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 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(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 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(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(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_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_encut():
from os.path import dirname
from pickle import loads, dumps
from quantities import eV, hartree
import quantities
import numpy
from pylada.vasp import Vasp
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")
a = Vasp()
a.add_specie = "Si", "{0}/pseudos/Si".format(dirname(__file__))
o = a._input['encut']
d = {'Encut': o.__class__}
d.update(quantities.__dict__)
d.update(numpy.__dict__)
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 == 'encut'
assert loads(dumps(o)).output_map() is None
a.encut = 1e0
assert abs(a.encut - 1e0) < 1e-8
assert abs(
float(o.output_map(structure=structure, vasp=a)['encut']) -
245.345) < 1e-8
assert abs(
float(
eval(repr(o), d).output_map(structure=structure, vasp=a)['encut'])
- 245.345) < 1e-8
assert abs(
float(
loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) -
245.345) < 1e-8
assert abs(eval(repr(o), d).value - 1.0) < 1e-8
assert abs(loads(dumps(o)).value - 1.0) < 1e-8
a.encut = 0.8
assert abs(a.encut - 0.8) < 1e-8
assert abs(
float(o.output_map(structure=structure, vasp=a)['encut']) -
245.345 * 0.8) < 1e-8
assert abs(
float(
eval(repr(o), d).output_map(structure=structure, vasp=a)['encut'])
- 245.345 * 0.8) < 1e-8
assert abs(
float(
loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) -
245.345 * 0.8) < 1e-8
assert abs(eval(repr(o), d).value - 0.8) < 1e-8
assert abs(loads(dumps(o)).value - 0.8) < 1e-8
a.encut = 200
assert abs(a.encut - 200) < 1e-8
assert abs(
float(o.output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(
float(
eval(repr(o), d).output_map(structure=structure, vasp=a)['encut'])
- 200) < 1e-8
assert abs(
float(
loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) -
200) < 1e-8
assert abs(eval(repr(o), d).value - 200) < 1e-8
assert abs(loads(dumps(o)).value - 200) < 1e-8
a.encut = 200 * eV
assert abs(a.encut - 200 * eV) < 1e-8
assert a.encut.units == eV
assert abs(
float(o.output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(
float(
eval(repr(o), d).output_map(structure=structure, vasp=a)['encut'])
- 200) < 1e-8
assert abs(
float(
loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) -
200) < 1e-8
assert abs(eval(repr(o), d).value - 200 * eV) < 1e-8
assert abs(loads(dumps(o)).value - 200 * eV) < 1e-8
assert eval(repr(o), d).value.units == eV
assert loads(dumps(o)).value.units == eV
a.encut = (200 * eV).rescale(hartree)
assert a.encut.units == hartree
assert abs(a.encut - 200 * eV) < 1e-8
assert abs(
float(o.output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(
float(
eval(repr(o), d).output_map(structure=structure, vasp=a)['encut'])
- 200) < 1e-7
assert abs(
float(
loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) -
200) < 1e-8
assert abs(eval(repr(o), d).value - 200 * eV) < 1e-8
assert abs(loads(dumps(o)).value - 200 * eV) < 1e-8
assert eval(repr(o), d).value.units == hartree
assert loads(dumps(o)).value.units == hartree
o = a._input['encutgw']
d = {'EncutGW': o.__class__}
d.update(quantities.__dict__)
d.update(numpy.__dict__)
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 == 'encutgw'
assert loads(dumps(o)).output_map() is None
a.encutgw = (200 * eV).rescale(hartree)
assert a.encutgw.units == hartree
assert abs(a.encutgw - 200 * eV) < 1e-8
assert abs(
float(o.output_map(structure=structure, vasp=a)['encutgw']) -
200) < 1e-8
assert abs(
float(
eval(repr(o), d).output_map(structure=structure, vasp=a)
['encutgw']) - 200) < 1e-7
assert abs(
float(
loads(dumps(o)).output_map(structure=structure, vasp=a)['encutgw'])
- 200) < 1e-8
assert abs(eval(repr(o), d).value - 200 * eV) < 1e-6
assert abs(loads(dumps(o)).value - 200 * eV) < 1e-8
assert eval(repr(o), d).value.units == hartree
assert loads(dumps(o)).value.units == hartree
if n2==0:n2=1
if n3==0:n3=1
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
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_encut():
from os.path import dirname
from pickle import loads, dumps
from quantities import eV, hartree
import quantities
import numpy
from pylada.vasp import Vasp
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")
a = Vasp()
a.add_specie = "Si", "{0}/pseudos/Si".format(dirname(__file__))
o = a._input['encut']
d = {'Encut': o.__class__}
d.update(quantities.__dict__)
d.update(numpy.__dict__)
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 == 'encut'
assert loads(dumps(o)).output_map() is None
a.encut = 1e0
assert abs(a.encut - 1e0) < 1e-8
assert abs(float(o.output_map(structure=structure, vasp=a)['encut']) - 245.345) < 1e-8
assert abs(float(eval(repr(o), d).output_map(
structure=structure, vasp=a)['encut']) - 245.345) < 1e-8
assert abs(float(loads(dumps(o)).output_map(
structure=structure, vasp=a)['encut']) - 245.345) < 1e-8
assert abs(eval(repr(o), d).value - 1.0) < 1e-8
assert abs(loads(dumps(o)).value - 1.0) < 1e-8
a.encut = 0.8
assert abs(a.encut - 0.8) < 1e-8
assert abs(float(o.output_map(structure=structure, vasp=a)['encut']) - 245.345 * 0.8) < 1e-8
assert abs(float(eval(repr(o), d).output_map(
structure=structure, vasp=a)['encut']) - 245.345 * 0.8) < 1e-8
assert abs(float(loads(dumps(o)).output_map(
structure=structure, vasp=a)['encut']) - 245.345 * 0.8) < 1e-8
assert abs(eval(repr(o), d).value - 0.8) < 1e-8
assert abs(loads(dumps(o)).value - 0.8) < 1e-8
a.encut = 200
assert abs(a.encut - 200) < 1e-8
assert abs(float(o.output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(float(eval(repr(o), d).output_map(
structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(float(loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(eval(repr(o), d).value - 200) < 1e-8
assert abs(loads(dumps(o)).value - 200) < 1e-8
a.encut = 200 * eV
assert abs(a.encut - 200 * eV) < 1e-8
assert a.encut.units == eV
assert abs(float(o.output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(float(eval(repr(o), d).output_map(
structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(float(loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(eval(repr(o), d).value - 200 * eV) < 1e-8
assert abs(loads(dumps(o)).value - 200 * eV) < 1e-8
assert eval(repr(o), d).value.units == eV
assert loads(dumps(o)).value.units == eV
a.encut = (200 * eV).rescale(hartree)
assert a.encut.units == hartree
assert abs(a.encut - 200 * eV) < 1e-8
assert abs(float(o.output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(float(eval(repr(o), d).output_map(
structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(float(loads(dumps(o)).output_map(structure=structure, vasp=a)['encut']) - 200) < 1e-8
assert abs(eval(repr(o), d).value - 200 * eV) < 1e-8
assert abs(loads(dumps(o)).value - 200 * eV) < 1e-8
assert eval(repr(o), d).value.units == hartree
assert loads(dumps(o)).value.units == hartree
o = a._input['encutgw']
d = {'EncutGW': o.__class__}
d.update(quantities.__dict__)
d.update(numpy.__dict__)
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 == 'encutgw'
assert loads(dumps(o)).output_map() is None
a.encutgw = (200 * eV).rescale(hartree)
assert a.encutgw.units == hartree
assert abs(a.encutgw - 200 * eV) < 1e-8
assert abs(float(o.output_map(structure=structure, vasp=a)['encutgw']) - 200) < 1e-8
assert abs(float(eval(repr(o), d).output_map(
structure=structure, vasp=a)['encutgw']) - 200) < 1e-8
assert abs(float(loads(dumps(o)).output_map(
structure=structure, vasp=a)['encutgw']) - 200) < 1e-8
assert abs(eval(repr(o), d).value - 200 * eV) < 1e-8
assert abs(loads(dumps(o)).value - 200 * eV) < 1e-8
assert eval(repr(o), d).value.units == hartree
assert loads(dumps(o)).value.units == hartree
