def calc_elast_dipole_dft(input_file, vasp_calc=True):
"""Reads OUTCAR file in the same directory with one shot forces
induced by removal of defect. Reads defect position
from .xyz file (which contains the defect) defined by `input_file`
calculates and returns the elastic dipole tensor of the defect.
Args:
input_file(str): name of input .xyz file containing defect cell.
Returns:
Elastic Dipole Tensor 3x3 numpy array.
"""
elastic = ElasticDipole()
ats_def = Atoms(input_file)
defect = find_h_atom(ats_def)
if vasp_calc:
import ase.io.vasp as vasp
ats_pos = vasp.read_vasp()
ats = vasp.read_vasp_out()
ats = Atoms(ats)
else:
pass
print 'Defect index', defect.index, 'Position', defect.position, 'Type: ', defect.number
f = ats.get_forces()
ats.add_property('force', f.T)
ats.write('force.xyz')
return elastic.compute_vacancy_dipole(defect,
ats_pos.copy(),
forces=ats.get_forces())
def gen_super(self, grain=None, rbt=None, sup_v=6, sup_bxv=2, rcut=2.0):
""" :method:`gen_super` Creates a :class:SubGrainBoundary super cell according to
conventions described in Rittner and Seidman (PRB 54 6999).
Args:
grain(:class:`ase.Atoms`): atoms object passed from gen_super_rbt.
rbt (list): rigid body translation as fractional translations of the supercell.
sup_v(int): Size of supercell along v.
sup_bxv(int): Size of supercell along boundary_plane_normal crossed with v.
rcut(float): Atom deletion criterion in angstrom.
"""
io = ImeallIO()
if rbt == None:
x = Atoms('{0}.xyz'.format(os.path.join(self.grain_dir, self.gbid)))
else:
x = Atoms(grain)
struct_dir = os.path.join(self.grain_dir, 'structs')
self.name = '{0}_v{1}bxv{2}_tv{3}bxv{4}_d{5}z'.format(self.gbid,
str(sup_v), str(sup_bxv), '0.0', '0.0', str(rcut))
#TODO fix this so it is more transparent.
#if rcut = 0 then only a super cell is generated with no deletion of atoms.
if rcut > 0.0:
x.set_cutoff(2.4)
x.calc_connect()
x.calc_dists()
rem = []
u = np.zeros(3)
for i in range(x.n):
for n in range(x.n_neighbours(i)):
j = x.neighbour(i, n, distance=3.0, diff=u)
if x.distance_min_image(i,j) < rcut and j != i:
rem.append(sorted([j,i]))
rem = list(set([a[0] for a in rem]))
if len(rem) > 0:
x.remove_atoms(rem)
else:
print 'No duplicate atoms in list.'
else:
x = x*(sup_v, sup_bxv, 1)
x.set_scaled_positions(x.get_scaled_positions())
if rbt == None:
self.struct_file = self.name
self.subgrain_dir = io.make_dir(self.calc_dir, self.name)
try:
with open('{0}/subgb.json'.format(self.subgrain_dir), 'r') as f:
j_dict = json.load(f)
except IOError:
j_dict = {}
j_dict['name'] = self.name
j_dict['param_file'] = self.param_file
j_dict['rbt'] = [0.0, 0.0]
j_dict['rcut'] = rcut
with open('{0}/subgb.json'.format(self.subgrain_dir), 'w') as f:
json.dump(j_dict, f, indent=2)
else:
return sup_v, sup_bxv, x
def test_gb(GB9, tmpdir):
"""Tests the basic grain boundary instance attributes and methods
(i.e., those that don't interact with other modules).
"""
assert len(GB9) == 644
a = GB9.atoms
assert a.n == 644
fxyz = str(tmpdir.join("s9.xyz"))
GB9.save_xyz(fxyz, "Ni")
from quippy import Atoms
A = Atoms(fxyz)
B = Atoms("tests/gb/s9.xyz")
assert A.equivalent(B)
def castep_write(atoms,
filename='default.cell',
optimise=False,
fix_lattice=False,
kpoint_spacing=0.03):
"""Write atoms a castep cell file and param file."""
atoms = Atoms(atoms)
local_cell = BASE_CELL.copy()
# Set some extra parameters
local_cell['kpoint_mp_spacing'] = kpoint_spacing
if fix_lattice:
local_cell['fix_all_cell'] = 'true'
if filename.endswith('.cell'):
cell_filename = filename
param_filename = filename[:-5] + '.param'
else:
cell_filename = filename + '.cell'
param_filename = filename + '.param'
local_param = BASE_PARAM.copy()
if optimise:
local_param['task'] = 'GeometryOptimization'
cell = CastepCell(cellfile=local_cell, atoms=atoms)
cell.update_from_atoms(atoms)
cell.write(cell_filename)
param = CastepParam(paramfile=local_param, atoms=atoms)
param.write(param_filename)
def gen_screw_dislocation_quad(self):
# Easy core
screw_slab_unit = BodyCenteredCubic(directions = [self.x, self.y, self.z],
size = (1,1,1), symbol='Fe', pbc=(1,1,1),
latticeconstant = alat)
screw_slab_unit = Atoms(screw_slab_unit)
# set the supercell:
n_x = int(18.0/screw_slab_unit.get_cell()[0,0])
n_y = int(18.0/screw_slab_unit.get_cell()[1,1])
n_z = 2
ref_slab = screw_slab_unit*(n_x,n_y,n_z)
ref_slab.write('ref_slab.xyz')
screw_slab_super = supercell(screw_slab_unit, n_x, n_y, n_z)
b = screw_slab_unit.get_cell()[2,2]
brg_vec = b*np.array([0,0,1])
disloc_l = np.array([0,0,1])
super_slab = screw_slab_super.copy()
L_x = screw_slab_super.lattice[0,0]
L_y = screw_slab_super.lattice[1,1]
L_z = screw_slab_super.lattice[2,2]
core = [(np.array([(L_x)/2., (L_y)/2., L_z/2.]), brg_vec),
np.array([(L_x)/2., (L_y)/2., L_z/2.]),
np.array([(L_x)/2., (L_y)/2., L_z/2.]),
np.array([(L_x)/2., (L_y)/2., L_z/2.])]
def gen_edge_dislocation(self):
screw_slab_unit = BodyCenteredCubic(directions = [self.x, self.y, self.z],
size = (1,1,1), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.83)
screw_slab_unit = Atoms(screw_slab_unit)
n_x = int(self.l_x/screw_slab_unit.get_cell()[0,0])
n_y = int(self.l_y/screw_slab_unit.get_cell()[1,1])
n_z = 1
screw_slab_super = supercell(screw_slab_unit, n_x, n_y, n_z)
screw_slab_unit.write('ref_slab.xyz')
b = screw_slab_unit.get_cell()[0,0]
brg_vec = b*np.array([1,0,0])
vacuum = 70.
screw_slab_super.lattice[1,1] += vacuum
disloc_l = np.array([0,0,1])
screw_slab_super.set_lattice(screw_slab_super.get_cell(), scale_positions=False)
super_slab = screw_slab_super.copy()
L_x = screw_slab_super.lattice[0,0]
L_y = screw_slab_super.lattice[1,1]
L_z = screw_slab_super.lattice[2,2]
#Maintain Periodicity along x and z for an edge dislocation:
core = np.array([(L_x)/2., (L_y-vacuum)/2., (L_z)/2.])
screw_slab_super.set_cutoff(3.0)
screw_slab_super.calc_connect()
disloc_noam(screw_slab_super, core, disloc_l, brg_vec)
screw_slab_super.info['core'] = core
screw_slab_super.write('e{0}.xyz'.format(self.name))
def update_json(self, filename):
"""
This function was originally written to update all keys in the
json dictionaries in the grain boundary directories.
The pattern is quite general and can be adapted to just add
new keys delete old keys consider it a dictionary migration
routine.
"""
new_json = {}
with open(filename, 'r') as json_old:
old_json = json.load(json_old)
new_json['zplanes'] = old_json['zplanes']
new_json['orientation_axis'] = old_json['orientation axis']
new_json['boundary_plane'] = old_json['boundary plane']
new_json['coincident_sites'] = old_json['coincident sites']
new_json['angle'] = old_json['angle']
new_json['gbid'] = old_json['gbid']
new_json['n_at'] = old_json['n_unit_cell']
new_json['type'] = 'symmetric tilt boundary'
dir_path = os.path.join('/'.join((filename.split('/'))[:-1]),
old_json['gbid'])
at = Atoms('{0}.xyz'.format(dir_path, old_json['gbid']))
cell = at.get_cell()
A = cell[0, 0] * cell[1, 1]
new_json['A'] = A
json_path = filename
with open(json_path, 'w') as json_new_file:
json.dump(new_json, json_new_file, indent=2)
def del_atoms(x=None):
rcut = 2.0
#x = Atoms('crack.xyz')
if x == None:
x = Atoms('1109337334_frac.xyz')
else:
pass
x.set_cutoff(3.0)
x.calc_connect()
x.calc_dists()
rem=[]
r = farray(0.0)
u = fzeros(3)
print len(x)
for i in frange(x.n):
for n in frange(x.n_neighbours(i)):
j = x.neighbour(i, n, distance=3.0, diff=u)
if x.distance_min_image(i, j) < rcut and j!=i:
rem.append(sorted([j,i]))
if i%10000==0: print i
rem = list(set([a[0] for a in rem]))
if len(rem) > 0:
print rem
x.remove_atoms(rem)
else:
print 'No duplicate atoms in list.'
x.write('crack_nodup.xyz')
return x
def gen_interface():
"""Selects an interfacial region of a bicrystal
based on common neighbour analysis. The width of the interfacial region
is equal to 2*(gb_max-gb_min) where gb_max is the z-coordinate of the highest
non-bcc atom, and gb_min is the lowest non-bcc atom.
The method creates a file `interface.xyz` in the working directory,
with the interface centered in a unit cell with 1 angstrom vacuum
on each side.
Returns:
:class:`ase.Atoms`: Atoms object of the interfacial slab in same
coordinates as original bicrystal.
"""
#output.xyz must have structure_type property attached.
ats = Atoms('output.xyz')
cell_midpoint = ats.get_cell()[2,2]/2.0
#select non-BCC sites are 0 otherwise 3.
struct_type = np.array(ats.properties['structure_type'])
struct_mask = [not struct for struct in struct_type]
interface = ats.select(struct_mask)
#select upper interface to decorate.
interface = interface.select([at.position[2] > cell_midpoint for at in interface])
z_vals = [at.position[2] for at in interface]
z_min = min(z_vals)
z_max = max(z_vals)
#take slice of interface max uncoordinated with min uncoordinated.
z_width = (z_max-z_min)/2.0
z_center = z_width + z_min
gb_max = z_max + 1.0*z_width
gb_min = z_min - 1.0*z_width
zint = ats.select([(gb_min <= at.position[2] <= gb_max) for at in ats])
#make a copy to return
int_ats = zint.copy()
zint.center(vacuum=1.0, axis=2)
zint.write('interface.xyz')
#Write POSCAR to use interstitial site generator:
ats = Atoms('interface.xyz')
#vasp_args=dict(xc='PBE', amix=0.01, amin=0.001, bmix=0.001, amix_mag=0.01, bmix_mag=0.001,
# kpts=[3, 3, 3], kpar=9, lreal='auto', ibrion=-1, nsw=0, nelmdl=-15, ispin=2,
# nelm=100, algo='VeryFast', npar=24, lplane=False, lwave=False, lcharg=False, istart=0,
# voskown=0, ismear=1, sigma=0.1, isym=2)
#vasp = Vasp(**vasp_args)
#vasp.initialize(ats)
#write_vasp('POSCAR', vasp.atoms_sorted, symbol_count=vasp.symbol_count, vasp5=True)
return int_ats
def delete_atoms(self, grain=None, rcut=2.0):
"""
Delete atoms below a certain distance threshold.
Args:
grain(:class:`quippy.Atoms`): Atoms object of the grain.
rcut(float): Atom deletion criterion.
Returns:
:class:`quippy.Atoms` object with atoms nearer than deletion criterion removed.
"""
io = ImeallIO()
if grain == None:
x = Atoms('{0}.xyz'.format(os.path.join(self.grain_dir,
self.gbid)))
else:
x = Atoms(grain)
x.set_cutoff(2.4)
x.calc_connect()
x.calc_dists()
rem = []
u = fzeros(3)
for i in frange(x.n):
for n in frange(x.n_neighbours(i)):
j = x.neighbour(i, n, distance=3.0, diff=u)
if x.distance_min_image(i, j) < rcut and j != i:
rem.append(sorted([j, i]))
rem = list(set([a[0] for a in rem]))
if len(rem) > 0:
x.remove_atoms(rem)
else:
print 'No duplicate atoms in list.'
if grain == None:
self.name = '{0}_d{1}'.format(self.gbid, str(rcut))
self.subgrain_dir = io.make_dir(self.calc_dir, self.name)
self.struct_file = gbid + '_' + 'n' + str(
len(rem)) + 'd' + str(rcut)
x.write('{0}.xyz'.format(
os.path.join(self.subgrain_dir, self.struct_file)))
return len(rem)
else:
return x
def add_key_to_dict(self, dirname):
os.path.join(dirname, 'subgb.json')
new_json = {}
with open(json_path, 'r') as json_old:
old_json = json.load(json_old)
for key in old_json.keys():
new_json[key] = old_json[key]
at = Atoms('{0}.xyz'.format(os.path.join(dirname, )))
cell = at.get_cell()
A = cell[0, 0] * cell[1, 1]
new_json['A'] = A
new_json['n_at'] = len(at)
def calc_elast_dipole_eam(input_file, force_tol, relax_cell):
"""
Calculate elastic dipole using an Embedded Atom Potential.
Args:
input_file (str): Name of .xyz file contains unitcell with defect.
force_tol (float): Force tolerance to stop relaxation.
relax_cell (bool): Relax lattice vectors.
Returns:
Elastic Dipole Tensor 3x3 numpy array.
"""
try:
POT_DIR = os.environ['POTDIR']
except KeyError:
sys.exit("PLEASE SET export POTDIR='path/to/potfiles/'")
elastic = ElasticDipole()
eam_pot = os.path.join(POT_DIR, 'PotBH.xml')
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(1.00894848312),
param_filename=eam_pot)
ats = Atoms(input_file)
ats.set_calculator(pot)
init_vol = ats.get_volume()
print 'Initial Vol.', init_vol
elastic.relax_defect_cell(ats, force_tol=force_tol, relax_cell=relax_cell)
final_vol = ats.get_volume()
print 'Final Vol.', final_vol
print 'Volume Diff.', final_vol - init_vol
ats = Atoms('defect_cell_relaxed.xyz')
defect = find_h_atom(ats)
print 'Defect index', defect.index, 'Position', defect.position, 'Type: ', defect.number
ats.set_calculator(pot)
return elastic.compute_vacancy_dipole(defect, ats.copy(), pot)
def calc_chemoelast(input_file):
"""Adds the structure type using an ovitos script to the :py:class:`Atoms` object
and calculates the breakdown of the energy contributions.
Args:
input_file(str):Relaxed grain boundary structure file.
Returns:
list(float):[(chemical_energy/total_energy)*gb_energy, (elastic_energy/total_energy)*gb_energy, gb_energy]
"""
potparam = PotentialParameters()
ener_bulk_dict = potparam.gs_ener_per_atom()
r_scale_dict = potparam.eam_rscale()
r_scale = r_scale_dict['PotBH.xml']
E_bulk = ener_bulk_dict['PotBH.xml']
try:
POT_DIR = os.environ['POTDIR']
except KeyError:
sys.exit("PLEASE SET export POTDIR='path/to/potfiles/'")
eam_pot = 'PotBH.xml'
eam_pot = os.path.join(POT_DIR, eam_pot)
pot = Potential(
'IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(r_scale),
param_filename=eam_pot)
ats = AtomsReader(input_file)[-1]
ats.set_calculator(pot)
gb_energy = potparam.calc_e_gb(ats, E_bulk)
print gb_energy, 'J/^2m'
ats.write('full.xyz')
elastic_energy = strain_energy(ats)
with open('elast.dat', 'w') as f:
for x in elastic_energy:
print >> f, x[0], x[1]
#generates output.xyz
imeall_root = os.path.join(app.root_path, 'ovito_scripts/attach_cna.py')
args_str = 'ovitos {imeall_root} -i {input_file}'.format(
imeall_root=app.root_path, input_file='full.xyz').split()
job = subprocess.Popen(args_str)
job.wait()
ats = Atoms('output.xyz')
#print the three contributions
x = calc_chemomechanical(ats)
try:
assert round(gb_energy, 2) == round(x[2], 2)
except AssertionError:
print "WARNING ENERGIES DON'T MATCH", gb_energy, x[2]
return x
def get_cosangle(conf, csvfile):
from quippy import Atoms
at = Atoms(conf)
with open(csvfile, 'r') as fff:
fff.readline()
line = fff.readline()
tipatoms = line.split(',')[2:]
tipatoms = [int(i) for i in tipatoms]
p1, p2 = at.positions[tipatoms]
dvec = p2[:2] - p1[:2]
d = np.linalg.norm(dvec)
cosangle = dvec[1] / d
print(tipatoms)
return cosangle
def relax_structure(system,
potential,
potential_filename=None,
relax_positions=True,
relax_cell=True):
"""
Run a geometry optimisation on the structure to find the energy minimum.
Parameters
----------
system : ase.Atoms
A system of atoms to run the minimisation on. The structure is
altered in-place.
potential : Potential or str
A quippy Potential object with the desired potential, or a
potential_str to initialise a new potential.
Returns
-------
minimised_structure : Atoms
The geometry optimised structure.
"""
info("Inside minimiser.")
qsystem = Atoms(system)
if not isinstance(potential, Potential):
if potential_filename:
potential = Potential(potential, param_filename=potential_filename)
else:
potential = Potential(potential)
qsystem.set_calculator(potential)
minimiser = Minim(qsystem,
relax_positions=relax_positions,
relax_cell=relax_cell)
with Capturing(debug_on_exit=True):
minimiser.run()
system.set_cell(qsystem.cell)
system.set_positions(qsystem.positions)
system.energy = qsystem.get_potential_energy()
info("Minimiser done.")
return system
def h2_formation_energy(pot):
"""
Given a potential calculate the H2 formation energy and
equilibrium bond spacing.
Args:
pot(:quippy:class:`Potential`) potential object.
Returns:
float: Hydrogen molecule formation energy.
"""
h2 = aseAtoms('H2', positions=[[0, 0, 0], [0, 0, 0.7]])
h2 = Atoms(h2)
h2.set_calculator(pot)
opt = BFGS(h2)
opt.run(fmax=0.0001)
E_h2 = h2.get_potential_energy()
return E_h2
def decorate_interface():
ats = Atoms('interface.xyz')
dataset = spglib.get_symmetry_dataset(ats, symprec=1e-5)
with open('unique_lattice_sites.json', 'w') as f:
json.dump([
list(ats[site_num].position)
for site_num in np.unique(dataset['equivalent_atoms'])
], f)
unique_atoms = []
for at in ats:
unique_atoms.append(at.position)
voronoi = Voronoi(limits=tuple(np.diag(ats.cell)),
periodic=(True, True, False))
cntr = voronoi.compute_voronoi(unique_atoms)
ints_list = []
for site_num in np.unique(dataset['equivalent_atoms']):
for vert in voronoi.get_vertices(site_num, cntr):
ints_list.append(vert.tolist())
for unique in ints_list:
ats.add_atoms(unique, 1)
for i in range(len(ats)):
ats.id[i] = i
#remove voronoi duplicates
print 'Fe_H atoms', len(ats)
ats.wrap()
del_ats = aseAtoms()
for at in ats:
del_ats.append(at)
geometry.get_duplicate_atoms(del_ats, cutoff=0.2, delete=True)
ats = del_ats.copy()
print 'Fe_H atoms remove duplicates', len(ats)
#select unique hydrogens
#for i in range(len(ats)):
# ats.id[i] = i
ints_list = [at.position for at in ats if at.number == 1]
with open('unique_h_sites.json', 'w') as f:
json.dump([list(u) for u in ints_list], f)
ats.write('hydrogenated_grain.xyz')
def pull_file(args, dir_name=None):
if dir_name == None:
ats = read(args.input, index=":")
else:
ats = read(os.path.join(dir_name, args.input), index=":")
if not args.full_qm:
init_ats = Atoms("crack_sim.xyz")
crack_pos = init_ats.info["CrackPos"]
qm_radius = 3.0
buff = 8.0
mm_pos = init_ats.get_positions()
x, y, z = init_ats.positions.T
#radius1 = np.sqrt((x - crack_pos[0])**2 + (y-crack_pos[1])**2 + (z-crack_pos[2])**2)
radius1 = np.sqrt((x - crack_pos[0])**2 + (y - crack_pos[1])**2)
qm_region_mask = (radius1 < qm_radius)
qm_pos = init_ats.get_positions()[qm_region_mask]
qm_com = qm_pos.mean(axis=0) # just to avoid pbc errors..
cell_center = np.diag(ats[0].get_cell()) / 2.0
print cell_center
print 'Full Cell CrackPos: ', crack_pos
crack_pos = crack_pos - qm_com + cell_center
print 'Shift CrackPos', crack_pos
print 'QM Radius', qm_radius
print len(ats)
for at in ats[args.start:args.end]:
#mark quantum atoms
x, y, z = at.positions.T
radius1 = np.sqrt((x - crack_pos[0])**2 + (y - crack_pos[1])**2 +
(z - crack_pos[2])**2)
qm_region_mask = np.array(map(int, (radius1 <= qm_radius)))
print sum(qm_region_mask)
at.new_array("qm_atoms", qm_region_mask, dtype=float)
at.set_array("qm_atoms", qm_region_mask)
write_xyz(args.output, at, append=True)
else:
for at in ats[args.start:args.end]:
write_xyz(args.output, at, append=True)
def gen_screw_dislocation(self):
screw_slab_unit = BodyCenteredCubic(directions = [self.x, self.y, self.z],
size = (1,1,1), symbol='Fe', pbc=(1,1,1),
latticeconstant = 2.83)
screw_slab_unit = Atoms(screw_slab_unit)
# set the supercell:
n_x = int(self.l_x/screw_slab_unit.get_cell()[0,0])
n_y = int(self.l_y/screw_slab_unit.get_cell()[1,1])
n_z = 2
screw_slab_super = supercell(screw_slab_unit, n_x, n_y, n_z)
ref_slab = screw_slab_unit*(n_x,n_y,n_z)
ref_slab.write('ref_slab.xyz')
#Burgers vector modulus:
b = screw_slab_unit.get_cell()[2,2]
brg_vec = b*np.array([0,0,1])
print b
vacuum = 70.
screw_slab_super.lattice[0,0] += vacuum
screw_slab_super.lattice[1,1] += vacuum
disloc_l = np.array([0,0,1])
screw_slab_super.set_lattice(screw_slab_super.get_cell(), scale_positions=False)
super_slab = screw_slab_super.copy()
L_x = screw_slab_super.lattice[0,0]
L_y = screw_slab_super.lattice[1,1]
L_z = screw_slab_super.lattice[2,2]
core = np.array([(L_x-vacuum)/2., (L_y-vacuum)/2., L_z/2.])
screw_slab_super.set_cutoff(3.0)
screw_slab_super.calc_connect()
disloc_noam(screw_slab_super, core, disloc_l, brg_vec)
screw_slab_super.info['core'] = core
screw_slab_super.write('s{0}.xyz'.format(self.name))
sc = SumCalculator(pot, cc)
atoms.set_constraint(FixAtoms(mask=fix_line_mask))
atoms.set_calculator(sc)
LBFGS(atoms, use_armijo=False).run(fmax=0.2)
fix_line = [FixedLine(i, np.array([0, 1, 0])) for i in fix_line_idx]
atoms.set_array('fix_line_mask', fix_line_mask)
atoms.set_constraint(fix_line + springs)
atoms.set_calculator(pot)
opt = vanillaLBFGS(atoms)
else:
print("Method not understood")
return
opt.attach(trajectory_write, interval=5)
opt.run(fmax=fmax)
return
if __name__ == '__main__':
pot = Potential('IP TS', param_filename="../ts_params.xml")
in_file = sys.argv[1]
out_file = os.path.splitext(in_file)[0] + '_relaxed.xyz'
atoms = Atoms(in_file)
minim_precon(atoms)
atoms.write(out_file)
def constrained_minim(atoms,
method='LBFGS',
vacuum=20.0,
k_spring=0.6,
clamp_mask=None,
initial_positions=None,
fmax=0.05,
spring='point'):
c = np.ptp(atoms.positions, axis=0)
c += vacuum
atoms.set_cell(np.diag(c))
if clamp_mask is None:
at_help = Atoms('crack.xyz')
clamp_mask = at_help.get_array('clamp_mask')
if initial_positions is None:
at_help = Atoms('crack.xyz')
at_help.get_array('pos_orig')
if spring == 'plane':
springs = [
Hookean(a1=i,
a2=[0, -1, 0, initial_positions[i, 1]],
k=k_spring,
rt=0) for i in np.where(clamp_mask)[0]
]
else:
springs = [
Hookean(a1=i, a2=initial_positions[i], k=k_spring, rt=0)
for i in np.where(clamp_mask)[0]
]
from quippy.io import AtomsWriter
out = AtomsWriter("traj-relax_structure.xyz")
trajectory_write = lambda: out.write(atoms)
if method == "LBFGS":
pot = atoms.calc
cc = ConstraintCalculator(springs)
sc = SumCalculator(pot, cc)
left, bottom, _ = initial_positions.min(axis=0)
fix_line_mask = (initial_positions[:, 0] < left + 6.5)
fix_line = FixAtoms(mask=fix_line_mask)
atoms.set_array('fix_line_mask', fix_line_mask)
atoms.set_constraint(fix_line)
atoms.set_calculator(sc)
opt = LBFGS(atoms, use_armijo=False)
elif method == "FIRE":
right, top, _ = initial_positions.max(axis=0)
left, bottom, _ = initial_positions.min(axis=0)
fix_line_mask = np.logical_or(initial_positions[:, 0] > right - 6.5,
initial_positions[:, 0] < left + 6.5)
fix_line_idx = np.where(fix_line_mask)[0]
fix_line = [FixedLine(i, np.array([0, 1, 0])) for i in fix_line_idx]
atoms.set_array('fix_line_mask', fix_line_mask)
atoms.set_constraint(fix_line + springs)
opt = FIRE(atoms, dtmax=2.5, maxmove=0.5)
elif method == "mix":
# do a first opt by keeping vertical edges fixed, then make them move along y
right, top, _ = initial_positions.max(axis=0)
left, bottom, _ = initial_positions.min(axis=0)
fix_line_mask = np.logical_or(initial_positions[:, 0] > right - 6.5,
initial_positions[:, 0] < left + 6.5)
fix_line_idx = np.where(fix_line_mask)[0]
pot = atoms.calc
cc = ConstraintCalculator(springs)
sc = SumCalculator(pot, cc)
atoms.set_constraint(FixAtoms(mask=fix_line_mask))
atoms.set_calculator(sc)
LBFGS(atoms, use_armijo=False).run(fmax=0.2)
fix_line = [FixedLine(i, np.array([0, 1, 0])) for i in fix_line_idx]
atoms.set_array('fix_line_mask', fix_line_mask)
atoms.set_constraint(fix_line + springs)
atoms.set_calculator(pot)
opt = vanillaLBFGS(atoms)
else:
print("Method not understood")
return
opt.attach(trajectory_write, interval=5)
opt.run(fmax=fmax)
return
#For edge z is dislocation line
z = [0, 1, 1]
s_system = list(x)
s_system.extend(y)
name = ''.join(map(str, s_system)).replace('-', '')
print x, y, z
disloc = Dislocation(x=x, y=y, z=z, name=name)
disloc.gen_edge_dislocation()
POT_DIR = '/Users/lambert/pymodules/imeall/imeall/potentials'
eam_pot = os.path.join(POT_DIR, 'Fe_Mendelev.xml')
print 'Open Atoms'
at = Atoms('e{0}.xyz'.format(name))
at.set_cutoff(3.0)
at.calc_connect()
print 'Delete atoms'
at = gbr.delete_atoms(grain=at, rcut=1.5)
at.info['OrigHeight'] = at.positions[:, 1].max() - at.positions[:, 1].min()
r_scale = 1.00894848312
rem = []
for atom in at:
if atom.position[0] <= 0.00 and atom.position[1] <= 100.0:
rem.append(atom.index + 1)
print 'Removing ', len(rem), ' atoms.'
if len(rem) > 0:
at.remove_atoms(rem)
else:
POT_DIR = os.environ['POTDIR']
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 = 2.82893
#could just use the proper one as well....
alat = 2.837666
sup_cell = args.supercellsize
tetra_pos = alat*np.array([0.5, 0.0, 0.75])
octa_pos = alat*np.array([0.5, 0.5, 0.0])
#Structures
gb = BodyCenteredCubic(directions = [[1,0,0], [0,1,0], [0,0,1]],
size = (sup_cell[0],sup_cell[1],sup_cell[2]), symbol='Fe', pbc=(1,1,1),
latticeconstant = alat)
mid_point = 0.5*(np.diag(gb.get_cell()))
mid_point = [((sup_cell[0]-1)/2.)*alat for sp in sup_cell]
gb = Atoms(gb)
if args.tetra:
print 'Tetrahedral Defect'
tetra_pos += mid_point
gb.add_atoms(tetra_pos, 1)
gb.write('bcc_h.xyz')
elif args.octa:
print 'Octahedral Defect'
octa_pos += mid_point
gb.add_atoms(octa_pos, 1)
gb.write('bcc_h.xyz')
else:
gb.write('bcc.xyz')
def NetCDFReader(source, frame=None, start=0, stop=None, step=1, format=None):
opened = False
if isinstance(source, str):
opened = True
source = netcdf_file(source)
from quippy import Atoms
DEG_TO_RAD = pi/180.0
remap_names = {'coordinates': 'pos',
'velocities': 'velo',
'cell_lengths': None,
'cell_angles': None,
'cell_lattice': None,
'cell_rotated': None}
prop_type_to_value = {PROPERTY_INT: 0,
PROPERTY_REAL: 0.0,
PROPERTY_STR: "",
PROPERTY_LOGICAL: False}
prop_dim_to_ncols = {('frame','atom','spatial'): 3,
('frame','atom','label'): 1,
('frame', 'atom'): 1}
if frame is not None:
start = frame
stop = frame+1
step = 1
else:
if stop is None:
stop = source.variables['cell_lengths'].shape[0]
for frame in range(start, stop, step):
cl = source.variables['cell_lengths'][frame]
ca = source.variables['cell_angles'][frame]
lattice = make_lattice(cl[0],cl[1],cl[2],ca[0]*DEG_TO_RAD,ca[1]*DEG_TO_RAD,ca[2]*DEG_TO_RAD)
at = Atoms(n=netcdf_dimlen(source, 'atom'), lattice=lattice, properties={})
for name, var in source.variables.iteritems():
name = remap_names.get(name, name)
if name is None:
continue
name = str(name) # in case it's a unicode string
if 'frame' in var.dimensions:
if 'atom' in var.dimensions:
# It's a property
value = var[frame]
if value.dtype.kind != 'S': value = value.T
at.add_property(name, value)
else:
# It's a param
if var.dimensions == ('frame','string'):
# if it's a single string, join it and strip it
at.params[name] = ''.join(var[frame]).strip()
else:
if name == 'cutoff':
at.cutoff = var[frame]
elif name == 'cutoff_skin':
at.cutoff_skin = var[frame]
elif name == 'nneightol':
at.nneightol = var[frame]
elif name == 'pbc':
at.pbc = var[frame]
else:
at.params[name] = var[frame].T
if 'cell_rotated' in source.variables:
cell_rotated = source.variables['cell_rotated'][frame]
orig_lattice = source.variables['cell_lattice'][frame]
#if cell_rotated == 1:
at.set_lattice(orig_lattice, True)
yield at
def close(self):
if self.opened: source.close()
def pp_nye_tensor(at, rr=15.0, dis_type='edge'):
# Post Processing routine to append nye tensor information
# to atoms object.
# Load reference slab and calculate connectivity
ref_slab = Atoms('./ref_slab.xyz')
at.set_cutoff(3.0)
at.calc_connect()
ref_slab.set_cutoff(3.0)
ref_slab.calc_connect()
core = np.zeros(3)
# To save time it is possible to only
# calculate the nye tensor for a 'core' region
# determined by cutting out a cluster:
if dis_type in ['edge', 'screw']:
try:
core = at.info['core']
except:
sys.exit('No Core Info')
print '\t Core Position: ', core
elif dis_type == 'crack':
core = at.info['CrackPos']
print '\t Crack Position: ', core
fixed_mask = (np.sqrt((at.positions[:, 0] - core[0])**2 +
(at.positions[:, 1] - core[1])**2) < rr)
if dis_type in ['edge', 'screw']:
at.add_property('edgex', 0.0)
at.add_property('edgey', 0.0)
at.add_property('screw', 0.0)
#Going to append full nye tensor to the crack tip:
elif dis_type == 'crack':
at.add_property('nye', 0.0, n_cols=9, overwrite=True)
cl = at.select(mask=fixed_mask, orig_index=True)
print '\t Size of cluster: ', len(cl)
# Append screw and edge information
# Probably should just pass an array at this stage?
alpha = calc_nye_tensor(cl, ref_slab, 3, 3, cl.n)
cl.edgex = alpha[2, 0, :]
cl.edgey = alpha[2, 1, :]
cl.screw = alpha[2, 2, :]
# Update quantum region according to the
# position of the dislocation core:
if dis_type in ['edge', 'screw']:
if dis_type == 'screw':
defect_pos = cl.screw
elif dis_type == 'edge':
defect_pos = cl.edgex
total_def = 0.
c = np.array([0., 0., 0.])
for i in range(len(cl)):
total_def = total_def + defect_pos[i]
c[0] = c[0] + cl.positions[i, 0] * defect_pos[i]
c[1] = c[1] + cl.positions[i, 1] * defect_pos[i]
c[0] = c[0] / total_def
c[1] = c[1] / total_def
c[2] = cl.lattice[2, 2] / 2.
core[:] = c.copy()
if dis_type in ['edge', 'screw']:
for index, screw, edgex, edgey in zip(cl.orig_index, cl.screw,
cl.edgex, cl.edgey):
# Now thread atoms back in looks like select will have indices in the fortran convention.
at.screw[index - 1] = screw
at.edgex[index - 1] = edgex
at.edgey[index - 1] = edgey
elif dis_type == 'crack':
for orig_index, index in zip(cl.orig_index, range(len(cl))):
at.nye[:, orig_index - 1] = alpha[:, :, index].T.reshape(9)
return core
print '\tCalculate Dynamics: ', run_dyn
print '\tCalculate Nye Tensor: ', calc_nye
print '\tInput File: ', input_file
print '\tPotential: ', pot_type
if pot_type == 'EAM':
global potdir
potdir = os.environ['POTDIR']
eam_pot = os.path.join(potdir, '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)
elif pot_type == 'TB':
tb = TightBindingPot(alat=1.00, nk=12)
screw_slab_unit = Atoms(screw_slab_unit)
center_cell = np.diag(screw_slab_unit.get_cell()) / 2.
screw_slab_unit.add_atoms(center_cell, 1)
#screw_slab_unit.add_atoms(center_cell*0.76, 6)
screw_slab_unit.set_atoms(screw_slab_unit.Z)
print len(screw_slab_unit)
tb.write_control_file('ctrl.fe', screw_slab_unit)
pot = Potential('IP LMTO_TBE',
param_str="""
<params>
<LMTO_TBE_params n_types="2" control_file="ctrl.fe">
<per_type_data type="1" atomic_num="26"/>
<per_type_data type="2" atomic_num="1"/>
</LMTO_TBE_params>
</params>""")
from quippy import Atoms, bcc
from matscipy.socketcalc import VaspClient, SocketCalculator
#look for mpirun and vasp on $PATH
#mpirun = spawn.find_executable('mpirun')
#vasp = spawn.find_executable('vasp')
#vasp = '/home/eng/essswb/vasp5/vasp.5.3.new/vasp'
mpirun = '/usr/bin/cobalt-mpirun'
vasp = '/projects/SiO2_Fracture/iron/vasp.bgq'
npj = 512 # nodes per job
ppn = 4
njobs = 1
nodes = npj * njobs
job_xyz = glob.glob('feb*.xyz')[0]
bulk = Atoms(job_xyz)
line = []
for at in bulk:
line.append(FixedLine(at.index, (0, 0, 1)))
bulk.set_constraint(line)
hostname, ip = get_hostname_ip()
partsize, partition, job_name = get_cobalt_info()
blocks = get_bootable_blocks(partition, nodes)
print('Available blocks: %s' % blocks)
boot_blocks(blocks)
block, corner, shape = list(block_corner_iter(blocks, npj))[0]
print block, corner, shape
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
sparse_file = 'gp33b.xml.sparseX.GAP_2016_10_3_60_19_29_10_8911'
gap_pot_sparse = os.path.join(POT_DIR, sparse_file)
shutil.copy(gap_pot, './')
shutil.copy(gap_pot_sparse, './')
qm_pot = Potential('IP GAP', param_filename=gap_pot)
else:
print ("Using PURE EAM POTENTIAL")
qm_pot = Potential('IP EAM_ErcolAd do_rescale_r=T r_scale={0}'.format(1.00894848312), param_filename=eam_pot)
nebpath = NEBPaths()
nebanalysis = NEBAnalysis()
if args.auto_gen:
disloc_ini, disloc_fin = nebpath.build_h_nebpath(neb_path=np.array(args.neb_path), fmax = args.fmax, sup_cell=args.sup_cell)
else:
disloc_ini = Atoms('disloc_0.xyz')
disloc_fin = Atoms('disloc_1.xyz')
n_knots = args.knots
images = [disloc_ini] + \
[disloc_ini.copy() for i in range(n_knots)] + \
[disloc_fin]
#copied this from Tom's scripts: need to check and understand
#Will turn these on after the initial run throughs to check the difference.
#alpha = dft_alat/eam_alat
#eam_bulk_mod = (eam_C11 + 2.0*eam_C12)/3.0
#dft_bulk_mod = (dft_C11 + 2.0*dft_C12)/3.0
#beta = eam_bulk_mod/dft_bulk_mod/alpha/alpha/alpha
qmmm_pot = ForceMixingCarvingCalculator(disloc_ini, qm_region_mask,
h_pos = h + lat
h_list.append(np.array(h_pos))
h_list = self.append_if_thresh(h_list, rcut = d_H)
#for h_pos in h_list:
# cl.add_atoms(h_pos,1)
else:
#In this case we just add to the octahedral or in a non-bulk
#environment largest volume sites.
h_list = []
for h in oct_sites:
h_list.append(h)
h_list = self.append_if_thresh(h_list, rcut = d_H)
return h_list
if __name__=='__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-p','--pattern', default="1.traj.xyz")
args = parser.parse_args()
pattern = args.pattern
jobs = glob.glob(pattern)
print jobs
hydrify = Hydrify()
scratch = os.getcwd()
for job in jobs:
os.chdir(job)
ats = Atoms('crack.xyz')
hydrify.hydrogenate_gb(mode='CrackTip')