def write_interstitials(structure, ttol=0.5):
""" function to write POSCAR with interstitials
Parameters:
host = pylada structure object, bulk supercell recommended
ttol = tolerance for finding interstitials
Return:
POSCAR file with interstitials, atom type "B"
"""
struct = deepcopy(structure)
ints = get_interstitials(struct, ttol)
test_str = deepcopy(struct)
for nn in range(len(ints)):
test_str.add_atom(
np.array(ints[nn])[0],
np.array(ints[nn])[1],
np.array(ints[nn])[2], 'B')
print('Writing file POSCAR_ints with "B" type atoms as interstitials')
with open("POSCAR_ints", "w") as file:
write.poscar(test_str, file, vasp5=True)
def write_tcl_one(options, A, tag):
""" write tcl file for viz in VMD """
with open("POSCAR_A.%s" % tag, "w") as f:
pcwrite.poscar(A, f, vasp5=True)
write_xyz(options, A, "A.%s" % tag, options.output_tiles)
fout = file("struct.%s.tcl" % tag, "w")
center = False
write_struct(fout, A, "A.%s.xyz" % tag, 0, center)
fout.close()
def pylada_to_pmg(pylada_structure):
'''
Converts a pylada structure to a pymatgen structure via a temporary file
:param pylada_structure: Pylada structure to convert
:return: Structure
'''
with tempfile.NamedTemporaryFile() as tmp:
name = tmp.name
write.poscar(pylada_structure, name, vasp5=True)
pymatgen_structure = Poscar.from_file(
name).structure # pymatgen.core.Structure
return pymatgen_structure
def strainstructure(orgposcar, strain, direct):
import os
import numpy as np
from pylada.crystal import write, read
outdir = gettmpdir()
tmp_file_name = "POSCAR"
tmp_path = os.path.join(outdir, tmp_file_name)
structure = read.poscar(orgposcar)
a = np.array([1.0, 1.0, 1.0])
if direct == "a":
a[0] = strain
elif direct == "b":
a[1] = strain
elif direct == "c":
a[2] = strain
A = np.diag(a)
structure.cell = structure.cell * A
for atom in structure:
atom.pos = atom.pos * a
write.poscar(structure, tmp_path, vasp5=True)
return tmp_path
def write_tcl(options, A, B, pairs, tag="", center=False):
""" write tcl file for viz in VMD """
AA = deepcopy(A)
BB = deepcopy(B)
if pairs != None and len(pairs) > 0:
for p in pairs:
ia = p[0]
ib = p[1]
AA[ia].pos = p[3]
BB[ib].pos = p[4]
with open("POSCAR_A.%s" % tag, "w") as f:
pcwrite.poscar(AA, f, vasp5=True)
with open("POSCAR_B.%s" % tag, "w") as f:
pcwrite.poscar(BB, f, vasp5=True)
write_xyz(options, AA, "A.%s" % tag, options.output_tiles)
write_xyz(options, BB, "B.%s" % tag, options.output_tiles)
fout = file("plotpairs.%s.tcl" % tag, "w")
write_struct(fout, AA, "A.%s.xyz" % tag, 0, center)
write_struct(fout, BB, "B.%s.xyz" % tag, 1, center)
linestr = "draw color green; graphics top line {%f %f %f} {%f %f %f} width 3 style dashed\n"
# sum = 0
for p in pairs:
print p
ia = p[0]
ib = p[1]
p1 = AA.scale * AA[ia].pos
p2 = BB.scale * BB[ib].pos
## double check! print "TCL types: %s %s" % (A[ia].type, B[ib].type)
# val = npl.norm(np.array(p1)-np.array(p2))
# sum += val
# print "write_tcl pairing: ", p1, p2, val
fout.write(linestr % (p1[0], p1[1], p1[2], p2[0], p2[1], p2[2]))
# print "write_tcl total pairing dist: ", sum
fout.close()
def test_istruc():
from collections import namedtuple
from pickle import loads, dumps
from os import remove
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import POSCAR, CONTCAR
from pylada.vasp import Vasp
from pylada.crystal import Structure, read, specieset, write
from pylada.error import ValueError
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
Extract = namedtuple("Extract", ['directory', 'success', 'structure'])
a = Vasp()
o = a._input['istruc']
d = {'IStruc': o.__class__}
directory = mkdtemp()
try:
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
assert exists(join(directory, POSCAR))
remove(join(directory, POSCAR))
# check reading from outcar but only on success.
a.restart = Extract(directory, False, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# check reading from outcar but only on success.
a.restart = Extract(directory, True, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) > 1e-8
assert abs(other[1].pos[0] - 0.27) < 1e-8
# Now check CONTCAR
write.poscar(structure, join(directory, CONTCAR))
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory, structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR), types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# Check some failure modes.
write.poscar(structure, join(directory, CONTCAR))
structure[0].type = 'Ge'
a.restart = None
try: o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError: pass
else: raise Exception()
structure[0].type = 'Si'
structure.add_atom(0.25,0,0, 'Si')
try: o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError: pass
else: raise Exception()
finally: rmtree(directory)
def raw_anim(A, B, options):
# just animate between A and B, straight up!
### this option is under development
savedir = os.getcwd()
os.chdir(options.trajdir)
structure = pcread.poscar(options.A)
structure = pcread.poscar(options.B)
print "saving starting anim"
Bpath = deepcopy(B)
tag = "Bpath0"
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# now write frames
dt = 1.0 / (options.frames - 1)
t = 0
iter = 0
eps = 1e-6
curpos = []
while t <= 1 + eps:
Bpath = deepcopy(B)
Bpath.cell = t * A.cell + (1.0 - t) * B.cell
for i in range(len(apos)):
pos = t * A[i].pos[i] + (1.0 - t) * B[i].pos[i]
if (iter == 0):
Bpath[i].pos = into_cell(
pos, Bpath.cell) # then make sure it's _in_ the unit cell
curpos.append(Bpath[i].pos)
else:
Bpath[i].pos = closest_to(pos, Bpath.cell, curpos[i])
curpos[i] = Bpath[i].pos
if (iter == 0): ## testing/bug fixing
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "src has cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "src has %d syms and sg %s" % (len(spacegroup), str(sg))
Bstart = deepcopy(Bpath)
sg = spglib.get_spacegroup(Bpath, symprec=1e-4, angle_tolerance=2.0)
# sg = spglib.get_spacegroup(Bpath, symprec=1e-1, angle_tolerance=10.0) ### debugging
print t, sg, tag
if (iter == options.frames - 1): ## testing/bug fixing
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "target has cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "target has %d syms and sg %s" % (len(spacegroup), str(sg))
Bend = deepcopy(Bpath)
tag = "traj.%d" % iter
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# write poscar we can analyze later
# bigB = supercell(Bpath, np.dot(eye2,Bpath.cell)) # for writing a big poscar
with open("%s.POSCAR" % tag, "w") as f:
pcwrite.poscar(Bpath, f, vasp5=True)
t += dt
iter += 1
os.chdir(savedir)
if (options.verbose > 2):
write_tcl(options, Bend, Bstart, pairs[1], "pairs")
# some special work to verify we really arrived at B:
# Borig = pcread.poscar(options.A)
# M = np.dot(Borig.cell, npl.inv(Bpath.cell))
# Bfinal = transform_cell(M,Bpath)
# bigB = supercell(Bfinal, np.dot(eye2,Bfinal.cell)) ## this is a special "doubling" test
# with open("final.POSCAR", "w") as f: pcwrite.poscar(bigB, f, vasp5=True)
# with open("final.POSCAR", "w") as f: pcwrite.poscar(Bfinal, f, vasp5=True)
# sg = spglib.get_spacegroup(Bfinal, symprec=1e-4, angle_tolerance=2.0) ## this is "B in A coords"
# print "spacegroup of final structure: ", sg
sg = spglib.get_spacegroup(B, symprec=1e-4, angle_tolerance=2.0)
print "spacegroup of initial structure (B, [Bflip in code]) ", sg
sg = spglib.get_spacegroup(A, symprec=1e-4, angle_tolerance=2.0)
print "spacegroup of target structure (A) ", sg
def make_anim(A, B, Tm, shift, pairs, options):
# combined view of the unit call and atom transforms
# A is target, B is src, after src has been rotated and its unit cell axes permuted so that they
# "most align" with those of A. Then transform is just two parts: first is unit cell Tform "Tm"
# next is mapping in pairs
### no longer true: which is expressed in 3N-dim space as bigA.
from copy import deepcopy
from util import write_struct, write_xyz, transform_cell, write_tcl
if options.verbose > 1:
print "Exploring minimal path we have discovered..."
# the results come out a little convoluated b/c of all the steps, so here we gather the
# actual start and finish positions.
details = False
print B.cell
print "maps to"
print A.cell
print "with internal atom shift"
print shift
print "and atom idx pairing"
ppidx = pairs[0]
ppos = pairs[1]
ainv = npl.inv(A.cell)
apos = []
bpos = []
for i in range(len(ppidx)):
p = ppidx[i]
q = ppos[i]
print p, q ##, into_cell(np.dot(B.cell, np.dot(ainv, q[4])), B.cell)
apos.append(q[3]) # target atom position
bpos.append(q[4]) # src atom position
if (options.verbose > 2):
print "and A is just"
print A.cell
for a in A:
print a.pos, into_cell(a.pos, A.cell)
print "and B is just"
print B.cell
for b in B:
print b.pos, into_cell(b.pos, B.cell)
if (not os.path.exists(options.trajdir)):
os.mkdir(options.trajdir)
savedir = os.getcwd()
os.chdir(options.trajdir)
if (options.verbose > 1):
print "saving starting anim"
Bpath = deepcopy(B)
tag = "Bpath0"
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# now write frames
eye2 = 2.0 * np.identity(3) # for writing a big cell if we want
dt = 1.0 / (options.frames - 1)
t = 0
iter = 0
eps = 1e-6
curpos = []
while t <= 1 + eps:
Bpath = deepcopy(B)
Bpath.cell = t * A.cell + (1.0 - t) * B.cell
for i in range(len(apos)):
p = t * apos[i] + (1.0 - t) * bpos[
i] # this is an abs position, but in A's frame of reference (both apos and bpos are created with
# B.cell transformed to A.cell. Here we are mapping to cells in between original B.cell and A.cell)
# Note apos and bpos are not taken directly from A, B input cells but are part of the "pairing" data
c = np.dot(ainv, p) # so get the coords
pos = np.dot(Bpath.cell,
c) # and express it w.r.t. evolving Bpath frame
if (iter == 0):
Bpath[i].pos = into_cell(
pos, Bpath.cell) # then make sure it's _in_ the unit cell
curpos.append(Bpath[i].pos)
else:
Bpath[i].pos = closest_to(pos, Bpath.cell, curpos[i])
curpos[i] = Bpath[i].pos
if (iter == 0): ## testing/bug fixing
Bstart = deepcopy(Bpath)
if (options.verbose > 2):
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "src has primitive cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "src has %d syms and sg %s" % (len(spacegroup), str(sg))
sg = spglib.get_spacegroup(Bpath, symprec=1e-4, angle_tolerance=2.0)
# sg = spglib.get_spacegroup(Bpath, symprec=1e-1, angle_tolerance=10.0) ### debugging
if (options.verbose > 1):
print t, sg, tag
if (iter == options.frames - 1): ## testing/bug fixing
Bend = deepcopy(Bpath)
if (options.verbose > 2):
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "target has primitive cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "target has %d syms and sg %s" % (len(spacegroup),
str(sg))
tag = "traj.%d" % iter
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# write poscar we can analyze later
# bigB = supercell(Bpath, np.dot(eye2,Bpath.cell)) # for writing a big poscar
with open("%s.POSCAR" % tag, "w") as f:
pcwrite.poscar(Bpath, f, vasp5=True)
t += dt
iter += 1
os.chdir(savedir)
if (options.verbose > 2):
write_tcl(options, Bend, Bstart, pairs[1], "pairs")
# some special work to verify we really arrived at B:
# Borig = pcread.poscar(options.A)
# M = np.dot(Borig.cell, npl.inv(Bpath.cell))
# Bfinal = transform_cell(M,Bpath)
# bigB = supercell(Bfinal, np.dot(eye2,Bfinal.cell)) ## this is a special "doubling" test
# with open("final.POSCAR", "w") as f: pcwrite.poscar(bigB, f, vasp5=True)
# with open("final.POSCAR", "w") as f: pcwrite.poscar(Bfinal, f, vasp5=True)
# sg = spglib.get_spacegroup(Bfinal, symprec=1e-4, angle_tolerance=2.0) ## this is "B in A coords"
# print "spacegroup of final structure: ", sg
sg = spglib.get_spacegroup(B, symprec=1e-4, angle_tolerance=2.0)
if (options.verbose > 0):
print "spacegroup of initial structure (B, [Bflip in code]) ", sg
sg = spglib.get_spacegroup(A, symprec=1e-4, angle_tolerance=2.0)
if (options.verbose > 1):
print "spacegroup of target structure (A) ", sg
a1 = [-d/2., d * (2+sqrt(3))/2., 0] a2 = [d * (1+sqrt(3))/2., d * (3+sqrt(3))/2., 0] a3 = [0,0,1] l1 = d*sqrt(3)/2. l2 = d*(sqrt(3)-1)/2. h1 = 1.5*d h2 = d*(3+sqrt(3))/2. structure = pyc.Structure(np.transpose([a1,a2,a3]), scale=1.0) structure.add_atom(0,0,0, "Si") structure.add_atom(0,d,0, "Si") structure.add_atom(l1, h1, 0, "Si") structure.add_atom(l2, h2, 0, "Si") write.poscar(structure, file='fakeSiO2.POSCAR') write_xyz(None, structure, 'fakeSiO2', 6) ############### hn1 = -sqrt(3)/2. * d h0 = 0 h1 = d h2 = 1.5*d h3 = (2+sqrt(3))/2. * d h4 = (3+sqrt(3))/2. * d h5 = (5+sqrt(3))/2. * d h6 = (5+2*sqrt(3))/2. * d h7 = (6+sqrt(3))/2. * d h8 = (6+2*sqrt(3))/2. * d l0 = 0
slab = minimize_broken_bonds(bulk=bulk,slab=slab,vacuum=vacuum,charge=charge,minimize_total=True)
except AssertionError:
print("Charges do not sum up to zero for %s, the charges are:"%(files[f]), charge)
print("Going to the next structure.")
break
# print("Done with the supercell construction, now shaping it")
cell=transpose(slab.cell)
cell[2][0]=0.
cell[2][1]=0.
slab.cell=transpose(cell)
r=diag([1,1,1])
slab=supercell(slab,dot(slab.cell,r))
write.poscar(structure=slab,file=outdir_cur + '/POSCAR_%s%s%s_%slay_%svac' %(miller[0],miller[1],miller[2],nlayers,vacuum),vasp5=True)
file.write('% 2i % 2i % 2i broken_bonds %2.4f %2.4f polar=%s\n' %(miller[0],miller[1],miller[2],count_broken_bonds(bulk=bulk,slab=slab),count_broken_bonds_per_area(bulk=bulk,slab=slab),is_polar(slab=slab,charge=charge)))
file.flush()
else:
file.write('DONE %d\n'%(miller_bounds))
file.flush()
file.close()
print("%s on core %d: DONE"%(files[f], rank))
continue
file.write('FAILED\n')
file.flush()
file.close()
print("%s on core %d: FAILED"%(files[f], rank))
def make_surfaces_to_pylada(root, bulk_structure, incar_settings=None, label='', depth=8, frozen_depth=2, override=[], kpt_modifier=1):
'''
:param root: root directory of run
:param bulk_structure: pylada bulk strucutre
:param incar_settings: location of INCAR.defaults
:return:
'''
from pylada.crystal import write
from Generate_Surface import Generate_Surface
from Helpers import pyl_to_pmg, pmg_to_pyl
from Generate_Surface import get_bottom, get_SD_along_vector
# small_surfaces = Generate_Surface(pyl_to_pmg(bulk_structure), 1, 1, 1, 3, vacuum=8, orth=True)
for i, surface in enumerate(Generate_Surface(pyl_to_pmg(bulk_structure), 1, 1, 1, depth, vacuum=8, orth=False)):
# Frozen Surface
# surface_small = small_surfaces[i]
surf_folder = root / label / str(i).zfill(2)
surf_folder.functional = WSBulkToFrozenSurfacePBE(Vasp(), bulk_structure=bulk_structure,
incar_settings=incar_settings, override=override,
kpt_modifier=kpt_modifier)
surf_folder.params['structure'] = pmg_to_pyl(surface).copy()
os.makedirs(surf_folder.name[1:], exist_ok=True)
surface.to('poscar', os.path.join(surf_folder.name[1:], 'surface.vasp'))
with open(os.path.join(surf_folder.name[1:], 'DATABASE'), 'w') as f:
f.write('''
surface
surface_cut {}
surface_termination {}
convergence_study
convergence_type surface
misc_labels {}
'''.format(i, 'None', label))
# Frozen Surfaces
for frozen_region in ['top', 'bottom']:
froz_folder = surf_folder / frozen_region
froz_folder.functional = WSBulkToSurfacePBE(Vasp(), bulk_structure=bulk_structure,
incar_settings=incar_settings, override=override,
kpt_modifier=kpt_modifier)
surface_frozen = surface.copy()
# print(surface_frozen)
sd = get_SD_along_vector(surface_frozen, 2, get_bottom(surface_frozen, length=frozen_depth, region=frozen_region))
# Poscar(surface_frozen, selective_dynamics=sd).write_file(os.path.join(froz_folder.name[1:], 'surface.vasp'))
surface_frozen_pyl = pmg_to_pyl(surface_frozen)
# sd_small = get_SD_along_vector(surface_frozen, frozen_depth, get_bottom(surface_frozen, region=frozen_region))
for (atom, sd) in zip(surface_frozen_pyl, sd):
if sd[0]:
atom.freeze = 'xyz'
os.makedirs(froz_folder.name[1:], exist_ok=True)
write.poscar(surface_frozen_pyl, os.path.join(froz_folder.name[1:], 'surface.vasp'), vasp5=True)
froz_folder.params['structure'] = surface_frozen_pyl.copy()
os.makedirs(froz_folder.name[1:], exist_ok=True)
with open(os.path.join(froz_folder.name[1:], 'DATABASE'), 'w') as f:
f.write('''
surface
surface_cut {}
surface_termination {}
misc_labels {}
'''.format(i, frozen_region, label))
def test_istruc():
from collections import namedtuple
from pickle import loads, dumps
from os import remove
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import POSCAR, CONTCAR
from pylada.vasp import Vasp
from pylada.crystal import Structure, read, specieset, write
from pylada.error import ValueError
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
.add_atom(0, 0, 0, "Si")\
.add_atom(0.25, 0.25, 0.25, "Si")
Extract = namedtuple("Extract", ['directory', 'success', 'structure'])
a = Vasp()
o = a._input['istruc']
d = {'IStruc': o.__class__}
directory = mkdtemp()
try:
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
assert exists(join(directory, POSCAR))
remove(join(directory, POSCAR))
# check reading from outcar but only on success.
a.restart = Extract(directory, False, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR),
types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# check reading from outcar but only on success.
a.restart = Extract(directory, True, structure.copy())
a.restart.structure[1].pos[0] += 0.02
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR),
types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) > 1e-8
assert abs(other[1].pos[0] - 0.27) < 1e-8
# Now check CONTCAR
write.poscar(structure, join(directory, CONTCAR))
assert a.istruc == 'auto'
assert o.output_map(vasp=a, outdir=directory,
structure=structure) is None
assert exists(join(directory, POSCAR))
other = read.poscar(join(directory, POSCAR),
types=specieset(structure))
assert abs(other[1].pos[0] - 0.25) < 1e-8
assert abs(other[1].pos[0] - 0.27) > 1e-8
# Check some failure modes.
write.poscar(structure, join(directory, CONTCAR))
structure[0].type = 'Ge'
a.restart = None
try:
o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError:
pass
else:
raise Exception()
structure[0].type = 'Si'
structure.add_atom(0.25, 0, 0, 'Si')
try:
o.output_map(vasp=a, outdir=directory, structure=structure)
except ValueError:
pass
else:
raise Exception()
finally:
rmtree(directory)
def save_struct(options, A, tag):
print "tag ", tag
pcwrite.poscar(A, "%s.%s" % (options.A, tag), vasp5=True)
write_tcl_one(options, A, tag)