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 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)
