, displacement=z,
adatom_on_lig=iface.adatom_on_lig,
adsorb_on_species=iface.adsorb_on_species,
primitive=False, from_ase=True,
x_shift=x, y_shift=y)
iface.create_interface()
energy = iface.calc_energy()
iface.sort()
if energy < ecut:
ifaces.append((energy, iface))
# ifaces.zip(energy, iface)
return ifaces
# firework 3 and firework 2
# at thickness and vac spacing of firework 4
# firework 5 firetask1: Interface relaxation , firetask2: slab relaxation
interface_firetasks = []
interface_fireworks = []
interface = Interface(bulk, hkl=[1,0,0], min_thick=10, min_vac=10,
supercell=[1,1,1], name=None, adsorb_on_species='Pb',
adatom_on_lig='O', ligand=ligand, displacement=3.0,
surface_coverage=0.01, scell_nmax=10, coverage_tol=0.25,
solvent="amine", start_from_slab=False, validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=False, primitive = True,
from_ase=True, x_shift= 0, y_shift= 0)
interface.create_interface() #with pre-configure as true, will generate different
#ligand interface configurations
interface.sort()
slab = interface.slab
slab.sort()
# create interface firetasks: interface relaxation and slab relaxation
interface_firetasks.append(get_calibration_task(structure=interface, \
incar_params = {'NSW':100}, \
other_params = {'job_dir': 'InterfaceRelax'}))
interface_firetasks.append(get_calibration_task(structure=slab, \
incar_params = {'NSW':100}))
interface_fireworks.append(Firework(interface_firetasks, name='interface_convergence'))
workflows.append(get_workflow(interface_fireworks, name='Interface'))
def coloumb_configured_interface(iface, random=True,
translations= None,
rotations=None,
samples=10, lowest=5, ecut=None):
"""
Creates Ligand Slab interfaces of user specified translations
and rotations away from the initial guess of binding site
configuration, returns lowest energy structure according to
Coulomb model
Args:
Interface: Interface object: initial interface object
random: True for using Gaussian sampled random numbers for
rotations and translations
translations: list of [x,y,z] translations to be performed
rotation: list of [a,b,c] rotations to be performed w.r.t
Ligand axis
samples: number of interfaces to create
lowest: number of structures to return according to order of
minimum energies
Returns:
list of lowest energy interface objects
"""
ifaces= []
transform= []
for i in range(samples):
if random:
x = np.random.normal() # shift along x direction
y = np.random.normal() # shift along y direction
z = np.random.normal() # shift aling z direction
a= SymmOp.from_axis_angle_and_translation(axis=[1,0,0],\
angle=np.random.normal(0,180))
b= SymmOp.from_axis_angle_and_translation(axis=[0,1,0],\
angle=np.random.normal(0,180))
c= SymmOp.from_axis_angle_and_translation(axis=[0,0,1],\
angle=np.random.normal(0,180))
ligand=iface.ligand
ligand.apply_operation(a)
ligand.apply_operation(b)
ligand.apply_operation(c)
# check if created interface maintains the ligand adsorbed
# over the surface
for j in iface.top_atoms:
if not iface.cart_coords[j][2] + iface.displacement > \
min(ligand.cart_coords[:,2]):
transform.append(True)
if all(transform):
iface= Interface(iface.strt, hkl=iface.hkl,
min_thick=iface.min_thick,
min_vac=iface.min_vac,
supercell=iface.supercell,
surface_coverage=iface.surface_coverage,
ligand=iface.ligand, displacement=z,
adatom_on_lig=iface.adatom_on_lig,
adsorb_on_species=iface.adsorb_on_species,
primitive= False, from_ase=True,
x_shift=x, y_shift=y)
iface.create_interface()
energy= iface.calc_energy()
iface.sort()
if energy<ecut:
ifaces.append((energy,iface))
# ifaces.zip(energy, iface)
return ifaces
scell_nmax=10,
coverage_tol=0.25,
solvent="amine",
start_from_slab=False,
validate_proximity=False,
to_unit_cell=False,
coords_are_cartesian=False,
primitive=True,
from_ase=True,
x_shift=0,
y_shift=0)
interface.create_interface(
) #with pre-configure as true, will generate different
#ligand interface configurations
interface.sort()
slab = interface.slab
slab.sort()
# create interface firetasks: interface relaxation and slab relaxation
interface_firetasks.append(get_calibration_task(structure=interface, \
incar_params = {'NSW':100}, \
other_params = {'job_dir': 'InterfaceRelax'}))
interface_firetasks.append(get_calibration_task(structure=slab, \
incar_params = {'NSW':100}))
interface_fireworks.append(
Firework(interface_firetasks, name='interface_convergence'))
workflows.append(get_workflow(interface_fireworks, name='Interface'))