def test(tmpdir, path):
from numpy import abs
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.relax import epitaxial
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0, 0, 0, "Si")\
.add_atom(0.25, 0.25, 0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
result = epitaxial(vasp,
structure,
outdir=str(tmpdir),
epiconv=1e-5,
comm=default_comm)
assert result.success
assert abs(result.stress[2, 2]) < 1.0
def test(tmpdir, path):
from numpy import abs
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.emass import effective_mass, EMass
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0, 0, 0, "Si")\
.add_atom(0.25, 0.25, 0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 25e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
emass = EMass(copy=vasp)
assert abs(emass.encut - 1.4) < 1e-8
assert abs(emass.ediff - 25e-5) < 1e-10
result = effective_mass(vasp, structure, outdir=str(tmpdir), comm=default_comm,
emassparams={'ediff': 1e-8})
result.emass
assert result.success
result = emass(structure, outdir=str(tmpdir), comm=default_comm,
emassparams={'ediff': 1e-8})
assert result.success
def test(path):
from shutil import rmtree
from tempfile import mkdtemp
from pylada.crystal import Structure
from pylada.vasp import Vasp
from epirelax import epitaxial
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
try:
result = epitaxial(vasp, structure, outdir=directory, epiconv=1e-4, comm=default_comm)
assert result.success
finally:
rmtree(directory)
pass
def test(path):
from os import makedirs
from os.path import exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada import default_comm
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
if directory == '/tmp/test' or directory == '/tmp/test/':
if exists(directory): rmtree(directory)
makedirs(directory)
try:
result = vasp(structure, outdir=directory, comm=default_comm)
assert result.success
finally:
if directory != '/tmp/test' and directory != '/tmp/test/':
rmtree(directory)
def test(path):
from os import makedirs
from os.path import exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada import default_comm
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
if directory == '/tmp/test' or directory == '/tmp/test/':
if exists(directory): rmtree(directory)
makedirs(directory)
try:
result = vasp(structure, outdir=directory, comm=default_comm)
assert result.success
finally:
if directory != '/tmp/test' and directory != '/tmp/test/':
rmtree(directory)
def test(tmpdir, path):
from numpy import all, abs
from quantities import kbar, eV, angstrom
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.relax import Relax
from pylada import default_comm
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
functional = Relax(copy=vasp)
assert abs(functional.ediff - 1e-5) < 1e-8
assert functional.prec == 'Accurate'
result = functional(structure, outdir=str(tmpdir), comm=default_comm,
relaxation="volume ionic cellshape")
assert result.success
assert result.stress.units == kbar and all(abs(result.stress) < 1e0)
assert result.forces.units == eV / angstrom and all(abs(result.forces) < 1e-1)
assert result.total_energy.units == eV and all(
abs(result.total_energy + 10.668652 * eV) < 1e-2)
def test_incar():
from shutil import rmtree
from tempfile import mkdtemp
from os.path import join, dirname
from quantities import eV
from pylada.vasp import Vasp, read_incar
from pylada.crystal import Structure
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "metal"
vasp.sigma = 0.06
vasp.relaxation = "volume"
vasp.add_specie = "Si", join(dirname(__file__), 'pseudos', 'Si')
directory = mkdtemp()
try:
vasp.write_incar(path=join(directory, 'INCAR'), structure=structure)
other = read_incar(join(directory, 'INCAR'))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == 'atomic'
assert other.isif == 7
assert other.ismear == 'metal'
assert other.istart == 'scratch'
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == 'volume'
assert other.system == 'has a name'
with open(join(directory, 'INCAR'), 'a') as file:
file.write('\nSOMETHing = 0.5\n')
other = read_incar(join(directory, 'INCAR'))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == 'atomic'
assert other.isif == 7
assert other.ismear == 'metal'
assert other.istart == 'scratch'
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == 'volume'
assert other.system == 'has a name'
assert 'something' in other._input
assert isinstance(other.something, float)
assert abs(other.something - 0.5) < 1e-8
finally:
rmtree(directory)
pass
def test(path):
from shutil import rmtree
from tempfile import mkdtemp
from os.path import join
from quantities import eV
from pylada.vasp import Vasp, read_incar
from pylada.crystal import Structure
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "metal"
vasp.sigma = 0.06
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
try:
vasp.write_incar(path=join(directory, 'INCAR'), structure=structure)
other = read_incar(join(directory, 'INCAR'))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == 'atomic'
assert other.isif == 7
assert other.ismear == 'metal'
assert other.istart == 'scratch'
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == 'volume'
assert other.system == 'has a name'
with open(join(directory, 'INCAR'), 'a') as file:
file.write('\nSOMETHing = 0.5\n')
other = read_incar(join(directory, 'INCAR'))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == 'atomic'
assert other.isif == 7
assert other.ismear == 'metal'
assert other.istart == 'scratch'
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == 'volume'
assert other.system == 'has a name'
assert 'something' in other._input
assert isinstance(other.something, float)
assert abs(other.something - 0.5) < 1e-8
finally:
rmtree(directory)
pass
def vasp():
from os.path import join, dirname
from pylada.vasp import Vasp
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "metal"
vasp.sigma = 0.06
vasp.relaxation = "volume"
vasp.add_specie = "Si", join(dirname(__file__), 'pseudos', 'Si')
return vasp
def vasp():
from os.path import join, dirname
from pylada.vasp import Vasp
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "metal"
vasp.sigma = 0.06
vasp.relaxation = "volume"
vasp.add_specie = "Si", join(dirname(__file__), 'pseudos', 'Si')
return vasp
def test(path):
from shutil import rmtree
from os.path import exists
from os import makedirs
from tempfile import mkdtemp
from numpy import abs
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.emass import effective_mass, EMass
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 25e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
emass = EMass(copy=vasp)
assert abs(emass.encut - 1.4) < 1e-8
assert abs(emass.ediff - 25e-5) < 1e-10
directory = "/tmp/test" #mkdtemp()
if exists(directory) and directory == '/tmp/test': rmtree(directory)
if not exists(directory): makedirs(directory)
try:
result = effective_mass(vasp,
structure,
outdir=directory,
comm=default_comm,
emassparams={'ediff': 1e-8})
result.emass
assert result.success
result = emass(structure,
outdir=directory,
comm=default_comm,
emassparams={'ediff': 1e-8})
assert result.success
finally:
if directory != '/tmp/test': rmtree(directory)
pass
def test(path):
from glob import glob
from os.path import join
from shutil import rmtree
from tempfile import mkdtemp
from numpy import all, abs
from quantities import kbar, eV, angstrom
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.relax import Relax
from pylada import default_comm
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
try:
functional = Relax(copy=vasp)
assert abs(functional.ediff - 1e-5) < 1e-8
assert functional.prec == 'Accurate'
result = functional(structure, outdir=directory, comm=default_comm,
relaxation="volume ionic cellshape")
assert result.success
def sortme(a): return int(a.split('/')[-1])
dirs = sorted(glob(join(join(directory, '*'), '[0-9]')), key=sortme)
# for previous, current in zip(dirs, dirs[1:]):
# assert len(check_output(['diff', join(previous, 'CONTCAR'), join(current, 'POSCAR')])) == 0
# assert len(check_output(['diff', join(current, 'CONTCAR'), join(directory, 'POSCAR')])) == 0
assert result.stress.units == kbar and all(abs(result.stress) < 1e0)
assert result.forces.units == eV/angstrom and all(abs(result.forces) < 1e-1)
assert result.total_energy.units == eV and all(abs(result.total_energy + 10.668652*eV) < 1e-2)
finally:
if directory != '/tmp/test/relax': rmtree(directory)
pass
def test(path):
from shutil import rmtree
from os.path import exists
from os import makedirs
from tempfile import mkdtemp
from numpy import abs
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.emass import effective_mass, EMass
from pylada import default_comm
structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 25e-5
vasp.encut = 1.4
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
emass = EMass(copy=vasp)
assert abs(emass.encut - 1.4) < 1e-8
assert abs(emass.ediff - 25e-5) < 1e-10
directory = "/tmp/test" #mkdtemp()
if exists(directory) and directory == '/tmp/test': rmtree(directory)
if not exists(directory): makedirs(directory)
try:
result = effective_mass(vasp, structure, outdir=directory, comm=default_comm,
emassparams={'ediff': 1e-8})
result.emass
assert result.success
result = emass(structure, outdir=directory, comm=default_comm,
emassparams={'ediff': 1e-8})
assert result.success
finally:
if directory != '/tmp/test': rmtree(directory)
pass
def test(tmpdir, path):
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada import default_comm
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
result = vasp(structure, outdir=str(tmpdir), comm=default_comm)
assert result.success
def test(tmpdir, path):
from numpy import all, abs
from quantities import kbar, eV, angstrom
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.relax import Relax
from pylada import default_comm
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")
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.prec = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "fermi"
vasp.sigma = 0.01
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
functional = Relax(copy=vasp)
assert abs(functional.ediff - 1e-5) < 1e-8
assert functional.prec == 'Accurate'
result = functional(structure,
outdir=str(tmpdir),
comm=default_comm,
relaxation="volume ionic cellshape")
assert result.success
assert result.stress.units == kbar and all(abs(result.stress) < 1e0)
assert result.forces.units == eV / angstrom and all(
abs(result.forces) < 1e-1)
assert result.total_energy.units == eV and all(
abs(result.total_energy + 10.668652 * eV) < 1e-2)
def test_ediff():
from pickle import loads, dumps
from pylada.vasp import Vasp
from pylada.crystal import Structure
a = Vasp()
u = 0.25
x, y = u, 0.25-u
structure = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "Mg") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "Mg") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "Mg") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "Mg") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "Al") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "Al") \
.add_atom( x, x, x, "O") \
.add_atom( x, y, y, "O") \
.add_atom( y, x, y, "O") \
.add_atom( y, y, x, "O") \
.add_atom( -x, -x, -x, "O") \
.add_atom( -x, -y, -y, "O") \
.add_atom( -y, -x, -y, "O") \
.add_atom( -y, -y, -x, "O")
N = float(len(structure))
o = a._input['ediff']
d = {'Ediff': o.__class__}
assert a.ediff is None
assert a.ediff_per_atom is None
assert o.output_map() is None
assert eval(repr(o), d).output_map() is None
assert eval(repr(o), d).keyword == 'ediff'
assert loads(dumps(o)).output_map() is None
a.ediff_per_atom = 1e-5
a.ediff = 2e-4
assert abs(a.ediff - 2e-4) < 1e-8
assert a.ediff_per_atom is None
assert abs(float(o.output_map(structure=structure)['ediff']) - a.ediff) < a.ediff * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediff']) - a.ediff) < a.ediff * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediff']) - a.ediff) < a.ediff * 1e-2
a.ediff = -1
assert abs(a.ediff) < 1e-8
assert abs(float(o.output_map(structure=structure)['ediff'])) < 1e-8
a = Vasp()
o = a._input['ediff_per_atom']
d = {'EdiffPerAtom': o.__class__}
assert a.ediff_per_atom is None
assert a.ediff is None
assert o.output_map() is None
assert eval(repr(o), d).output_map() is None
assert eval(repr(o), d).keyword == 'ediff'
assert loads(dumps(o)).output_map() is None
a.ediff = 1e-5
a.ediff_per_atom = 2e-4
assert abs(a.ediff_per_atom - 2e-4) < 1e-8
assert a.ediff is None
assert abs(float(o.output_map(structure=structure)['ediff']) - 2e-4 * N) < 2e-4 * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediff']) - 2e-4 * N) < 2e-4 * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediff']) - 2e-4 * N) < 2e-4 * 1e-2
a.ediff = 1e-4
a.ediff_per_atom = None
assert abs(a.ediff-1e-4) < 1e-8
assert a.ediff_per_atom is None
a.ediff_per_atom = 1e-4
a.ediff = None
assert abs(a.ediff_per_atom-1e-4) < 1e-8
assert a.ediff is None
return "\n0\nGamma\n%2i %2i %2i\n 0. 0. 0.\n" %(n1,n2,n3) ############### setting up the functional vasp=Vasp() vasp.program = '/home/vstevano/bin/vasp' pseudoDir = '/home/vstevano/software/pseudos' vasp.add_specie = "In", pseudoDir + "/In" vasp.add_specie = "O", pseudoDir + "/O" vasp.prec = "accurate" vasp.encut = 340. vasp.ismear = 0 vasp.sigma = 0.05 vasp.ediff = 1.0e-6 vasp.ediffg = -0.01 vasp.convergence= 1.0e-6 vasp.nsw = 1 vasp.lwave = True vasp.lorbit = 10 vasp.lplane = True vasp.addgrid = True vasp.npar = 8 vasp.isym = 0 vasp.lcharg = True vasp.lwave = True vasp.lmaxmix = 4 vasp.loptics = False vasp.lpead = False vasp.algo = "Normal"
def test(path):
from shutil import rmtree
from tempfile import mkdtemp
from os.path import join
from quantities import eV
from pylada.vasp import Vasp, read_incar
from pylada.crystal import Structure
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")
)
vasp = Vasp()
vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
vasp.precision = "accurate"
vasp.ediff = 1e-5
vasp.encut = 1
vasp.ismear = "metal"
vasp.sigma = 0.06
vasp.relaxation = "volume"
vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
directory = mkdtemp()
try:
vasp.write_incar(path=join(directory, "INCAR"), structure=structure)
other = read_incar(join(directory, "INCAR"))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == "atomic"
assert other.isif == 7
assert other.ismear == "metal"
assert other.istart == "scratch"
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == "volume"
assert other.system == "has a name"
with open(join(directory, "INCAR"), "a") as file:
file.write("\nSOMETHing = 0.5\n")
other = read_incar(join(directory, "INCAR"))
assert abs(other.ediff - 1e-5) < 1e-8
assert abs(other.encut - 245.345) < 1e-8
assert abs(other.sigma - 0.06 * eV) < 1e-8
assert other.ibrion == 2
assert other.icharg == "atomic"
assert other.isif == 7
assert other.ismear == "metal"
assert other.istart == "scratch"
assert other.lcharg == False
assert other.nsw == 50
assert other.relaxation == "volume"
assert other.system == "has a name"
assert "something" in other._input
assert isinstance(other.something, float)
assert abs(other.something - 0.5) < 1e-8
finally:
rmtree(directory)
pass
def test_ediff():
from pickle import loads, dumps
from pylada.vasp import Vasp
from pylada.crystal import Structure
a = Vasp()
u = 0.25
x, y = u, 0.25-u
structure = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "Mg") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "Mg") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "Mg") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "Mg") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "Al") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "Al") \
.add_atom( x, x, x, "O") \
.add_atom( x, y, y, "O") \
.add_atom( y, x, y, "O") \
.add_atom( y, y, x, "O") \
.add_atom( -x, -x, -x, "O") \
.add_atom( -x, -y, -y, "O") \
.add_atom( -y, -x, -y, "O") \
.add_atom( -y, -y, -x, "O")
N = float(len(structure))
o = a._input['ediff']
d = {'Ediff': o.__class__}
assert a.ediff is None
assert a.ediff_per_atom is None
assert o.output_map() is None
assert eval(repr(o), d).output_map() is None
assert eval(repr(o), d).keyword == 'ediff'
assert loads(dumps(o)).output_map() is None
a.ediff_per_atom = 1e-5
a.ediff = 2e-4
assert abs(a.ediff - 2e-4) < 1e-8
assert a.ediff_per_atom is None
assert abs(float(o.output_map(structure=structure)['ediff']) - a.ediff) < a.ediff * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediff']) - a.ediff) < a.ediff * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediff']) - a.ediff) < a.ediff * 1e-2
a.ediff = -1
assert abs(a.ediff) < 1e-8
assert abs(float(o.output_map(structure=structure)['ediff'])) < 1e-8
a = Vasp()
o = a._input['ediff_per_atom']
d = {'EdiffPerAtom': o.__class__}
assert a.ediff_per_atom is None
assert a.ediff is None
assert o.output_map() is None
assert eval(repr(o), d).output_map() is None
assert eval(repr(o), d).keyword == 'ediff'
assert loads(dumps(o)).output_map() is None
a.ediff = 1e-5
a.ediff_per_atom = 2e-4
assert abs(a.ediff_per_atom - 2e-4) < 1e-8
assert a.ediff is None
assert abs(float(o.output_map(structure=structure)['ediff']) - 2e-4 * N) < 2e-4 * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediff']) - 2e-4 * N) < 2e-4 * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediff']) - 2e-4 * N) < 2e-4 * 1e-2
a.ediff = 1e-4
a.ediff_per_atom = None
assert abs(a.ediff-1e-4) < 1e-8
assert a.ediff_per_atom is None
a.ediff_per_atom = 1e-4
a.ediff = None
assert abs(a.ediff_per_atom-1e-4) < 1e-8
assert a.ediff is None