def pre_prepare_ase_after_relax_AB(initial_XV, final_XV, Ghost):
"""
"""
import sisl
trace_atom_A_initial = sisl.Geometry(initial_XV.xyz[-2],
atoms=initial_XV.atoms.Z[-2])
trace_atom_B_initial = sisl.Geometry(initial_XV.xyz[-1],
atoms=initial_XV.atoms.Z[-1])
#trace_atom_A_final = sisl.Geometry(final_XV.xyz[-2],
# atoms = final_XV.atoms.Z[-2])
trace_atom_B_final = sisl.Geometry(final_XV.xyz[-1],
atoms=final_XV.atoms.Z[-1])
initial_XV = initial_XV.remove([-1])
#initial_XV = initial_XV.remove([-1])
final_XV = final_XV.remove([-1])
#final_XV = final_XV.remove([-2])
info_sisl = {
'initial': initial_XV,
'final': final_XV,
'trace_atom_A_initial': trace_atom_A_initial,
'trace_atom_B_initial': trace_atom_B_initial,
#'trace_atom_A_final' : trace_atom_A_final,
'trace_atom_B_final': trace_atom_B_final,
}
return info_sisl
def pre_prepare_ase_after_relax_to_be_deleted(initial_XV,final_XV):
"""
"""
import sisl
trace_atom_A_initial = sisl.Geometry(initial_XV.xyz[-2],
atoms = initial_XV.atoms.Z[-2])
trace_atom_A_final = sisl.Geometry( final_XV.xyz[-2],
atoms = final_XV.atoms.Z[-2])
trace_atom_B_initial = sisl.Geometry( initial_XV.xyz[-1],
atoms= initial_XV.atoms.Z[-1])
trace_atom_B_kicked = sisl.Geometry(final_XV.xyz[-1],
atoms= final_XV.atoms.Z[-1])
#trace_atom_A_initial = sisl.Geometry(initial_XV.xyz[-2],
# atoms = initial_XV.atoms.Z[-2])
#trace_atom_B_initial = sisl.Geometry(initial_XV.xyz[-1],
# atoms = initial_XV.atoms.Z[-1])
initial_XV = initial_XV.remove([-1])
final_XV = final_XV.remove([-1])
info_sisl = {'initial' : initial_XV,
'final' : final_XV,
'trace_atom_A_initial' : trace_atom_A_initial,
'trace_atom_A_final' : trace_atom_A_final,
'trace_atom_B_initial' : trace_atom_B_initial,
'trace_atom_B_kicked' : trace_atom_B_kicked,
}
return info_sisl
def pre_prepare_ase_after_relax(initial_XV,final_XV,Ghost):
"""
"""
import sisl
if Ghost ==True:
print ('Finding Ghosts in XV')
#Ghost_initial = sisl.Geometry(initial_XV.xyz[-2],
# atoms = initial_XV.atoms.Z[-2])
#Ghost_final = sisl.Geometry(initial_XV.xyz[-1],
# atoms = initial_XV.atoms.Z[-1])
Ghost_initial_Info = sisl.Atom(-1 * initial_XV.atoms[-2].Z)
Ghost_initial = sisl.Geometry( initial_XV.xyz[-2],
atoms= sisl.Atom( -1* Ghost_initial_Info.Z , tag=Ghost_initial_Info.symbol+"_ghost"))
Ghost_final_Info = sisl.Atom(-1 * initial_XV.atoms[-1].Z)
Ghost_final = sisl.Geometry( initial_XV.xyz[-1],
atoms=sisl.Atom( -1* Ghost_final_Info.Z,tag = Ghost_final_Info.symbol+"_ghost" ))
trace_atom_initial = sisl.Geometry(initial_XV.xyz[-3],
atoms = initial_XV.atoms.Z[-3])
trace_atom_final = sisl.Geometry(final_XV.xyz[-3],
atoms = final_XV.atoms.Z[-3])
initial_XV = initial_XV.remove([-1])
initial_XV = initial_XV.remove([-1])
final_XV = final_XV.remove([-1])
final_XV = final_XV.remove([-1])
info_sisl = {'initial' : initial_XV,
'final' : final_XV,
'trace_atom_initial' : trace_atom_initial,
'trace_atom_final' : trace_atom_final,
'Ghost_initial' : Ghost_initial,
'Ghost_final' : Ghost_final,
}
else:
trace_atom_initial = initial_XV[-1]
trace_atom_final = final_XV[-1]
info_sisl ={'initial' : initial_XV,
'final' : final_XV,
'trace_atom_initial' : trace_atom_initial,
'trace_atom_final' : trace_atom_final,
}
return info_sisl
def test_tshs_error(sisl_files, sisl_tmp):
si = sisl.get_sile(sisl_files(_dir, 'si_pdos_kgrid.TSHS'))
# check number of orbitals
geom = si.read_geometry()
geom = sisl.Geometry(np.random.rand(geom.na + 1, 3))
si.read_hamiltonian(geometry=geom)
def GrapheneSheet(nx, ny):
Graphene = si.Geometry([[0.62, 3.55, 25], [0.62, 0.71, 25],
[1.85, 2.84, 25], [1.85, 1.42, 25]], [Atom('C')],
[2.46, 4.26, 0])
Graphene = Graphene.tile(nx, 0).tile(ny, 1)
# Graphene = Graphene.sort(axes=(1, 0, 2))
return Graphene
def test_tshs_error(sisl_files):
# reading with a wrong geometry
si = sisl.get_sile(sisl_files(_dir, 'si_pdos_kgrid.TSHS'))
# check number of orbitals
geom = si.read_geometry()
geom = sisl.Geometry(np.random.rand(geom.na + 1, 3))
with pytest.raises(sisl.SileError):
si.read_hamiltonian(geometry=geom)
def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name.startswith("siesta_PDOS_file"):
spin_type = name.split("_")[-1]
n_spin, filename = {
"unpolarized": (1, "SrTiO3.PDOS"),
"polarized": (2, "SrTiO3_polarized.PDOS"),
"noncollinear": (4, "SrTiO3_noncollinear.PDOS")
}[spin_type]
init_func = sisl.get_sile(siesta_test_files(filename)).plot
attrs = {
"na": 5,
"no": 72,
"n_spin": n_spin,
"species": ('Sr', 'Ti', 'O')
}
elif name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[-1]
n_spin, H = {
"unpolarized": (1, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (4, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (4, H.transform(spin=sisl.Spin.SPINORBIT))
}[spin_type]
init_func = partial(H.plot.pdos, Erange=[-5, 5])
attrs = {"na": 2, "no": 2, "n_spin": n_spin, "species": ('C', )}
elif name == "wfsx_file":
# From a siesta .WFSX file
# Since there is no hamiltonian for bi2se3_3ql.fdf, we create a dummy one
wfsx = sisl.get_sile(siesta_test_files("bi2se3_3ql.bands.WFSX"))
geometry = sisl.get_sile(
siesta_test_files("bi2se3_3ql.fdf")).read_geometry()
geometry = sisl.Geometry(geometry.xyz, atoms=wfsx.read_basis())
H = sisl.Hamiltonian(geometry, dim=4)
init_func = partial(H.plot.pdos,
wfsx_file=wfsx,
entry_points_order=["wfsx file"])
attrs = {"na": 15, "no": 195, "n_spin": 4, "species": ('Bi', 'Se')}
return init_func, attrs
class TestGeometryPlot(GeometryPlotTester):
run_for = {
"sisl_geom": {
"init_func": sisl.geom.graphene(orthogonal=True).plot
},
"ghost_atoms": {
"init_func":
sisl.Geometry([[0, 0, 1], [1, 0, 0]],
atoms=[sisl.Atom(6), sisl.Atom(-6)]).plot
}
}
def init_func_and_attrs(self, request):
name = request.param
if name == "sisl_geom":
init_func = sisl.geom.graphene(orthogonal=True).plot
elif name == "ghost_atoms":
init_func = sisl.Geometry([[0, 0, 1], [1, 0, 0]],
atoms=[sisl.Atom(6),
sisl.Atom(-6)]).plot
attrs = {}
return init_func, attrs
def Import(nx, contactrep
): # Function takes in number of device and contact repitition
filename = input('Enter filename: ') # Filename of fdf structure
filename = filename + '.fdf' # Add file ending
fdf = si.get_sile(filename) # Import the system
geom = fdf.read_geometry(output=False) # Load geometry from fdf file
C_list = (geom.atoms.Z == 6).nonzero()[0] # List of carbon atoms
O_list = (geom.atoms.Z == 8).nonzero()[0] # List of oxygen atoms
C_O_list = np.concatenate((C_list, O_list)) # Add lists
Subbed = geom.sub(C_O_list) # Keep only C or O atoms in geometry
Subbed.reduce() # Remove "empty" atom places
geom = Subbed
cellsize = geom.xyz.shape[0] # Determine number of atoms
geom = geom.tile(nx + 4 * contactrep, 1) # Repeat structure
geom = geom.rotate(270, v=[0, 0, 1],
origo=geom.center(what='xyz')) # Rotate structure
xyz = geom.xyz
xyz = np.round(xyz, decimals=1) # Round off coordinates
# Create geometry based on coordinates
geom = si.Geometry(xyz, [Atom('C')], [2.46, 4.26, 0])
# geom = geom.sort(axes=(2,1,0))
LatticeVectors = fdf.get('LatticeVectors') # Gather lattice vectors
UY = np.fromstring(LatticeVectors[0], dtype=float, sep=' ')[0] # ... in Y
UX = np.fromstring(LatticeVectors[1], dtype=float, sep=' ')[1] # ... in X
print('Unit Cell x: {}'.format(UX))
print('Unit Cell y: {}'.format(UY))
xyz = geom.xyz
dgeom = geom
plt.scatter(xyz[:, 0], xyz[:, 1])
plt.axis('equal')
for i in range(xyz[:, 0].shape[0]):
s = i
xy = (xyz[i, 0], xyz[i, 1])
plt.annotate(s, xy)
plt.grid(b=True, which='both', axis='both')
plt.show()
return xyz, UX, UY, filename, dgeom, cellsize
def Generate_Kick_Images(self):
"""
"""
from .Utils.utils_siesta import read_siesta_fdf, read_siesta_XV, FixingSislImages
from .Utils.utils_kick import pre_prepare_sisl, is_frac_or_cart_or_index, pre_prepare_ase_after_relax
import os
import glob, shutil
import numpy as np
import sys
from .BarriersIO import SiestaBarriersIO
import sisl
from ase.neb import NEB
if self.relaxed == True:
print("=================================================")
print(" The Relaxed Kick Image Generation ... ")
print("=================================================")
if self.initial_relaxed_path == None or self.final_relaxed_path == None:
sys.exit("intial/final relaxed path not provided")
if self.initial_relaxed_fdf_name == None or self.final_relaxed_fdf_name == None:
sys.exit("intial/final relaxed fdf not provided")
#self.host_structure = read_siesta_fdf(self.host_path,self.host_fdf_name)
self.initial_structure = read_siesta_XV(
self.initial_relaxed_path, self.initial_relaxed_fdf_name)
self.final_structure = read_siesta_XV(self.final_relaxed_path,
self.final_relaxed_fdf_name)
self.test = pre_prepare_ase_after_relax(
self.initial_structure['XV'], self.final_structure['XV'])
initial = sisl.Geometry.toASE(self.test['initial'])
final = sisl.Geometry.toASE(self.test['final'])
else:
print("=================================================")
print(" The Initial Kick Image Generation ... ")
print("=================================================")
#self.host_structure = read_siesta_fdf(self.host_path,self.host_fdf_name)
frac_or_cart_or_index = is_frac_or_cart_or_index(
self.trace_atom_initial_position)
self.test = pre_prepare_sisl(
frac_or_cart_or_index,
#self.host_structure['Geometry'],
self.host_structure,
self.trace_atom_initial_position,
self.trace_atom_final_position,
self.kicked_atom_final_position,
self.rtol,
self.atol,
)
initial = sisl.Geometry.toASE(self.test['initial'])
final = sisl.Geometry.toASE(self.test['final'])
#%%*****************************************************************
#%% Do the Image Creation with ASE Here
#%%*****************************************************************
if self.relaxed == True:
print("NEB Interpolation for : Relaxed Structures")
else:
print("NEB Interpolation for : UnRelaxed Structures")
print("Copying ASE For NEB Image 0 : initial image ")
self.images = [initial]
for i in range(self.number_of_images):
print("Copying ASE For NEB Image {} : images ".format(i + 1))
self.images.append(initial.copy())
self.images.append(final)
print("Copying ASE For NEB Image {} : final image".format(i + 2))
#%%
self.neb = NEB(self.images)
self.neb.interpolate(self.interpolation_method)
self.sisl_images = []
for i in range(self.number_of_images + 2):
#self.sisl_images.append(sisl.Geometry.fromASE(self.images[i]))
temp = sisl.Geometry.fromASE(self.images[i])
self.sisl_images.append(
FixingSislImages(self.test['initial'], temp, "ghost",
self.relaxed))
#-------------------------------------------------------------------
# For Kick
#-------------------------------------------------------------------
if self.relaxed == True:
#d = self.test['trace_atom_A_final'] - self.test[]
d = self.trace_atom_final_position - self.trace_atom_initial_position
else:
d = self.trace_atom_final_position - self.trace_atom_initial_position
Steps = d / (self.number_of_images + 1)
if self.relaxed == True:
FinalAtomPositionKick = self.test['trace_atom_B_initial'].xyz[0]
else:
FinalAtomPositionKick = self.trace_atom_final_position
MovingAtomIndex = len(self.neb.images[0].get_positions())
MovingAtomKick = np.array([])
for l in range(self.neb.nimages):
if l == 0:
MovingAtomKick = np.append(MovingAtomKick,
FinalAtomPositionKick)
if l > 0:
MovingAtomKick = np.append(MovingAtomKick,
FinalAtomPositionKick + Steps)
FinalAtomPositionKick = FinalAtomPositionKick + Steps
MovingAtomKick = MovingAtomKick.reshape(self.number_of_images + 2, 3)
if self.relaxed == True:
steps_x = np.divide(
self.test['trace_atom_B_kicked'].xyz[0][0] -
MovingAtomKick[0][0], len(MovingAtomKick))
steps_y = np.divide(
self.test['trace_atom_B_kicked'].xyz[0][1] -
MovingAtomKick[0][1], len(MovingAtomKick))
steps_z = np.divide(
self.test['trace_atom_B_kicked'].xyz[0][2] -
MovingAtomKick[0][2], len(MovingAtomKick))
else:
steps_x = np.divide(
self.kicked_atom_final_position[0] - MovingAtomKick[0][0],
len(MovingAtomKick))
steps_y = np.divide(
self.kicked_atom_final_position[1] - MovingAtomKick[0][1],
len(MovingAtomKick))
steps_z = np.divide(
self.kicked_atom_final_position[2] - MovingAtomKick[0][2],
len(MovingAtomKick))
print(steps_x)
print(steps_y)
print(steps_z)
#Offset
Offset = np.array([])
for l in range(len(MovingAtomKick)):
if l == 0:
Offset = np.append(Offset, 0.0)
Offset = np.append(Offset, 0.0)
Offset = np.append(Offset, 0.0)
else:
Offset = np.append(Offset, steps_x * l + steps_x)
Offset = np.append(Offset, steps_y * l + steps_y)
Offset = np.append(Offset, steps_z * l + steps_z)
Offset = Offset.reshape(len(MovingAtomKick), 3)
MovingAtomKick = Offset + MovingAtomKick[0]
self.MovingAtomKick = MovingAtomKick
print("DEBUG: {}".format(self.MovingAtomKick))
sisl_moving = []
# Fixing the Tag
self.KickedAtomInfo = self.test['trace_atom_B_kicked']
print("DEBUG: {}".format(self.KickedAtomInfo))
#KickedAtomInfo = sisl.Atom(self.test['trace_atom_B_kicked'].atoms.Z)
for i in range(self.number_of_images + 2):
#sisl_moving.append(sisl.Geometry(MovingAtomKick[i],atoms= sisl.Atom (KickedAtomInfo.Z,tag=KickedAtomInfo.symbol+"_kicked")))
sisl_moving.append(
sisl.Geometry(
xyz=self.MovingAtomKick[i],
atoms=sisl.Atom(
Z=self.KickedAtomInfo.atom[0].Z,
tag=self.KickedAtomInfo.atoms.atom[0].symbol +
"_kicked")))
#sisl_moving.append(sisl.Geometry(MovingAtomKick[i],atoms=self.test['trace_atom_B_kicked'].atoms.Z))
print(" Putting Kicked Specie in Sisl Geometry Object ")
for i in range(self.number_of_images + 2):
self.sisl_images[i] = self.sisl_images[i].add(sisl_moving[i])
# self.sisl_images[i] = self.sisl_images[i].add(moving_specie_B[i])
self.IO = SiestaBarriersIO(
neb_type='kick',
sisl_images=self.sisl_images,
flos_path=self.flos_path,
flos_file_name_relax=self.flos_file_name_relax,
flos_file_name_neb=self.flos_file_name_neb,
number_of_images=self.number_of_images,
initial_relaxed_path=self.initial_relaxed_path,
final_relaxed_path=self.final_relaxed_path,
initial_relaxed_fdf_name=self.final_relaxed_path,
final_relaxed_fdf_name=self.final_relaxed_fdf_name,
relax_engine=self.relax_engine,
relaxed=self.relaxed,
ghost=self.ghost,
)
def si_pdos_kgrid_geom():
return sisl.Geometry([[0, 0, 0], [1, 1, 1]],
sisl.Atom('Si', R=np.arange(13) + 1))
def pre_prepare_sisl(frac_or_cart_or_index, Initial_Geom, InitialAtomPosition,
FinalAtomPosition, rtol, atol):
"""
"""
import sisl
if frac_or_cart_or_index == 'cartesian':
print("Cartesian ...")
#Initial_Geom = Fdf.read_geometry()
XYZ = Initial_Geom.xyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print("Removing Vacancies Ang/Bohr")
print("Removing Index for Initial Atom:{}".format(
AtomIndex(XYZ, InitialAtomPosition, rtol, atol)))
print("Removing Index for Final Atom:{}".format(
AtomIndex(XYZ, FinalAtomPosition, rtol, atol)))
trace_atom_initial = sisl.Geometry(
Initial_Geom.xyz[AtomIndex(XYZ, InitialAtomPosition, rtol, atol)],
atoms=Initial_Geom.atoms.Z[AtomIndex(XYZ, InitialAtomPosition,
rtol, atol)])
trace_atom_final = sisl.Geometry(
Initial_Geom.xyz[AtomIndex(XYZ, FinalAtomPosition, rtol, atol)],
atoms=Initial_Geom.atoms.Z[AtomIndex(XYZ, FinalAtomPosition, rtol,
atol)])
InitialASEXYZ = InitialASEXYZ.remove(
AtomIndex(XYZ, InitialAtomPosition, rtol, atol))
FinalASEXYZ = FinalASEXYZ.remove(
AtomIndex(XYZ, FinalAtomPosition, rtol, atol))
if AtomIndex(XYZ, FinalAtomPosition, rtol, atol) > AtomIndex(
XYZ, InitialAtomPosition, rtol, atol):
print("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(
AtomIndex(XYZ, FinalAtomPosition, rtol, atol) - 1)
FinalASEXYZ = FinalASEXYZ.remove(
AtomIndex(XYZ, InitialAtomPosition, rtol, atol))
if AtomIndex(XYZ, FinalAtomPosition, rtol, atol) < AtomIndex(
XYZ, InitialAtomPosition, rtol, atol):
print("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(
AtomIndex(XYZFull, FinalAtomPosition, rtol, atol))
FinalASEXYZ = FinalASEXYZ.remove(
AtomIndex(XYZFull, InitialAtomPosition, rtol, atol) - 1)
elif frac_or_cart_or_index == 'frac':
#print ("Removing Vacancies Fractional NOT Implemented")
print("Fractional ...")
Frac = Initial_Geom.fxyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print("Removing Vacancies Ang/Bohr")
print("Removing Index for Initial Atom:{}".format(
AtomIndex(Frac, InitialAtomPosition, rtol, atol)))
print("Removing Index for Final Atom:{}".format(
AtomIndex(Frac, FinalAtomPosition, rtol, atol)))
trace_atom_initial = sisl.Geometry(
Initial_Geom.xyz[AtomIndex(Frac, InitialAtomPosition, rtol, atol)],
atoms=Initial_Geom.atoms.Z[AtomIndex(Frac, InitialAtomPosition,
rtol, atol)])
trace_atom_final = sisl.Geometry(
Initial_Geom.xyz[AtomIndex(Frac, FinalAtomPosition, rtol, atol)],
atoms=Initial_Geom.atoms.Z[AtomIndex(Frac, FinalAtomPosition, rtol,
atol)])
InitialASEXYZ = InitialASEXYZ.remove(
AtomIndex(Frac, InitialAtomPosition, rtol, atol))
FinalASEXYZ = FinalASEXYZ.remove(
AtomIndex(Frac, FinalAtomPosition, rtol, atol))
if AtomIndex(Frac, FinalAtomPosition, rtol, atol) > AtomIndex(
Frac, InitialAtomPosition, rtol, atol):
print("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(
AtomIndex(Frac, FinalAtomPosition, rtol, atol) - 1)
FinalASEXYZ = FinalASEXYZ.remove(
AtomIndex(Frac, InitialAtomPosition, rtol, atol))
if AtomIndex(Frac, FinalAtomPosition, rtol, atol) < AtomIndex(
Frac, InitialAtomPosition, rtol, atol):
print("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(
AtomIndex(Frac, FinalAtomPosition, rtol, atol))
FinalASEXYZ = FinalASEXYZ.remove(
AtomIndex(Frac, InitialAtomPosition, rtol, atol) - 1)
else:
print('index')
#Frac = Initial_Geom.fxyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print("Removing Vacancies Ang/Bohr")
print("Removing Index for Initial Atom:{}".format(InitialAtomPosition -
1))
print("Removing Index for Final Atom:{}".format(FinalAtomPosition - 1))
#trace_atom_A_initial = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
# atoms= Initial_Geom.atoms.Z[InitialAtomPosition-1])
#trace_atom_B_final = sisl.Geometry(Initial_Geom.xyz[FinalAtomPosition-1],
# atoms= Initial_Geom.atoms.Z[FinalAtomPosition-1])
trace_atom_A_initial = sisl.Geometry(
Initial_Geom.xyz[InitialAtomPosition - 1],
atoms=Initial_Geom.atoms.Z[InitialAtomPosition - 1])
trace_atom_A_final = sisl.Geometry(
Initial_Geom.xyz[FinalAtomPosition - 1],
atoms=Initial_Geom.atoms.Z[InitialAtomPosition - 1])
trace_atom_B_initial = sisl.Geometry(
Initial_Geom.xyz[FinalAtomPosition - 1],
atoms=Initial_Geom.atoms.Z[FinalAtomPosition - 1])
trace_atom_B_final = sisl.Geometry(
Initial_Geom.xyz[InitialAtomPosition - 1],
atoms=Initial_Geom.atoms.Z[FinalAtomPosition - 1])
InitialASEXYZ = InitialASEXYZ.remove(InitialAtomPosition - 1)
FinalASEXYZ = FinalASEXYZ.remove(FinalAtomPosition - 1)
if (FinalAtomPosition - 1) > (InitialAtomPosition - 1):
print("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(FinalAtomPosition - 2)
FinalASEXYZ = FinalASEXYZ.remove(InitialAtomPosition - 1)
if (FinalAtomPosition - 1) < (InitialAtomPosition - 1):
print("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(FinalAtomPosition - 1)
FinalASEXYZ = FinalASEXYZ.remove(InitialAtomPosition - 2)
InitialASEXYZ = InitialASEXYZ.add(trace_atom_A_final)
FinalASEXYZ = FinalASEXYZ.add(trace_atom_A_initial)
info_sisl = {
'initial': InitialASEXYZ,
'final': FinalASEXYZ,
'trace_atom_A_initial': trace_atom_A_initial,
'trace_atom_A_final': trace_atom_A_final,
'trace_atom_B_initial': trace_atom_B_initial,
'trace_atom_B_final': trace_atom_B_final,
}
return info_sisl
def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[2]
n_spin, H = {
"unpolarized": (1, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (1, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (1, H.transform(spin=sisl.Spin.SPINORBIT))
}.get(spin_type)
n_states = 2
if H.spin.is_spinorbit or H.spin.is_noncolinear:
n_states *= 2
# Directly creating a BandStructure object
if name.endswith("jump"):
names = ["Gamma", "M", "M", "K"]
bz = sisl.BandStructure(H, [[0, 0, 0], [2 / 3, 1 / 3, 0], None,
[2 / 3, 1 / 3, 0], [1 / 2, 0, 0]],
6, names)
nk = 7
tickvals = [0., 1.70309799, 1.83083034, 2.68237934]
else:
names = ["Gamma", "M", "K"]
bz = sisl.BandStructure(
H, [[0, 0, 0], [2 / 3, 1 / 3, 0], [1 / 2, 0, 0]], 6, names)
nk = 6
tickvals = [0., 1.70309799, 2.55464699]
init_func = bz.plot.fatbands
attrs = {
"bands_shape":
(nk, n_spin, n_states) if H.spin.is_polarized else
(nk, n_states),
"weights_shape":
(n_spin, nk, n_states, 2) if H.spin.is_polarized else
(nk, n_states, 2),
"ticklabels":
names,
"tickvals":
tickvals,
"gap":
0,
"spin_texture":
not H.spin.is_diagonal,
"spin":
H.spin
}
elif name == "wfsx file":
# From a siesta bands.WFSX file
# Since there is no hamiltonian for bi2se3_3ql.fdf, we create a dummy one
wfsx = sisl.get_sile(siesta_test_files("bi2se3_3ql.bands.WFSX"))
geometry = sisl.get_sile(
siesta_test_files("bi2se3_3ql.fdf")).read_geometry()
geometry = sisl.Geometry(geometry.xyz, atoms=wfsx.read_basis())
H = sisl.Hamiltonian(geometry, dim=4)
init_func = partial(H.plot.fatbands,
wfsx_file=wfsx,
E0=-51.68,
entry_points_order=["wfsx file"])
attrs = {
"bands_shape": (16, 8),
"weights_shape": (16, 8, 195),
"ticklabels": None,
"tickvals": None,
"gap": 0.0575,
"spin_texture": False,
"spin": sisl.Spin("nc")
}
return init_func, attrs
def pre_prepare_sisl (frac_or_cart_or_index,Initial_Geom,InitialAtomPosition,FinalAtomPosition,rtol,atol,Ghost):
"""
"""
import sisl
if frac_or_cart_or_index == 'cartesian':
print ("Cartesian ...(BUGGGGGGGG! SHOULD FIX)")
#Initial_Geom = Fdf.read_geometry()
XYZ = Initial_Geom.xyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print ("Removing Vacancies Ang/Bohr")
print ("Removing Index for Initial Atom:{}".format(AtomIndex(XYZ,InitialAtomPosition,rtol,atol)))
print ("Removing Index for Final Atom:{}".format(AtomIndex(XYZ,FinalAtomPosition,rtol,atol)))
if Ghost == True:
Ghost_initial = sisl.Geometry(Initial_Geom.xyz[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)],
atoms= -1* Initial_Geom.atoms.Z[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)]
)
Ghost_final = sisl.Geometry(Initial_Geom.xyz[AtomIndex(XYZ,FinalAtomPosition,rtol,atol)],
atoms= -1* Initial_Geom.atoms.Z[AtomIndex(XYZ,FinalAtomPosition,rtol,atol)]
)
trace_atom_initial = sisl.Geometry(Initial_Geom.xyz[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)],
atoms= Initial_Geom.atoms.Z[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)]
)
trace_atom_final = sisl.Geometry(Initial_Geom.xyz[AtomIndex(XYZ,FinalAtomPosition,rtol,atol)],
atoms= Initial_Geom.atoms.Z[AtomIndex(XYZ,FinalAtomPosition,rtol,atol)]
)
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(XYZ,InitialAtomPosition,rtol,atol))
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(XYZ,FinalAtomPosition,rtol,atol))
if AtomIndex(XYZ,FinalAtomPosition,rtol,atol) > AtomIndex(XYZ,InitialAtomPosition,rtol,atol):
print ("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(XYZ,FinalAtomPosition,rtol,atol)-1)
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(XYZ,InitialAtomPosition,rtol,atol))
if AtomIndex(XYZ,FinalAtomPosition,rtol,atol) < AtomIndex(XYZ,InitialAtomPosition,rtol,atol):
print ("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(XYZ,FinalAtomPosition,rtol,atol))
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(XYZ,InitialAtomPosition,rtol,atol)-1)
elif frac_or_cart_or_index == 'frac':
#print ("Removing Vacancies Fractional NOT Implemented")
print ("Fractional ... (BUGGGGGGGG SHOULD FIX)")
Frac = Initial_Geom.fxyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print ("Removing Vacancies Ang/Bohr")
print ("Removing Index for Initial Atom:{}".format(AtomIndex(Frac,InitialAtomPosition,rtol,atol)))
print ("Removing Index for Final Atom:{}".format(AtomIndex(Frac,FinalAtomPosition,rtol,atol)))
if Ghost == True:
Ghost_initial = sisl.Geometry(Initial_Geom.xyz[AtomIndex(Frac,InitialAtomPosition,rtol,atol)],
atoms= -1* Initial_Geom.atoms.Z[AtomIndex(Frac,InitialAtomPosition,rtol,atol)]
)
Ghost_final = sisl.Geometry(Initial_Geom.xyz[AtomIndex(Frac,FinalAtomPosition,rtol,atol)],
atoms= -1* Initial_Geom.atoms.Z[AtomIndex(Frac,FinalAtomPosition,rtol,atol)]
)
trace_atom_initial = sisl.Geometry(Initial_Geom.xyz[AtomIndex(Frac,InitialAtomPosition,rtol,atol)],
atoms= Initial_Geom.atoms.Z[AtomIndex(Frac,InitialAtomPosition,rtol,atol)]
)
trace_atom_final = sisl.Geometry(Initial_Geom.xyz[AtomIndex(Frac,FinalAtomPosition,rtol,atol)],
atoms= Initial_Geom.atoms.Z[AtomIndex(Frac,FinalAtomPosition,rtol,atol)]
)
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(Frac,InitialAtomPosition,rtol,atol))
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(Frac,FinalAtomPosition,rtol,atol))
if AtomIndex(Frac,FinalAtomPosition,rtol,atol) > AtomIndex(Frac,InitialAtomPosition,rtol,atol):
print ("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(Frac,FinalAtomPosition,rtol,atol)-1)
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(Frac,InitialAtomPosition,rtol,atol))
if AtomIndex(Frac,FinalAtomPosition,rtol,atol) < AtomIndex(Frac,InitialAtomPosition,rtol,atol):
print ("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(Frac,FinalAtomPosition,rtol,atol))
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(Frac,InitialAtomPosition,rtol,atol)-1)
else:
print('index')
#Frac = Initial_Geom.fxyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print ("Removing Vacancies Ang/Bohr")
print ("Removing Index for Initial Atom:{}".format(InitialAtomPosition-1))
print ("Removing Index for Final Atom:{}".format(FinalAtomPosition-1))
if Ghost == True:
#Ghost_initial = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
# atoms= -1* Initial_Geom.atoms.Z[InitialAtomPosition-1]
# )
#Ghost_final = sisl.Geometry(Initial_Geom.xyz[FinalAtomPosition-1],
# atoms= -1* Initial_Geom.atoms.Z[FinalAtomPosition-1]
# )
Ghost_initial_Info = sisl.Atom(Initial_Geom.atoms.Z[InitialAtomPosition-1])
Ghost_initial = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
atoms= sisl.Atom( -1* Ghost_initial_Info.Z , tag=Ghost_initial_Info.symbol+"_ghost"))
Ghost_final_Info = sisl.Atom(Initial_Geom.atoms.Z[FinalAtomPosition-1])
Ghost_final = sisl.Geometry(Initial_Geom.xyz[ FinalAtomPosition-1 ],
atoms=sisl.Atom( -1* Ghost_final_Info.Z,tag = Ghost_final_Info.symbol+"_ghost" ))
trace_atom_initial = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
atoms= Initial_Geom.atoms.Z[InitialAtomPosition-1]
)
trace_atom_final = sisl.Geometry(Initial_Geom.xyz[FinalAtomPosition-1],
atoms= Initial_Geom.atoms.Z[FinalAtomPosition-1]
)
InitialASEXYZ = InitialASEXYZ.remove(InitialAtomPosition-1)
FinalASEXYZ = FinalASEXYZ.remove(FinalAtomPosition-1)
if (FinalAtomPosition-1) > (InitialAtomPosition-1):
print ("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(FinalAtomPosition-2)
FinalASEXYZ = FinalASEXYZ.remove(InitialAtomPosition-1)
if (FinalAtomPosition-1) < (InitialAtomPosition-1):
print ("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(FinalAtomPosition-1)
FinalASEXYZ = FinalASEXYZ.remove(InitialAtomPosition-2)
InitialASEXYZ = InitialASEXYZ.add(trace_atom_final)
FinalASEXYZ = FinalASEXYZ.add(trace_atom_initial)
if Ghost == True:
info_sisl = {'initial' : InitialASEXYZ,
'final' : FinalASEXYZ,
'trace_atom_initial' : trace_atom_initial,
'trace_atom_final' : trace_atom_final,
'Ghost_initial' : Ghost_initial,
'Ghost_final' : Ghost_final,
}
else:
info_sisl = {'initial' : InitialASEXYZ,
'final' : FinalASEXYZ,
'trace_atom_initial' : trace_atom_initial,
'trace_atom_final' : trace_atom_final,
}
return info_sisl
def pre_prepare_sisl (frac_or_cart_or_index,Initial_Geom,InitialAtomPosition,FinalAtomPosition,KickedAtomPosition,rtol=1e-2,atol=1e-2):
"""
"""
import sisl
from sisl import Atom
if frac_or_cart_or_index == 'cartesian':
print ("Cartesian ...")
#Initial_Geom = Fdf.read_geometry()
XYZ = Initial_Geom.xyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print ("Removing Vacancies Ang/Bohr")
print ("Removing Index for Initial Atom:{}".format(AtomIndex(XYZ,InitialAtomPosition,rtol,atol)))
print ("Removing Index for Final Atom:{}".format(AtomIndex(XYZ,FinalAtomPosition,rtol,atol)))
# Fixing tags
TraceAtom_Initial_Info = sisl.Atom(Initial_Geom.atoms.Z[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)])
TraceAtom_Initial = sisl.Geometry(xyz=Initial_Geom.xyz[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)],
atoms= sisl.Atom(TraceAtom_Initial_Info.Z,tag=TraceAtom_Initial_Info.symbol+'_i' ))
Ghost_initial = sisl.Geometry(xyz=Initial_Geom.xyz[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)],
atoms= sisl.Atom(TraceAtom_Initial_Info.Z,tag=TraceAtom_Initial_Info.symbol+'_ghost' ))
TraceAtom_Final_Info = sisl.Atom(Initial_Geom.atoms.Z[AtomIndex(XYZ,InitialAtomPosition,rtol,atol)])
TraceAtom_Final = sisl.Geometry(xyz = FinalAtomPosition ,
atoms= sisl.Atom(TraceAtom_Final_Info.Z,tag=TraceAtom_Final_Info.symbol+'_i'))
Ghost_final = sisl.Geometry(xyz = FinalAtomPosition ,
atoms= sisl.Atom(TraceAtom_Final_Info.Z,tag=TraceAtom_Final_Info.symbol+'_ghost'))
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(XYZ,InitialAtomPosition,rtol,atol))
FinalASEXYZ = InitialASEXYZ
elif frac_or_cart_or_index == 'frac':
#print ("Removing Vacancies Fractional NOT Implemented")
print ("Fractional ...")
Frac = Initial_Geom.fxyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print ("Removing Vacancies Ang/Bohr")
print ("Removing Index for Initial Atom:{}".format(AtomIndex(Frac,InitialAtomPosition,rtol,atol)))
print ("Removing Index for Final Atom:{}".format(AtomIndex(Frac,FinalAtomPosition,rtol,atol)))
trace_atom_initial = sisl.Geometry(Initial_Geom.xyz[AtomIndex(Frac,InitialAtomPosition,rtol,atol)],
atoms= Initial_Geom.atoms.Z[AtomIndex(Frac,InitialAtomPosition,rtol,atol)])
trace_atom_final = sisl.Geometry(Initial_Geom.xyz[AtomIndex(Frac,FinalAtomPosition,rtol,atol)],
atoms= Initial_Geom.atoms.Z[AtomIndex(Frac,FinalAtomPosition,rtol,atol)])
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(Frac,InitialAtomPosition,rtol,atol))
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(Frac,FinalAtomPosition,rtol,atol))
if AtomIndex(Frac,FinalAtomPosition,rtol,atol) > AtomIndex(Frac,InitialAtomPosition,rtol,atol):
print ("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(Frac,FinalAtomPosition,rtol,atol)-1)
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(Frac,InitialAtomPosition,rtol,atol))
if AtomIndex(Frac,FinalAtomPosition,rtol,atol) < AtomIndex(Frac,InitialAtomPosition,rtol,atol):
print ("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(AtomIndex(Frac,FinalAtomPosition,rtol,atol))
FinalASEXYZ = FinalASEXYZ.remove(AtomIndex(Frac,InitialAtomPosition,rtol,atol)-1)
else:
print('index')
#Frac = Initial_Geom.fxyz
InitialASEXYZ = Initial_Geom
FinalASEXYZ = Initial_Geom
print ("Removing Vacancies Ang/Bohr")
print ("Removing Index for Initial Atom:{}".format(InitialAtomPosition-1))
print ("Removing Index for Final Atom:{}".format(FinalAtomPosition-1))
#trace_atom_A_initial = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
# atoms= Initial_Geom.atoms.Z[InitialAtomPosition-1])
#trace_atom_B_final = sisl.Geometry(Initial_Geom.xyz[FinalAtomPosition-1],
# atoms= Initial_Geom.atoms.Z[FinalAtomPosition-1])
trace_atom_A_initial = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
atoms= Initial_Geom.atoms.Z[InitialAtomPosition-1])
trace_atom_A_final = sisl.Geometry(Initial_Geom.xyz[FinalAtomPosition-1],
atoms= Initial_Geom.atoms.Z[InitialAtomPosition-1])
trace_atom_B_initial = sisl.Geometry(Initial_Geom.xyz[FinalAtomPosition-1],
atoms= Initial_Geom.atoms.Z[FinalAtomPosition-1])
trace_atom_B_final = sisl.Geometry(Initial_Geom.xyz[InitialAtomPosition-1],
atoms= Initial_Geom.atoms.Z[FinalAtomPosition-1])
InitialASEXYZ = InitialASEXYZ.remove(InitialAtomPosition-1)
FinalASEXYZ = FinalASEXYZ.remove(FinalAtomPosition-1)
if (FinalAtomPosition-1) > (InitialAtomPosition-1):
print ("Order : Final Atom Position > Initial Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(FinalAtomPosition-2)
FinalASEXYZ = FinalASEXYZ.remove(InitialAtomPosition-1)
if (FinalAtomPosition-1) < (InitialAtomPosition-1):
print ("Order : Initial Atom Position > Final Atom Position")
InitialASEXYZ = InitialASEXYZ.remove(FinalAtomPosition-1)
FinalASEXYZ = FinalASEXYZ.remove(InitialAtomPosition-2)
InitialASEXYZ = InitialASEXYZ.add(TraceAtom_Initial)
FinalASEXYZ = FinalASEXYZ.add(TraceAtom_Final)
info_sisl = {'initial' : InitialASEXYZ,
'final' : FinalASEXYZ,
'trace_atom_initial' : TraceAtom_Initial,
'trace_atom_final' : TraceAtom_Final,
'Ghost_initial' : Ghost_initial,
'Ghost_final' : Ghost_final,
}
return info_sisl
def Generate_Exchange_Images(self):
"""
"""
from .Utils.utils_siesta import read_siesta_fdf, read_siesta_XV
from .Utils.utils_exchange import pre_prepare_sisl, is_frac_or_cart_or_index, pre_prepare_ase_after_relax_AA, pre_prepare_ase_after_relax_AB, pre_prepare_ase_after_relax_A, pre_prepare_ase_after_relax_B
import os
import glob, shutil
import numpy as np
import sys
from .BarriersIO import SiestaBarriersIO
import sisl
from ase.neb import NEB
if self.relaxed == True:
print("=================================================")
print(" The Relaxed Exchange Image Generation ... ")
print("=================================================")
#self.host_structure = read_siesta_fdf(self.host_path,self.host_fdf_name)
self.initial_structure = read_siesta_XV(
self.initial_relaxed_path, self.initial_relaxed_fdf_name)
self.final_structure = read_siesta_XV(self.final_relaxed_path,
self.final_relaxed_fdf_name)
if self.check_AA_or_AB() == True:
self.test_A = pre_prepare_ase_after_relax_A(
self.initial_structure['XV'], self.final_structure['XV'])
self.test_B = pre_prepare_ase_after_relax_B(
self.initial_structure['XV'], self.final_structure['XV'])
else:
#print ("Not Implemented Yet!")
self.test_A = pre_prepare_ase_after_relax_A(
self.initial_structure['XV'], self.final_structure['XV'])
self.test_B = pre_prepare_ase_after_relax_B(
self.initial_structure['XV'], self.final_structure['XV'])
initial_A = sisl.Geometry.toASE(self.test_A['initial'])
final_A = sisl.Geometry.toASE(self.test_A['final'])
initial_B = sisl.Geometry.toASE(self.test_B['initial'])
final_B = sisl.Geometry.toASE(self.test_B['final'])
else:
print("=================================================")
print(" The Initial Exchange Image Generation ... ")
print("=================================================")
frac_or_cart_or_index = is_frac_or_cart_or_index(
self.trace_atom_initial_position)
self.test = pre_prepare_sisl(
frac_or_cart_or_index,
self.host_structure,
self.trace_atom_initial_position,
self.trace_atom_final_position,
self.rtol,
self.atol,
)
initial = sisl.Geometry.toASE(self.test['initial'])
final = sisl.Geometry.toASE(self.test['final'])
self.initial_structure = {}
self.final_structure = {}
self.initial_structure['XV'] = self.test['initial']
self.final_structure['XV'] = self.test['final']
self.check_AA_or_AB()
#%%*****************************************************************
#%% Do the Image Creation with ASE Here
#%%*****************************************************************
if self.relaxed == True:
print("NEB Interpolation for : Relaxed Structures")
print("Copying ASE For NEB Image 0 : initial image ")
self.images_A = [initial_A]
self.images_B = [initial_B]
for i in range(self.number_of_images):
print("Copying ASE For NEB Image {} : images ".format(i + 1))
self.images_A.append(initial_A.copy())
self.images_B.append(initial_B.copy())
self.images_A.append(final_A)
self.images_B.append(final_B)
print("Copying ASE For NEB Image {} : final image".format(i + 2))
#%%
self.neb_A = NEB(self.images_A)
self.neb_B = NEB(self.images_B)
self.neb_A.interpolate(self.interpolation_method)
self.neb_B.interpolate(self.interpolation_method)
self.sisl_images_A = []
self.sisl_images_B = []
for i in range(self.number_of_images + 2):
self.sisl_images_A.append(
sisl.Geometry.fromASE(self.images_A[i]))
self.sisl_images_B.append(
sisl.Geometry.fromASE(self.images_B[i]))
#-------------------------------------------------------------------
# For Exchange
#-------------------------------------------------------------------
moving_specie_A = {}
moving_specie_B = {}
for i in range(len(self.sisl_images_A)):
moving_specie_A[i] = sisl.Geometry(
self.sisl_images_A[i].xyz[-1],
atoms=self.sisl_images_A[i].atoms.Z[-1])
moving_specie_B[i] = sisl.Geometry(
self.sisl_images_B[i].xyz[-1],
atoms=self.sisl_images_B[i].atoms.Z[-1])
ni_list = []
for i in range(self.number_of_images + 2):
ni_list.append(int(i))
ni_list.sort(reverse=True)
j = 0
#for i in ni_list:
# #moving_specie_B[j] = sisl.Geometry(moving_specie_A[i].xyz,atoms=self.test['trace_atom_B_initial'].atoms.Z)
# moving_specie_B[j] = sisl.Geometry(moving_specie_A[i].xyz,atoms=self.test_B['trace_atom_B_initial'].atoms.Z)
# j = j+1
#moving_specie_B[0].xyz = self.test_B['trace_atom_B_initial'].xyz
#moving_specie_B[self.number_of_images+2] = self.test['trace_atom_B_final'].xyz
d = moving_specie_B[0].xyz - moving_specie_A[0].xyz
d = d.reshape(3, )
dsq = d**2
dsum = np.sum(dsq)
dsum = np.sqrt(dsum)
ToleranceRadius = self.tolerance_radius
#ToleranceRadius= np.array([-1.5,1.5,0.0]) #Ang
print("d", d)
print("dsum", dsum)
print("Tolernace Radius :{}".format(self.tolerance_radius))
Migration_Direction = self.exchange_direction
NumberOfImages = self.number_of_images
if Migration_Direction.lower() == "x":
d[0] = d[0] + dsum + ToleranceRadius[0]
Steps = d / NumberOfImages
print("Migration Direction Axis: x")
if Migration_Direction.lower() == "y":
d[1] = d[1] + dsum + ToleranceRadius[1]
Steps = d / NumberOfImages
print("Migration Direction Axis: y")
if Migration_Direction.lower() == "z":
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Axis: z")
if Migration_Direction.lower() == "xy":
d[0] = d[0] + dsum + ToleranceRadius[0]
d[1] = d[1] + dsum + ToleranceRadius[1]
Steps = d / NumberOfImages
print("Migration Direction Plane: xy")
if Migration_Direction.lower() == "xz":
d[0] = d[0] + dsum + ToleranceRadius[0]
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Plane: xz")
if Migration_Direction.lower() == "yz":
d[1] = d[1] + dsum + ToleranceRadius[1]
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Plane: yz")
if Migration_Direction.lower() == "xyz":
d[0] = d[0] + dsum + ToleranceRadius[0]
d[1] = d[1] + dsum + ToleranceRadius[1]
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Volume: xyz")
for l in range(1, NumberOfImages + 1):
print("Atom A ", l, moving_specie_A[l].xyz + Steps)
moving_specie_A[l].xyz = moving_specie_A[l].xyz + Steps
for l in range(1, NumberOfImages + 1):
print("Atom B ", l, moving_specie_B[l].xyz - Steps)
moving_specie_B[l].xyz = moving_specie_B[l].xyz - Steps
#print("DEBUG: {}".format(moving_specie_B[self.number_of_images+2]))
#moving_specie_B[self.number_of_images+2] = self.test['trace_atom_B_final'].xyz
#print("DEBUG: {}".format(moving_specie_B[self.number_of_images+2]))
for k in range(self.number_of_images + 2):
self.sisl_images_A[k] = self.sisl_images_A[k].remove([-1])
print(" Putting Specie A & B in Sisl Geometry Object ")
for i in range(self.number_of_images + 2):
self.sisl_images_A[i] = self.sisl_images_A[i].add(
moving_specie_A[i])
self.sisl_images_A[i] = self.sisl_images_A[i].add(
moving_specie_B[i])
self.sisl_images = self.sisl_images_A
else:
print("NEB Interpolation for : UnRelaxed Structures")
print("Copying ASE For NEB Image 0 : initial image ")
self.images = [initial]
for i in range(self.number_of_images):
print("Copying ASE For NEB Image {} : images ".format(i + 1))
self.images.append(initial.copy())
self.images.append(final)
print("Copying ASE For NEB Image {} : final image".format(i + 2))
#%%
self.neb = NEB(self.images)
self.neb.interpolate(self.interpolation_method)
self.sisl_images = []
for i in range(self.number_of_images + 2):
self.sisl_images.append(sisl.Geometry.fromASE(self.images[i]))
#-------------------------------------------------------------------
# For Exchange
#-------------------------------------------------------------------
moving_specie_A = {}
moving_specie_B = {}
for i in range(len(self.sisl_images)):
moving_specie_A[i] = sisl.Geometry(
self.sisl_images[i].xyz[-1],
atoms=self.sisl_images[i].atoms.Z[-1])
ni_list = []
for i in range(self.number_of_images + 2):
ni_list.append(int(i))
ni_list.sort(reverse=True)
j = 0
for i in ni_list:
moving_specie_B[j] = sisl.Geometry(
moving_specie_A[i].xyz,
atoms=self.test['trace_atom_B_initial'].atoms.Z)
#moving_specie_B[j] = sisl.Geometry(moving_specie_A[i].xyz,atoms=self.test['trace_atom_B_initial'].atoms.Z)
j = j + 1
#moving_specie_B[0].xyz = self.test['trace_atom_B_initial'].xyz
#moving_specie_B[self.number_of_images+2] = self.test['trace_atom_B_final'].xyz
d = moving_specie_B[0].xyz - moving_specie_A[0].xyz
d = d.reshape(3, )
dsq = d**2
dsum = np.sum(dsq)
dsum = np.sqrt(dsum)
ToleranceRadius = self.tolerance_radius
#ToleranceRadius= np.array([-1.5,1.5,0.0]) #Ang
print("d", d)
print("dsum", dsum)
print("Tolernace Radius :{}".format(self.tolerance_radius))
Migration_Direction = self.exchange_direction
NumberOfImages = self.number_of_images
if Migration_Direction.lower() == "x":
d[0] = d[0] + dsum + ToleranceRadius[0]
Steps = d / NumberOfImages
print("Migration Direction Axis: x")
if Migration_Direction.lower() == "y":
d[1] = d[1] + dsum + ToleranceRadius[1]
Steps = d / NumberOfImages
print("Migration Direction Axis: y")
if Migration_Direction.lower() == "z":
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Axis: z")
if Migration_Direction.lower() == "xy":
d[0] = d[0] + dsum + ToleranceRadius[0]
d[1] = d[1] + dsum + ToleranceRadius[1]
Steps = d / NumberOfImages
print("Migration Direction Plane: xy")
if Migration_Direction.lower() == "xz":
d[0] = d[0] + dsum + ToleranceRadius[0]
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Plane: xz")
if Migration_Direction.lower() == "yz":
d[1] = d[1] + dsum + ToleranceRadius[1]
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Plane: yz")
if Migration_Direction.lower() == "xyz":
d[0] = d[0] + dsum + ToleranceRadius[0]
d[1] = d[1] + dsum + ToleranceRadius[1]
d[2] = d[2] + dsum + ToleranceRadius[2]
Steps = d / NumberOfImages
print("Migration Direction Volume: xyz")
for l in range(1, NumberOfImages + 1):
print("Atom A ", l, moving_specie_A[l].xyz + Steps)
moving_specie_A[l].xyz = moving_specie_A[l].xyz + Steps
for l in range(1, NumberOfImages + 1):
print("Atom B ", l, moving_specie_B[l].xyz - Steps)
moving_specie_B[l].xyz = moving_specie_B[l].xyz - Steps
#print("DEBUG: {}".format(moving_specie_B[self.number_of_images+2]))
#moving_specie_B[self.number_of_images+2] = self.test['trace_atom_B_final'].xyz
#print("DEBUG: {}".format(moving_specie_B[self.number_of_images+2]))
for k in range(self.number_of_images + 2):
self.sisl_images[k] = self.sisl_images[k].remove([-1])
print(" Putting Specie A & B in Sisl Geometry Object ")
for i in range(self.number_of_images + 2):
self.sisl_images[i] = self.sisl_images[i].add(
moving_specie_A[i])
self.sisl_images[i] = self.sisl_images[i].add(
moving_specie_B[i])
self.IO = SiestaBarriersIO(
neb_type='exchange',
sisl_images=self.sisl_images,
flos_path=self.flos_path,
flos_file_name_relax=self.flos_file_name_relax,
flos_file_name_neb=self.flos_file_name_neb,
number_of_images=self.number_of_images,
initial_relaxed_path=self.initial_relaxed_path,
initial_relaxed_fdf_name=self.initial_relaxed_fdf_name,
final_relaxed_path=self.final_relaxed_path,
final_relaxed_fdf_name=self.final_relaxed_fdf_name,
relax_engine=self.relax_engine,
relaxed=self.relaxed,
ghost=self.ghost,
)
from hubbard import HubbardHamiltonian, sp2
import numpy as np
import sisl
for w in range(1, 25, 2):
g = sisl.geom.agnr(w)
H0 = sp2(g)
H = HubbardHamiltonian(H0, U=0)
zak = H.get_Zak_phase()
print(f'width={w:3}, zak={zak:7.3f}')
# SSH model, topological cell
g = sisl.Geometry([[0, 0, 0], [0, 1.65, 0]],
sisl.Atom(6, 1.001),
sc=[10, 3, 10])
g.set_nsc([1, 3, 1])
H0 = sp2(g)
H = HubbardHamiltonian(H0, U=0)
zak = H.get_Zak_phase(axis=1)
print(f'SSH topo : zak={zak:7.3f}')
# SSH model, trivial cell
g = sisl.Geometry([[0, 0, 0], [0, 1.42, 0]],
sisl.Atom(6, 1.001),
sc=[10, 3, 10])
g.set_nsc([1, 3, 1])
H0 = sp2(g)
H = HubbardHamiltonian(H0, U=0)
zak = H.get_Zak_phase(axis=1)
print(f'SSH triv : zak={zak:7.3f}')
def copy(self, *args, **kwargs):
copy = super().copy(*args, **kwargs)
copy.U = self.U
return copy
# Multi-orbital tight-binding Hamiltonian, set U in the geometry
pz = OrbitalU(1.42, q0=1.0, U=3.)
s = OrbitalU(1.42, q0=0, U=0.)
C = sisl.Atom(6, orbitals=[pz, s])
g = geom.zgnr(W, atoms=C)
# Add another atom to have heterogeneous number of orbitals per atoms
C2 = sisl.Atom(6, orbitals=[pz])
G_C2 = sisl.Geometry(g.xyz[0], atoms=C2)
g = g.replace(0, G_C2)
# Identify index for atoms
idx = g.a2o(range(len(g)))
# Build U for each orbital in each atom
#U = np.zeros(g.no)
#U[idx] = 3.
# Build TB Hamiltonian, zeroes for non-pz orbitals
TBham = sisl.Hamiltonian(g, spin='polarized')
for ia in g:
ib = g.close(ia, R=[0, 1.42 + 0.1])
io_a = g.a2o(ia, all=True)
for iib in ib[1]:
def FixingSislImages(initial,
SislStructure,
ghost_suffix='ghost',
relaxed=False,
moving_specie="initial"):
"""
"""
import sisl
AtomIndex = np.array([])
AtomSymbol = np.array([])
for i in range(SislStructure.na):
AtomIndex = np.append(AtomIndex, SislStructure.atoms.Z[i])
AtomSymbol = np.append(AtomSymbol, initial.atoms[i].tag)
for i in range(SislStructure.na):
if i == 0:
#print(i)
if AtomIndex[i] < 0:
ghost_name = sisl.Atom(-1 * AtomIndex[i])
Test = sisl.Geometry(
xyz=SislStructure.xyz[i],
#atoms=sisl.Atom(ghost_name,tag=ghost_name.symbol+"_"+ghost_suffix), Bug!
atoms=sisl.Atom(int(AtomIndex[i]),
tag=ghost_name.symbol + "_" +
ghost_suffix),
sc=SislStructure.cell)
else:
Test = sisl.Geometry(xyz=SislStructure.xyz[i],
atoms=sisl.Atom(AtomIndex[i],
tag=AtomSymbol[i]),
sc=SislStructure.cell)
#if i>0 and i<= SislStructure.na-2:
if 0 < i <= SislStructure.na - 2:
#print(i)
if AtomIndex[i] < 0:
ghost_name = sisl.Atom(-1 * AtomIndex[i])
Test += sisl.Geometry(
xyz=SislStructure.xyz[i],
#atoms=sisl.Atom(ghost_name,tag=ghost_name.symbol+"_"+ghost_suffix), Bug!!
atoms=sisl.Atom(int(AtomIndex[i]),
tag=ghost_name.symbol + "_" +
ghost_suffix),
sc=SislStructure.cell)
else:
Test += sisl.Geometry(xyz=SislStructure.xyz[i],
atoms=sisl.Atom(AtomIndex[i],
tag=AtomSymbol[i]),
sc=SislStructure.cell)
if SislStructure.na - 2 < i < SislStructure.na:
#print(i)
if relaxed:
Test += sisl.Geometry(
xyz=SislStructure.xyz[i],
#atoms=sisl.Atom(AtomIndex[i],tag=AtomSymbol[i]+suffix),
atoms=sisl.Atom(AtomIndex[i], tag=AtomSymbol[i]),
sc=SislStructure.cell)
else:
Test += sisl.Geometry(
xyz=SislStructure.xyz[i],
#atoms=sisl.Atom(AtomIndex[i],tag=AtomSymbol[i]+suffix),
atoms=sisl.Atom(AtomIndex[i],
tag=AtomSymbol[i] + "_" + moving_specie),
sc=SislStructure.cell)
return Test
