def build_tilt_sym_frac(self, bp=[-1,1,12], v=[1,1,0], c_space=None):
bpxv = [(bp[1]*v[2]-v[1]*bp[2]),(bp[2]*v[0]-bp[0]*v[2]),(bp[0]*v[1]- v[0]*bp[1])]
grain_a = BodyCenteredCubic(directions = [bpxv, bp, v],
size = (1,1,1), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.85)
n_grain_unit = len(grain_a)
n = 2
# Slightly different from slabmaker since in the fracture
# Simulations we want the grainboundary plane to be normal to y.
while(grain_a.get_cell()[1,1] < 120.0):
grain_a = BodyCenteredCubic(directions = [bpxv, bp, v],
size = (1,n,2), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.85)
n += 1
print '\t {0} repeats in z direction'.format(n)
grain_b = grain_a.copy()
grain_c = grain_a.copy()
print '\t', '{0} {1} {2}'.format(v[0],v[1],v[2])
print '\t', '{0} {1} {2}'.format(bpxv[0],bpxv[1],bpxv[2])
print '\t', '{0} {1} {2}'.format(bp[0], bp[1], bp[2])
if c_space==None:
s1 = surface('Fe', (map(int, bp)), n)
c_space = s1.get_cell()[2,2]/float(n) #-s1.positions[:,2].max()
s2 = surface('Fe', (map(int, v)), 1)
x_space = s2.get_cell()[0,0] #-s1.positions[:,2].max()
s3 = surface('Fe', (map(int, bpxv)), 1)
y_space = s3.get_cell()[1,1] #-s1.positions[:,2].max()
print '\t Interplanar spacing: ', x_space.round(2), y_space.round(2), c_space.round(2), 'A'
# Reflect grain b in z-axis (across mirror plane):
print grain_a.get_cell()[1,1]-grain_a.positions[:,1].max()
grain_b.positions[:,1] = -1.0*grain_b.positions[:,1]
grain_c.extend(grain_b)
grain_c.set_cell([grain_c.get_cell()[0,0], 2*grain_c.get_cell()[1,1], grain_c.get_cell()[2,2]])
grain_c.positions[:,1] += abs(grain_c.positions[:,1].min())
pos = [grain.position for grain in grain_c]
pos = sorted(pos, key= lambda x: x[2])
dups = get_duplicate_atoms(grain_c)
# now center fracture cell with plenty of vacuum
grain_c.center(vacuum=10.0,axis=1)
return grain_c
a = 5.7885/2
cell = [[1,0,0],[0,1,0],[0,0,1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5,5])
atoms.set_cell([a, a, a], scale_atoms=True)
carbon = Atom('C', position=(0,0.5*a,0.75*a), charge=0.4)
atoms = atoms*(2,2,2) + carbon
constraint = FixAtoms(indices=[8,10,12,14,16])
atoms.set_constraint(constraint)
atoms[-1].position = [0, 0.5*a, 0.75*a]
init = atoms.copy()
# view(init)
atoms[-1].position = [0, 0.75*a, 0.5*a]
final = atoms.copy()
# view(final)
def save( filename, arg ):
f = open(filename, 'a+t')
f.write('{0} \n'.format(arg))
f.close()
os.system('mkdir result')
print atoms.get_cell()
from matplotlib import mlab
from numpy import *
from ase.utils.eos import EquationOfState
from ase.lattice.cubic import BodyCenteredCubic
from ase import Atom
a = 2.8920
cell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5, 5])
carbon = Atom('C', position=(0, 0.5 * a, 0.5 * a), charge=0.4)
atoms = atoms * (2, 2, 2) + carbon
init = atoms.copy()
final = atoms.copy()
final[-1].position = [0, 0.5 * a, (0.5 + 1.0) * a]
images = [init]
for i in range(9):
os.system('mkdir 0{0}'.format(i + 1))
os.chdir('0{0}'.format(i + 1))
atoms = read('POSCAR')
# atoms[-1].position = [0,0.5*a,(0.5+(1./10.*i))*a]
# view(atoms)
images.append(atoms.copy())
# write('POSCAR', atoms)
os.chdir('..')
def make_edge_cyl(alat, C11, C12, C44,
cylinder_r=10, cutoff=5.5,
symbol='W'):
'''
makes edge dislocation using atomman library
cylinder_r - radius of cylinder of unconstrained atoms around the
dislocation in angstrom
cutoff - potential cutoff for marinica potentials for FS cutoff = 4.4
symbol : string
Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory
default is "W" for tungsten
'''
# Create a Stroh ojbect with junk data
stroh = am.defect.Stroh(am.ElasticConstants(C11=141, C12=110, C44=98),
np.array([0, 0, 1]))
axes = np.array([[1, 1, 1],
[1, -1, 0],
[1, 1, -2]])
c = am.ElasticConstants(C11=C11, C12=C12, C44=C44)
burgers = alat * np.array([1., 1., 1.])/2.
# Solving a new problem with Stroh.solve
# Does not work with the new version of atomman
stroh.solve(c, burgers, axes=axes)
unit_cell = BodyCenteredCubic(directions=axes.tolist(),
size=(1, 1, 1), symbol='W',
pbc=(False, False, True),
latticeconstant=alat)
bulk = unit_cell.copy()
# shift to make the zeros of the cell betweem the atomic planes
# and under the midplane on Y axes
X_midplane_shift = (1.0/3.0)*alat*np.sqrt(3.0)/2.0
Y_midplane_shift = 0.25*alat*np.sqrt(2.0)
bulk_shift = [X_midplane_shift,
Y_midplane_shift,
0.0]
bulk.positions += bulk_shift
tot_r = cylinder_r + cutoff + 0.01
Lx = int(round(tot_r/(alat*np.sqrt(3.0)/2.0)))
Ly = int(round(tot_r/(alat*np.sqrt(2.))))
# factor 2 to make shure odd number of images is translated
# it is important for the correct centering of the dislocation core
bulk = bulk * (2*Lx, 2*Ly, 1)
center_shift = [Lx * alat * np.sqrt(3.0)/2.,
Ly * alat * np.sqrt(2.),
0.0]
bulk.positions -= center_shift
ED = bulk.copy()
disp = stroh.displacement(ED.positions)
ED.positions += disp
x, y, z = ED.positions.T
radius_x_y_zero = np.sqrt(x**2 + y**2)
mask = radius_x_y_zero < tot_r
ED = ED[mask]
bulk = bulk[mask]
bulk.write("before.xyz")
ED.write("after_disp.xyz")
x, y, z = ED.positions.T
radius_x_y_zero = np.sqrt(x**2 + y**2)
mask_zero = radius_x_y_zero > cylinder_r
fix_atoms = FixAtoms(mask=mask_zero)
ED.set_constraint(fix_atoms)
x, y, z = bulk.positions.T
# move lower left segment
bulk.positions[(y < 0.0) & (x < X_midplane_shift)] -= \
[alat * np.sqrt(3.0) / 2.0, 0.0, 0.0]
# make the doslocation extraplane center
bulk.positions += [(1.0/3.0)*alat*np.sqrt(3.0)/2.0, 0.0, 0.0]
return ED, bulk
def make_edge_cyl_001_100(a0, C11, C12, C44,
cylinder_r,
cutoff=5.5,
tol=1e-6,
symbol="W"):
"""Function to produce consistent edge dislocation configuration.
Parameters
----------
alat : float
Lattice constant of the material.
C11 : float
C11 elastic constant of the material.
C12 : float
C12 elastic constant of the material.
C44 : float
C44 elastic constant of the material.
cylinder_r : float
Radius of cylinder of unconstrained atoms around the
dislocation in angstrom.
cutoff : float
Potential cutoff for determenition of size of
fixed atoms region (2*cutoff)
tol : float
Tolerance for generation of self consistent solution.
symbol : string
Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory
default is "W" for tungsten
Returns
-------
bulk : ase.Atoms object
Bulk configuration.
disloc : ase.Atoms object
Dislocation configuration.
disp : np.array
Correstonding displacement.
"""
# Create a Stroh ojbect with junk data
stroh = am.defect.Stroh(am.ElasticConstants(C11=141, C12=110, C44=98),
np.array([0, 0, 1]))
axes = np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]])
c = am.ElasticConstants(C11=C11, C12=C12, C44=C44)
burgers = a0 * np.array([1., 0., 0.])
# Solving a new problem with Stroh.solve
# Does not work with the new version of atomman
stroh.solve(c, burgers, axes=axes)
unit_cell = BodyCenteredCubic(directions=axes.tolist(),
size=(1, 1, 1), symbol=symbol,
pbc=(False, False, True),
latticeconstant=a0)
bulk = unit_cell.copy()
# shift to make the zeros of the cell betweem the atomic planes
# and under the midplane on Y axes
X_midplane_shift = -0.25*a0
Y_midplane_shift = -0.25*a0
bulk_shift = [X_midplane_shift,
Y_midplane_shift,
0.0]
bulk.positions += bulk_shift
tot_r = cylinder_r + 2*cutoff + 0.01
Lx = int(round(tot_r/a0))
Ly = int(round(tot_r/a0))
# factor 2 to make sure odd number of images is translated
# it is important for the correct centering of the dislocation core
bulk = bulk * (2*Lx, 2*Ly, 1)
center_shift = [Lx * a0, Ly * a0, 0.0]
bulk.positions -= center_shift
# bulk.write("before.xyz")
disp1 = stroh.displacement(bulk.positions)
disloc = bulk.copy()
res = np.inf
i = 0
while res > tol:
disloc.positions = bulk.positions + disp1
disp2 = stroh.displacement(disloc.positions)
res = np.abs(disp1 - disp2).max()
disp1 = disp2
print 'disloc SCF', i, '|d1-d2|_inf =', res
i += 1
if i > 10:
raise RuntimeError('Self-consistency did \
not converge in 10 cycles')
disp = disp2
x, y, z = disloc.positions.T
radius_x_y_zero = np.sqrt(x**2 + y**2)
mask = radius_x_y_zero < tot_r
disloc = disloc[mask]
bulk = bulk[mask]
# disloc.write("after_disp.xyz")
x, y, z = disloc.positions.T
radius_x_y_zero = np.sqrt(x**2 + y**2)
mask_zero = radius_x_y_zero > cylinder_r
fix_atoms = FixAtoms(mask=mask_zero)
disloc.set_constraint(fix_atoms)
return bulk, disloc, disp
def make_screw_quadrupole(alat,
left_shift=0,
right_shift=0,
n1u=5,
symbol="W"):
"""Generates a screw dislocation dipole configuration
for effective quadrupole arrangement. Works for BCC systems.
Parameters
----------
alat : float
Lattice parameter of the system in Angstrom.
left_shift : float, optional
Shift of the left dislocation core in number of dsitances to next
equivalent disocation core positions needed for creation for final
configuration for NEB. Default is 0.
right_shift : float, optional
shift of the right dislocation core in number of dsitances to next
equivalent disocation core positions needed for creation for final
configuration for NEB. Default is 0.
n1u : int, odd number
odd number! length of the cell a doubled distance between core along x.
Main parameter to calculate cell vectors
symbol : string
Symbol of the element to pass to ase.lattuce.cubic.SimpleCubicFactory
default is "W" for tungsten
Returns
-------
disloc_quadrupole : ase.Atoms
Resulting quadrupole configuration.
W_bulk : ase.Atoms
Perfect system.
dislo_coord_left : list of float
Coodrinates of left dislocation core [x, y]
dislo_coord_right : list of float
Coodrinates of right dislocation core [x, y]
Notes
-----
Calculation of cell vectors
+++++++++++++++++++++++++++
From [1]_ we take:
- Unit vectors for the cell are:
.. math::
u = \frac{1}{3}[1 \bar{2} 1];
.. math::
v = \frac{1}{3}[2 \bar{1} \bar{1}];
.. math::
z = b = \frac{1}{2}[1 1 1];
- Cell vectors are:
.. math::
C_1 = n^u_1 u + n^v_1 v + C^z_1 z;
.. math::
C_2 = n^u_2 u + n^v_2 v + C^z_2 z;
.. math::
C_3 = z
- For quadrupole arrangement n1u needs to be odd number,
for 135 atoms cell we take n1u=5
- To have quadrupole as as close as possible to a square one has to take:
.. math::
2 n^u_2 + n^v_2 = n^u_1
.. math::
n^v_2 \approx \frac{n^u_1}{\sqrt{3}}
- for n1u = 5:
.. math::
n^v_2 \approx \frac{n^u_1}{\sqrt{3}} = 2.89 \approx 3.0
.. math::
n^u_2 = \frac{1}{2} (n^u_1 - n^v_2) \approx \frac{1}{2} (5-3)=1
- Following [2]_ cell geometry is optimized by ading tilt compomemts
Cz1 and Cz2 for our case of n1u = 3n - 1:
Easy core
.. math::
C^z_1 = + \frac{1}{3}
.. math::
C^z_2 = + \frac{1}{6}
Hard core
.. math::
C^z_1 = + \frac{1}{3}
.. math::
C^z_2 = + \frac{1}{6}
may be typo in the paper check the original!
References:
+++++++++++
.. [1] Ventelon, L. & Willaime, F. J 'Core structure and Peierls potential
of screw dislocations in alpha-Fe from first principles: cluster versus
dipole approaches' Computer-Aided Mater Des (2007) 14(Suppl 1): 85.
https://doi.org/10.1007/s10820-007-9064-y
.. [2] Cai W. (2005) Modeling Dislocations Using a Periodic Cell.
In: Yip S. (eds) Handbook of Materials Modeling. Springer, Dordrecht
https://link.springer.com/chapter/10.1007/978-1-4020-3286-8_42
"""
unit_cell = BodyCenteredCubic(directions=[[1, -2, 1],
[2, -1, -1],
[1, 1, 1]],
symbol=symbol,
pbc=(True, True, True),
latticeconstant=alat, debug=0)
unit_cell_u, unit_cell_v, unit_cell_z = unit_cell.get_cell()
# calculate the cell vectors according to the Ventelon paper
# the real configrution depends on rounding check it here
n2v = int(np.rint(n1u/np.sqrt(3.0)))
# when the n1u - n2v difference is odd it is impossible to have
# perfect arrangemt of translation along x with C2 equal to 0.5*n1u
# choice of rounding between np.ceil() and np.trunc() makes a different
# configuration but of same quality of arrangement of quadrupoles (test)
n2u = np.ceil((n1u - n2v) / 2.)
n1v = 0
print("Not rounded values of C2 componets: ")
print("n2u: %.2f, n2v: %.2f" % ((n1u - n2v) / 2., n1u/np.sqrt(3.0)))
print("Calculated cell vectors from n1u = %i" % n1u)
print("n1v = %i" % n1v)
print("n2u = %i" % n2u)
print("n2v = %i" % n2v)
bulk = unit_cell.copy()*[n1u, n2v, 1]
# add another periodic shift in x direction to c2 vector
# for proper periodicity (n^u_2=1) of the effective quadrupole arrangement
bulk.cell[1] += n2u * unit_cell_u
C1_quadrupole, C2_quadrupole, C3_quadrupole = bulk.get_cell()
# calulation of dislocation cores positions
# distance between centers of triangles along x
# move to odd/even number -> get to upward/downward triangle
x_core_dist = alat * np.sqrt(6.)/6.0
# distance between centers of triangles along y
y_core_dist = alat * np.sqrt(2.)/6.0
# separation of the cores in a 1ux1v cell
nx_left = 2
nx_right = 5
if n2v % 2 == 0: # check if the number of cells in y direction is even
# Even: then introduce cores between two equal halfes of the cell
ny_left = -2
ny_right = -1
else: # Odd: introduce cores between two equal halfes of the cell
ny_left = 4
ny_right = 5
nx_left += 2.0 * left_shift
nx_right += 2.0 * right_shift
dislo_coord_left = np.array([nx_left * x_core_dist,
ny_left * y_core_dist,
0.0])
dislo_coord_right = np.array([nx_right * x_core_dist,
ny_right * y_core_dist,
0.0])
# caclulation of the shifts of the inital cores coordinates for the final
# quadrupole arrangements
# different x centering preferences for odd and even values
if n2v % 2 == 0: # check if the number of cells in y direction is even
# Even:
dislo_coord_left += (n2u - 1) * unit_cell_u
dislo_coord_right += (n2u - 1 + np.trunc(n1u/2.0)) * unit_cell_u
else: # Odd:
dislo_coord_left += n2u * unit_cell_u
dislo_coord_right += (n2u + np.trunc(n1u/2.0)) * unit_cell_u
dislo_coord_left += np.trunc(n2v/2.0) * unit_cell_v
dislo_coord_right += np.trunc(n2v/2.0) * unit_cell_v
u_quadrupole = dipole_displacement_angle(bulk,
dislo_coord_left,
dislo_coord_right)
# get the image contribution from the dipoles around
# (default value of N images to scan n_img=10)
u_img = get_u_img(bulk,
dislo_coord_left,
dislo_coord_right)
u_sum = u_quadrupole + u_img
# calculate the field of neghbouring cell to estimate
# linear u_err along C1 and C2 (see. Cai paper)
# u_err along C2
n1_shift = 0
n2_shift = 1
shift = n1_shift*C1_quadrupole + n2_shift*C2_quadrupole
u_quadrupole_shifted = dipole_displacement_angle(bulk,
dislo_coord_left + shift,
dislo_coord_right + shift,
shift=shift)
u_img_shifted = get_u_img(bulk,
dislo_coord_left,
dislo_coord_right,
n1_shift=n1_shift, n2_shift=n2_shift)
u_sum_shifted = u_quadrupole_shifted + u_img_shifted
delta_u = u_sum - u_sum_shifted
delta_u_C2 = delta_u.T[2].mean()
print("delta u c2: %.2f " % delta_u_C2)
# u_err along C1
n1_shift = 1
n2_shift = 0
shift = n1_shift*C1_quadrupole + n2_shift*C2_quadrupole
u_quadrupole_shifted = dipole_displacement_angle(bulk,
dislo_coord_left + shift,
dislo_coord_right + shift,
shift=shift)
u_img_shifted = get_u_img(bulk,
dislo_coord_left,
dislo_coord_right,
n1_shift=n1_shift, n2_shift=n2_shift)
u_sum_shifted = u_quadrupole_shifted + u_img_shifted
delta_u = u_sum - u_sum_shifted
delta_u_C1 = delta_u.T[2].mean()
print("delta u c1: %.3f" % delta_u_C1)
x_scaled, y_scaled, __ = bulk.get_scaled_positions(wrap=False).T
u_err_C2 = (y_scaled - 0.5)*delta_u_C2
u_err_C1 = delta_u_C1*(x_scaled - 0.5)
u_err = u_err_C1 + u_err_C2
# Calculate the u_tilt to accomodate the stress (see. Cai paper)
burgers = bulk.cell[2][2]
u_tilt = 0.5 * burgers * (y_scaled - 0.5)
final_u = u_sum
final_u.T[2] += u_err - u_tilt
disloc_quadrupole = bulk.copy()
disloc_quadrupole.positions += final_u
# tilt the cell according to the u_tilt
disloc_quadrupole.cell[1][2] -= burgers/2.0
bulk.cell[1][2] -= burgers/2.0
return disloc_quadrupole, bulk, dislo_coord_left, dislo_coord_right
def calc_bulk_dissolution(args):
"""Calculate the bulk dissolution energy for hydrogen
in a tetrahedral position in bcc iron.
Args:
args(list): determine applied strain to unit cell.
"""
POT_DIR = os.path.join(app.root_path, 'potentials')
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
r_scale = 1.00894848312
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
alat = 2.83
gb = BodyCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(6, 6, 6),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=alat)
cell = gb.get_cell()
print 'Fe Cell', cell
e1 = np.array([1, 0, 0])
e2 = np.array([0, 1, 0])
e3 = np.array([0, 0, 1])
if args.hydrostatic != 0.0:
strain_tensor = np.eye(3) + args.hydrostatic * np.eye(3)
cell = cell * strain_tensor
gb.set_cell(cell, scale_atoms=True)
print 'Hydrostatic strain', args.hydrostatic
print 'strain tensor', strain_tensor
print gb.get_cell()
elif args.stretch != 0.0:
strain_tensor = np.tensordot(e2, e2, axes=0)
strain_tensor = np.eye(3) + args.stretch * strain_tensor
cell = strain_tensor * cell
print 'Stretch strain'
print 'Cell:', cell
gb.set_cell(cell, scale_atoms=True)
elif args.shear != 0.0:
strain_tensor = np.tensordot(e1, e2, axes=0)
strain_tensor = np.eye(3) + args.shear * strain_tensor
cell = strain_tensor.dot(cell)
print 'Shear Strain', strain_tensor
print 'Cell:', cell
gb.set_cell(cell, scale_atoms=True)
gb.write('sheared.xyz')
else:
print 'No strain applied.'
tetra_pos = alat * np.array([0.25, 0.0, 0.5])
h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]])
h2 = Atoms(h2)
gb = Atoms(gb)
gb_h = gb.copy()
gb_h.add_atoms(tetra_pos, 1)
#caclulators
gb.set_calculator(pot)
h2.set_calculator(pot)
gb_h.set_calculator(pot)
gb_h.write('hydrogen_bcc.xyz')
#Calc Hydrogen molecule energy
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
h2.write('h2mol.xyz')
#strain_mask = [1,1,1,0,0,0]
strain_mask = [0, 0, 0, 0, 0, 0]
ucf = UnitCellFilter(gb_h, strain_mask)
#opt = BFGS(gb_h)
opt = FIRE(ucf)
opt.run(fmax=0.0001)
E_gb = gb.get_potential_energy()
E_gbh = gb_h.get_potential_energy()
E_dis = E_gbh - E_gb - 0.5 * E_h2
print 'E_gb', E_gb
print 'E_gbh', E_gbh
print 'H2 Formation Energy', E_h2
print 'Dissolution Energy', E_dis
cell = [[1,0,0],[0,1,0],[0,0,1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5,5])
atoms.set_cell([a,a,a], scale_atoms=True)
#atoms.set_cell([a,a,a])
carbon = Atom('C', position=(0,0.5*a,0.5*a), charge=0.4)
atoms = atoms*(2,2,2) + carbon
constraint = FixAtoms(indices=[8,10])
atoms.set_constraint(constraint)
init = atoms.copy()
final = atoms.copy()
final[-1].position = [0, 0.5*a, (0.5+0.25)*a]
for i in range(0,18):
os.system('mkdir {:02d}'.format(i))
os.chdir('{:02d}'.format(i))
atoms[-1].position = [0,0.5*a,(0.5+(0.25/17.*i))*a]
# view(atoms)
write('POSCAR', atoms)
os.chdir('..')
view(init)
view(final)
from numpy import *
from ase.utils.eos import EquationOfState
from ase.lattice.cubic import BodyCenteredCubic
from ase import Atom
a = 2.8920
cell = [[1,0,0],[0,1,0],[0,0,1]]
atoms = BodyCenteredCubic('Fe', directions=cell)
atoms.set_initial_magnetic_moments([5,5])
carbon = Atom('C', position=(0,0.5*a,0.5*a), charge=0.4)
atoms = atoms*(2,2,2) + carbon
init = atoms.copy()
final = atoms.copy()
final[-1].position = [0, 0.5*a, (0.5+1.0)*a]
images = [init]
for i in range(9):
os.system('mkdir 0{0}'.format(i+1))
os.chdir('0{0}'.format(i+1))
atoms = read('POSCAR')
# atoms[-1].position = [0,0.5*a,(0.5+(1./10.*i))*a]
# view(atoms)
images.append(atoms.copy())
# write('POSCAR', atoms)
os.chdir('..')
# NB: order of types must match order in control file
tb_pot = Potential('IP LMTO_TBE',
param_str="""
<params>
<LMTO_TBE_params n_types="3" control_file="ctrl.fe">
<per_type_data type="1" atomic_num="26"/>
<per_type_data type="2" atomic_num="6"/>
<per_type_data type="3" atomic_num="1"/>
</LMTO_TBE_params>
</params>""")
print tb_pot
# compute energies and forces for a range of lattice constants
if True:
a = np.linspace(2.5, 3.0, 5)
e = []
f = []
configs = []
for aa in a:
atoms = BodyCenteredCubic(symbol='Fe', latticeconstant=aa)
atoms *= [n, n, n]
atoms.set_calculator(tb_pot)
e.append(atoms.get_potential_energy())
f.append(atoms.get_forces()[0, 0])
configs.append(atoms.copy())
# print lattice constants, energies and forces
print 'a = ', list(a)
print 'e = ', list(e)
print 'f = ', list(f)
param_filename=eam_pot)
alat = 2.83
#Structures
gb = BodyCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(4, 4, 4),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=alat)
tetra_pos = alat * np.array([0.25, 0.0, 0.5])
h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]])
h2 = Atoms(h2)
gb = Atoms(gb)
gb_h = gb.copy()
gb_h.add_atoms(tetra_pos, 1)
#caclulators
gb.set_calculator(pot)
h2.set_calculator(pot)
gb_h.set_calculator(pot)
gb_h.write('hydrogen_bcc.xyz')
#Calc Hydrogen molecule energy
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
strain_mask = [1, 1, 1, 0, 0, 0]
ucf = UnitCellFilter(gb_h, strain_mask)
def gamma_surf(h_pos=np.array([1.41, 1.500, 22.48])):
"""
:method:`gamma_surf` generates a set of directories with the upper
half unit cell displaced along a certain distance
along a particular lattice vector. Hydrogens can be added by
setting vector in h_pos.
TODO:
h_pos should be a list of vectors and atom type for this to be more general.
"""
vasp_exe = '/projects/SiO2_Fracture/iron/vasp.bgq'
crack_geom = {
'cleavage_plane': (1, 1, 0),
'crack_front': (1, -1, 0),
'crack_direction': (0, 0, 1)
}
crack_direction = crack_geom['crack_direction']
crack_front = crack_geom['crack_front']
cleavage_plane = crack_geom['cleavage_plane']
fe_unit = BodyCenteredCubic(
directions=[crack_direction, crack_front, cleavage_plane],
size=(1, 1, 1),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=2.83)
nunits = 8
fe_bulk = BodyCenteredCubic(
directions=[crack_direction, crack_front, cleavage_plane],
size=(2, 2, nunits),
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=2.83)
fe_unit = Atoms(fe_unit)
fe_bulk = Atoms(fe_bulk)
ycut = 5.0 + float(nunits) / 2.0 * fe_unit.lattice[2, 2]
fe_bulk.center(vacuum=5.0, axis=2)
print 'lattice', fe_bulk.lattice[1, 1]
print 'ycut', ycut
a1 = fe_unit.lattice[0, 0]
a2 = fe_unit.lattice[1, 1]
POT_DIR = os.environ['POTDIR']
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
r_scale = 1.00894848312
#eam_pot = os.path.join(POT_DIR, 'iron_mish.xml')
#r_scale = 1.0129007626
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
fe_bulk.set_calculator(pot)
print 'Bulk Energy', fe_bulk.get_potential_energy()
refen = fe_bulk.get_potential_energy()
A = fe_bulk.get_volume() / fe_bulk.lattice[2, 2]
vasp_args = dict(
xc='PBE',
amix=0.01,
amin=0.001,
bmix=0.001,
amix_mag=0.01,
bmix_mag=0.001,
kpts=[8, 8, 1],
kpar=32,
lreal='auto',
ibrion=2,
nsw=40,
nelmdl=-15,
ispin=2,
nelm=100,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
istart=0,
voskown=1,
ismear=1,
sigma=0.1,
isym=2) # possibly try iwavpr=12, should be faster if it works
dir_name = 'b111shiftsym'
#dir_name = 'b001shiftsym'
f = open('_patdon123{0}H1.dat'.format(dir_name), 'w')
WRITEVASP = True
a0 = 2.83
for inum, ashift in enumerate(np.arange(0, 1.10, 0.10)):
try:
os.mkdir('{0}{1}'.format(dir_name, ashift))
except:
pass
print 'Directory already exists'
os.chdir('{0}{1}'.format(dir_name, ashift))
fe_shift = fe_bulk.copy()
fe_shift.set_calculator(pot)
for at in fe_shift:
if at.position[2] > ycut:
#[00-1](110)
# at.position += ashift*np.array([-a1,0,0])
#[1-11](110)
at.position += 0.5 * ashift * np.array([a1, a2, 0])
# print >> fil1, ashift, (units.m**2/units.J)*(fe_shift.get_potential_energy()-refen)/A
line = []
for at in fe_shift:
line.append(FixedLine(at.index, (0, 0, 1)))
#Now add Hydrogen
# fe_shift.add_atoms(np.array([0.53*a0, 0.53*a0, 21.0+a0/2]),1)
# at relaxed position:
fe_shift.add_atoms(h_pos, 1)
fix_atoms_mask = [at.number == 1 for at in fe_shift]
fixedatoms = FixAtoms(mask=fix_atoms_mask)
fe_shift.set_constraint(line + [fixedatoms])
opt = LBFGS(fe_shift)
opt.run(fmax=0.1, steps=1000)
if inum == 0:
print 'Setting Reference Energy'
refen = fe_shift.get_potential_energy()
print >> f, ashift, (units.m**2 / units.J) * (
fe_shift.get_potential_energy() - refen) / A
fe_shift.write('feb{0}.xyz'.format(ashift))
if WRITEVASP:
vasp = Vasp(**vasp_args)
vasp.initialize(fe_shift)
write_vasp('POSCAR',
vasp.atoms_sorted,
symbol_count=vasp.symbol_count,
vasp5=True)
vasp.write_incar(fe_shift)
vasp.write_potcar()
vasp.write_kpoints()
os.chdir('../')
f.close()
