def create_atoms(n_a, n_b, n_c):
unitcell = bulk('Ar', 'fcc', 1.5, orthorhombic=True) # ===> epsilon unit
atoms_a = unitcell
for i in range(n_a - 1):
atoms_a = stack(atoms_a, unitcell, axis=0)
atoms_b = atoms_a
for j in range(n_b - 1):
atoms_b = stack(atoms_b, atoms_a, axis=1)
all_atoms = atoms_b
for k in range(n_c - 1):
all_atoms = stack(all_atoms, atoms_b, axis=2)
return all_atoms
def test_surface_stack():
from ase.build.surface import _all_surface_functions
from ase.build import stack
from ase.calculators.calculator import compare_atoms
# The purpose of this test is to test the stack() function and verify
# that the various surface builder functions produce configurations
# consistent with stacking.
d = _all_surface_functions()
exclude = {'mx2', 'graphene'} # mx2 and graphene are not like the others
for name in sorted(d):
if name in exclude:
continue
func = d[name]
def has(var):
c = func.__code__
return var in c.co_varnames[:c.co_argcount]
for nlayers in range(1, 7):
atoms = func('Au', size=(2, 2, nlayers), periodic=True, a=4.0)
big_atoms = func('Au', size=(2, 2, 2 * nlayers), periodic=True, a=4.0)
stacked_atoms = stack(atoms, atoms)
changes = compare_atoms(stacked_atoms, big_atoms, tol=1e-11)
if not changes:
print('OK', name, nlayers)
break
else:
assert 0, 'Unstackable surface {}'.format(name)
def construct_db_clean():
db = connect(DB_NAME)
for rep in range(1, 12):
mgsi = get_mgsi() * (1, 1, rep)
al = get_al() * (1, 1, rep)
merged = stack(al, mgsi, axis=2)
db.write(merged, surface=1)
def construct_db_mixed():
db = connect(DB_NAME)
for rep in range(9, 12):
mgsi = get_mgsi() * (rep, 1, 1)
al = get_al() * (rep, 1, 1)
merged = stack(al, mgsi, axis=0)
db.write(merged, surface=0)
def construct_db_mgsi():
db = connect(DB_NAME)
for rep in range(1, 12):
mgsi = get_mgsi() * (1, 1, rep)
mgsi2 = get_mgsi()
mgsi2.rotate(90, "x")
mgsi2.wrap()
mgsi2 *= (1, 1, rep)
merged = stack(mgsi, mgsi2, axis=2)
db.write(merged, surface=2)
def merge_2D_slabs(b):
global view, view_2, struc1, struc2, s1, s2, slabgen1, slabgen2, s3, view_3, pressed
pressed = 1
a1_tmp = (s2.cell.lengths()[0] / (s1.cell.lengths()[0]))
a2_tmp = (s2.cell.lengths()[1] / (s1.cell.lengths()[1]))
a1 = 1
b1 = 1
a2 = 1
b2 = 1
if (a1_tmp >= 1):
a1 = int(np.round(a1))
else:
b1 = int(np.round(1 / a1))
if (a2_tmp >= 1):
a2 = int(np.round(a1))
else:
b2 = int(np.round(1 / a1))
s1 = s1.repeat((a1, a2, 1))
s2 = s2.repeat((b1, b2, 1))
if (substrate_slide.value == 1):
cell_final = s1.cell.copy()
fix_val = 0
else:
cell_final = s2.cell.copy()
fix_val = 1
vac = gap_slide.value / 2
s1.center(vacuum=vac, axis=2)
s2.center(vacuum=vac, axis=2)
s3, s1_strain, s2_strain = stack(s1,
s2,
axis=2,
fix=0,
cell=cell_final,
maxstrain=None,
distance=None,
output_strained=True)
strain1 = np.sqrt(((s1_strain.cell - s1.cell).sum(axis=0)**2).sum())
strain2 = np.sqrt(((s2_strain.cell - s2.cell).sum(axis=0)**2).sum())
view_3 = nglview.show_ase(s3)
view_3.add_representation('unitcell')
view_3.background = 'black'
view_3.camera = "orthographic"
with output_1:
output_1.clear_output()
print("Strain on cell of Material 1 is", strain1)
print("Strain on cell of Material 2 is", strain2)
display(view_3)
def create_atoms(n_a, n_b, n_c):
unitcell = bulk(
'Ar', 'fcc', np.power(2, (2. / 3)),
cubic=True) #,orthorhombic=True) # ===> 1.122 sigma (from geometry)
# unitcell = bulk('Ar', 'fcc', 5.4, orthorhombic=True)
# visualize.view(unitcell)
# print unitcell.get_cell()
atoms_a = unitcell
for i in range(n_a - 1):
atoms_a = stack(atoms_a, unitcell, axis=0)
atoms_b = atoms_a
for j in range(n_b - 1):
atoms_b = stack(atoms_b, atoms_a, axis=1)
all_atoms = atoms_b
for k in range(n_c - 1):
all_atoms = stack(all_atoms, atoms_b, axis=2)
# print all_atoms.get_cell()
print("The cell is= ", all_atoms.get_cell())
# visualize.view(all_atoms)
return all_atoms
def mgsi(interface):
atoms = bulk('Al', cubic=True)
mgsi = atoms.copy()
miller = (0, 0, 1)
if interface == SILICON or interface == MAGNESIUM:
miller = (1, 0, 0)
tags, levels = get_layers(mgsi, miller)
for i, atom in enumerate(mgsi):
if interface == SILICON or interface == ALTERNATING:
if tags[i] % 2 == 0:
atom.symbol = 'Mg'
else:
atom.symbol = 'Si'
elif interface == MAGNESIUM:
if tags[i] % 2 == 0:
atom.symbol = 'Si'
else:
atom.symbol = 'Mg'
# Tag all atoms to -1
for atom in mgsi:
atom.tag = -1
mgsi = mgsi * (4, 4, 4)
matrix = atoms.copy()
for atom in matrix:
atom.tag = -1
matrix = matrix * (4, 4, 4)
active_area = atoms.copy()
active_area = active_area * (4, 4, 4)
tags, layers = get_layers(active_area, (1, 0, 0))
for t, atom in zip(tags, active_area):
atom.tag = t
# Stack togeter
atoms = stack(mgsi, active_area, axis=0)
atoms = stack(atoms, matrix, axis=0)
atoms = wrap_and_sort_by_position(atoms)
write(f"data/mgsi_active_matrix_{interface}_interface.xyz", atoms)
cell = a_0 * identity(3)
atoms.set_cell(cell, scale_atoms=True)
unitCell = atoms.get_cell()
atomsLeft = Atoms(atoms)
atomsRight = Atoms(atoms)
atomsRight.rotate((0, 0, np.pi / 12), rotate_cell=True)
print atomsLeft.get_positions()
print atomsRight.get_positions()
print atomsLeft.get_cell()
print atomsRight.get_cell()
stackedAtoms = stack(atomsLeft,
atomsLeft,
axis=0,
cell=None,
fix=0,
maxstrain=None)
stackedAtoms = stack(stackedAtoms,
atomsLeft,
axis=0,
cell=None,
fix=0,
maxstrain=None)
stackedAtoms = stack(stackedAtoms,
atomsRight,
axis=0,
cell=None,
fix=0,
maxstrain=None)
stackedAtoms = stack(stackedAtoms,
def __call__(self, pot="test.set", X="Ni"):
"""
Objective function for fitting a single element (Ni) eam.
Arguments:
pot (str) : Name of the relevant potential file.
X (str) : Element name.
"""
# Starting points for lattice params
# Every lammps command needs to define a pair_style and corresponding potential.
cmds0 = ["pair_style eam/alloy", "pair_coeff * * {} {}".format(pot, X)]
r = 3 # Supercell size
# FCC structure properties.
Ni_fcc_prim = bulk(X, "fcc", cubic=True, a=self.a_fcc)
Ni_fcc = make_supercell(Ni_fcc_prim, r * np.eye(3))
N_fcc = Ni_fcc.get_global_number_of_atoms()
# Initial cell relaxation
# cmds = cmds0 +\
# ["fix 1 all box/relax iso 0.0 vmax 0.001",
# "min_style cg",
# "minimize 1e-12 1e-8 10000 100000"] # minimize etol ftol maxiter maxeval
# lammps = LAMMPSlibExt(lmpcmds=cmds,log_file="test_fcc_0.log",keep_alive=True)
# Ni_fcc.calc = lammps
# E_fcc = Ni_fcc.get_total_energy()
# a = convert(Ni_fcc.calc.lmp.extract_variable("a",None,0),"distance",Ni_fcc.calc.units,"ASE")
# b = convert(Ni_fcc.calc.lmp.extract_variable("b",None,0),"distance",Ni_fcc.calc.units,"ASE")
# c = convert(Ni_fcc.calc.lmp.extract_variable("c",None,0),"distance",Ni_fcc.calc.units,"ASE")
# a_fcc = (a+b+c)/3.
# Ni_fcc.set_cell([a,a,a],scale_atoms=True) # Update cell to optimal structure.
# Bulk modulus
# cmds = cmds0 +\
# ["min_style cg",
# "minimize 1e-12 1e-8 10000 100000"]
# Geometry optimisation
lammps_inst = LAMMPSlibExt(lmpcmds=cmds0,
log_file="test_fcc.log",
keep_alive=True)
Ni_fcc.calc = lammps_inst
try:
(a_fcc, b_fcc, c_fcc), E_fcc = geometry_opt(Ni_fcc, tol=1.e-6)
except Exception:
return 1.e8 * np.ones(self.n_out)
Ni_fcc.set_cell([a_fcc, a_fcc, a_fcc],
scale_atoms=True) # Update cell to optimal structure.
# Bulk modulus
lammps_inst = LAMMPSlibExt(lmpcmds=cmds0,
log_file="test_fcc_B.log",
keep_alive=True)
Ni_fcc.calc = lammps_inst
eos = calculate_eos(Ni_fcc, npoints=12, eps=0.3)
eos.eos_string = "birchmurnaghan" # Consistent with CASTEP
try:
v, e, B = eos.fit()
except:
Ni_fcc_prim = bulk(X, "fcc", cubic=True, a=self.a_fcc_0)
Ni_fcc = make_supercell(Ni_fcc_prim, r * np.eye(3))
Ni_fcc.calc = lammps_inst
eos = calculate_eos(Ni_fcc, npoints=12, eps=0.2)
eos.eos_string = "birchmurnaghan" # Consistent with CASTEP
try:
v, e, B = eos.fit()
except:
return 1.e8 * np.ones(self.n_out)
# Check if something has gone wrong.
if v < 0. or v == np.nan or v == None:
return 1.e8 * np.ones(self.n_out)
elif np.abs(
v**(1 / 3) / r - a_fcc / r
) > 1.5 or a_fcc / r > 2.5 * self.a_fcc_0 or a_fcc / r < self.a_fcc_0 / 2.:
return 1.e8 * np.ones(self.n_out)
# Calculate bulk modulus
B_fcc = B / kJ * 1.e24
#a_fcc = v**(1/3)
#E_fcc = e
Ni_fcc.set_cell([a_fcc, a_fcc, a_fcc],
scale_atoms=True) # Update cell to optimal structure.
# Elastic constants
elastic_consts = calculate_elastic_cubic(Ni_fcc, 5)
C11, C12, C44 = elastic_consts.fit_consts()
C11_fcc = C11 / kJ * 1.e24
C12_fcc = C12 / kJ * 1.e24
C44_fcc = C44 / kJ * 1.e24
# HCP structure properties.
a_hcp_guess = self.a_hcp * a_fcc / r / self.a_fcc
Ni_hcp_prim = bulk(X,
"hcp",
a=a_hcp_guess,
c=self.c2a_hcp * a_hcp_guess)
Ni_hcp = make_supercell(Ni_hcp_prim, r * np.eye(3))
N_hcp = Ni_hcp.get_global_number_of_atoms()
# Initial cell relaxation
# cmds = cmds0 +\
# ["fix 1 all box/relax iso 0.0 vmax 0.001",
# "min_style cg",
# "minimize 1e-8 1e-8 10000 100000"]
# lammps = LAMMPSlibExt(lmpcmds=cmds,log_file="test_fcc_0.log",keep_alive=True)
# Ni_hcp.calc = lammps
# E_hcp = Ni_hcp.get_total_energy()
# a = convert(Ni_hcp.calc.lmp.extract_variable("a",None,0),"distance",Ni_hcp.calc.units,"ASE")
# b = convert(Ni_hcp.calc.lmp.extract_variable("b",None,0),"distance",Ni_hcp.calc.units,"ASE")
# c = convert(Ni_hcp.calc.lmp.extract_variable("c",None,0),"distance",Ni_hcp.calc.units,"ASE")
# a_hcp = (a+b)/2
lammps_inst = LAMMPSlibExt(lmpcmds=cmds0,
log_file="test_hcp.log",
keep_alive=True)
Ni_hcp.calc = lammps_inst
try:
(a_hcp, b_hcp, c_hcp), E_hcp = geometry_opt(Ni_hcp, tol=1.e-3)
except Exception:
return 1.e8 * np.ones(self.n_out)
c2a_hcp = c_hcp / a_hcp
# DHCP structure properties.
Ni_hcp_r = Ni_hcp.copy()
p0 = Ni_hcp.get_positions()
R = np.array([[-0.5, np.sqrt(3) / 2, 0], [np.sqrt(3) / 2, 0.5, 0],
[0, 0, 1]]) # Householder reflection matrix for v=a-b
Ni_hcp_r.set_positions(p0 @ R.T)
Ni_dhcp = stack(Ni_hcp_r, Ni_hcp, axis=2)
N_dhcp = Ni_dhcp.get_global_number_of_atoms()
# Initial cell relaxation
# cmds = cmds0 +\
# ["fix 1 all box/relax iso 0.0 vmax 0.001",
# "min_style cg",
# "minimize 1e-8 1e-8 10000 100000"]
# lammps = LAMMPSlibExt(lmpcmds=cmds,log_file="test_fcc_0.log",keep_alive=True)
lammps_inst = LAMMPSlibExt(lmpcmds=cmds0,
log_file="test_dhcp.log",
keep_alive=True)
Ni_dhcp.calc = lammps_inst
try:
(a_dhcp, b_dhcp, c_dhcp), E_dhcp = geometry_opt(Ni_dhcp, tol=1.e-3)
except Exception:
return 1.e8 * np.ones(self.n_out)
c2a_dhcp = 0.5 * c_dhcp / a_dhcp
# Extrinsic properties
E_fcc /= N_fcc
E_hcp /= N_hcp
E_dhcp /= N_dhcp
a_fcc /= r
a_hcp /= r
a_dhcp /= r
# Set parameters that belong to self.
self.a_fcc = a_fcc
self.a_hcp = a_hcp
self.a_dhcp = a_dhcp
self.c2a_hcp = c2a_hcp
self.c2a_dhcp = c2a_dhcp
return np.array([
E_fcc, E_hcp, E_dhcp,
(4 * (E_hcp + 2 * E_dhcp - 3 * E_fcc) / a_fcc**2) * 1.6021773e4,
a_fcc, a_hcp, c2a_hcp, a_dhcp, c2a_dhcp, B_fcc, C11_fcc, C12_fcc,
C44_fcc
])
from numpy import identity
from ase import Atoms
from ase import Atom
import ase
from ase.build import stack
#Define BZ unit cell, with lattice parameter
atoms = Atoms('BaZrOOO', [(0.5, 0.5, 0.5), (0, 0, 0), (0.5, 0, 0), (0, 0.5, 0), (0, 0, 0.5)])
a_0 = 4.1972899437
cell = a_0*identity(3)
atoms.set_cell(cell, scale_atoms=True)
write("BZ1011.vasp", atoms)
atomsLeft = Atoms(atoms)
atomsRight = Atoms(atoms)
#atomsRight.rotate((0, 0, np.pi/6), rotate_cell=True)
atomsStacked = stack(atomsLeft, atomsRight, axis=0, cell=None, fix=0.5, maxstrain=None)
atomsStacked = stack(atomsStacked, atomsStacked, axis=0, cell=None, fix=0.5, maxstrain=None)
atomsStackRotated = Atoms(atomsStacked)
#Rotation about the center of the unit cell
atomsStackRotated.rotate((0, 0, np.pi/6), center=(0,0,0))
#print atomsStackRotated.get_positions()
superStack = stack(atomsStacked, atomsStackRotated, axis=0, cell=None, fix=0.5, maxstrain=None)
write("BZ_rotated.vasp", superStack)
from ase.calculators.calculator import compare_atoms
# The purpose of this test is to test the stack() function and verify
# that the various surface builder functions produce configurations
# consistent with stacking.
d = _all_surface_functions()
exclude = {'mx2'} # mx2 is not like the others
for name in sorted(d):
if name in exclude:
continue
func = d[name]
def has(var):
c = func.__code__
return var in c.co_varnames[:c.co_argcount]
for nlayers in range(1, 7):
atoms = func('Au', size=(2, 2, nlayers), periodic=True, a=4.0)
big_atoms = func('Au', size=(2, 2, 2 * nlayers), periodic=True, a=4.0)
stacked_atoms = stack(atoms, atoms)
changes = compare_atoms(stacked_atoms, big_atoms, tol=1e-11)
if not changes:
print('OK', name, nlayers)
break
else:
assert 0, 'Unstackable surface {}'.format(name)
n_unitcell = int(args.n_unitcell)
if a_repeat == b_repeat == c_repeat == 1:
a_repeat = b_repeat = c_repeat = n_unitcell
# latt const https://aip.scitation.org/doi/10.1063/1.1726009 ==>> angstrom
# Ar = bulk('Ar', 'fcc',5.3118)
# =======
unitcell = bulk('Ar', 'fcc', 1.5, orthorhombic=True) #===> epsilon unit
from ase import visualize
from ase.build import stack
from ase.io import write
import numpy as np
# Ars= Atoms(bulk, size=(10,10,10))
atoms_a = unitcell
for i in range(a_repeat - 1):
atoms_a = stack(atoms_a, unitcell, axis=0)
atoms_b = atoms_a
for j in range(b_repeat - 1):
atoms_b = stack(atoms_b, atoms_a, axis=1)
all_atoms = atoms_b
for k in range(c_repeat - 1):
all_atoms = stack(all_atoms, atoms_b, axis=2)
# write("initial_positions.xyz", all_atoms, format='xyz', parallel=True, append=False)
pos_ = all_atoms.get_positions()
# visualize.view(all_atoms)
# print("the cell is=",all_atoms.get_cell())
cell_ = np.array([[
all_atoms.get_cell()[0][0],
all_atoms.get_cell()[1][1],
def generate_interface(self):
"""
main function to generate interface from two cut_cells.
Returns .True. if an error occured, otherwise returns .False.
"""
# set up the output file so we can put the error messages
# in the output file
file = self.input.dict['output_file']
# copy over the atom units so that cut_cells are unchanged
unit_cell_a = self.cut_cell_a.copy()
unit_cell_b = self.cut_cell_b.copy()
# remove small numbers from computer error
# unit_cell_a.cell = self.check_zero_diag(unit_cell_a.cell)
# unit_cell_a = self.check_cell_rotation(unit_cell_a, unit_cell_b)
# =====Debug=====
if (self.input.dict['print_debug'] != 'False'):
printx("========Starting Cell 1========")
printx(str(unit_cell_a.cell))
printx("atoms = " + str(len(unit_cell_a)))
printx("========Starting Cell 2========")
printx(str(unit_cell_b.cell))
printx("atoms = " + str(len(unit_cell_b)))
# replicate the unit cells so that periodicity is always preserved
periodic_cell_a, max_coeff_a = self.protect_periodicity(unit_cell_a)
periodic_cell_b, max_coeff_b = self.protect_periodicity(unit_cell_b)
# populate the new cell using cookie cutter method on generated lattice
try:
self.super_cell1 = self.populate_new_cell(
unit_cell_a, periodic_cell_a, max_coeff_a)
self.super_cell2 = self.populate_new_cell(
unit_cell_b, periodic_cell_b, max_coeff_b)
except Exception as err:
[printx(x) for x in err.args]
raise Exception("Too many atoms, skipping to next step")
# =====Debug=====
if (self.input.dict['print_debug'] != 'False'):
printx("========Ortho Cell 1========")
printx(str(self.super_cell1.cell))
printx("atoms = " + str(len(self.super_cell1)))
printx("========Ortho Cell 2========")
printx(str(self.super_cell2.cell))
printx("atoms = " + str(len(self.super_cell2)))
# calculate the smallest supercells needed to minimize
# stress in the interface
P_list, R_list = self.generate_interface_transform(
self.super_cell1, self.super_cell2)
P_tuple = tuple(P_list + [int(self.input.dict['crys_a_layers'])])
R_tuple = tuple(R_list + [int(self.input.dict['crys_b_layers'])])
# generate new supercells
try:
self.super_cell1 *= P_tuple
except Exception as err:
raise Exception(
"Error in generating supercell_a in interface step")
try:
self.super_cell2 *= R_tuple
except Exception as err:
raise Exception(
"Error in generating supercell_b in interface step")
# =====Debug=====
if (self.input.dict['print_debug'] != 'False'):
printx("Replication A = " + str(P_tuple))
printx("Replication B = " + str(R_tuple))
# check that total size isn't too big before we continue
total = len(self.super_cell1) + len(self.super_cell2)
if (total >= int(self.input.dict['max_atoms'])):
raise Exception("Error: interface is too large: " + str(total))
# tag the two supercells so that they can be separated later
self.super_cell1.set_tags(1)
self.super_cell2.set_tags(2)
# add a vacuum between the layers.
if (self.distance is not None):
self.super_cell1.cell[2, 2] += self.distance
# =====Debug=====
if (self.input.dict['print_debug'] != 'False'):
printx("========Super Cell 1========")
printx(str(self.super_cell1.cell))
printx("atoms = " + str(len(self.super_cell1)))
printx("========Super Cell 2========")
printx(str(self.super_cell2.cell))
printx("atoms = " + str(len(self.super_cell2)))
# stack the supercells on top of each other and set pbc to xy-slab
try:
self.interface, self.super_cell1, self.supercell2 = stack(
self.super_cell1, self.super_cell2,
output_strained=True, maxstrain=None)
except Exception as err:
raise Exception(
"Error in generating interface during the stack step")
# set pbc to infinite slab or fully periodic setting
if (self.input.dict['full_periodicity'] != 'False'):
self.interface.pbc = [1, 1, 1]
else:
self.interface.pbc = [1, 1, 0]
#add explicit vacuum above and below
if (self.input.dict['z_axis_vacuum'] != '0.0'):
self.interface = self.z_insert_vacuum(self.interface)
# use merge sort to identify and remove duplicate atoms.
if (self.input.dict['remove_duplicates'] != 'False'):
try:
self.remove_duplicates(self.interface)
except Exception as err:
raise Exception("Error in checking for atom overlaps")
return
