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 getincar(incar): from pylada.vasp import read_incar vasp = read_incar(incar) @tools.layer def new(job): @tools.cellcall(job.params["call"]) def func(job): job.params['vasp'] = vasp job.params["call"] = func yield job return new
def test_read_from_incar_with_unknowns_params(tmpdir, vasp, structure):
from pylada.vasp import read_incar
vasp.write_incar(path=str(tmpdir.join('INCAR')), structure=structure)
with open(str(tmpdir.join('INCAR')), 'a') as file:
file.write('\nSOMETHing = 0.5\n')
other = read_incar(str(tmpdir.join('INCAR')))
check_vasp(other)
assert 'something' in other._input
assert isinstance(other.something, float)
assert abs(other.something - 0.5) < 1e-8
def test_read_from_incar_with_unknowns_params(tmpdir, vasp, structure):
from pylada.vasp import read_incar
vasp.write_incar(path=str(tmpdir.join("INCAR")), structure=structure)
with open(str(tmpdir.join("INCAR")), "a") as file:
file.write("\nSOMETHing = 0.5\n")
other = read_incar(str(tmpdir.join("INCAR")))
check_vasp(other)
assert "something" in other._input
assert isinstance(other.something, float)
assert abs(other.something - 0.5) < 1e-8
def compute(outdir, common, **kwargs):
from pylada.vasp import read_incar
from pylada.crystal import read
import os
structure = read.poscar(kwargs["poscar"])
vasp = read_incar(kwargs["incar"])
for pot in kwargs["potcar"]:
vasp.add_specie = pot.split("_")[0], os.path.join(
os.environ["PAW"], pot)
if "writechg" in kwargs.keys():
vasp.lcharg = kwargs["writechg"]
else:
vasp.lcharg = True
if "writewave" in kwargs.keys():
vasp.lwave = kwargs["writewave"]
else:
vasp.lwave = True
if "writeoptics" in kwargs.keys():
vasp.loptics = kwargs["writeoptics"]
else:
vasp.loptics = False
if "optcell" in kwargs.keys():
if kwargs["optcell"] is not None:
writeoptcell(outdir, kwargs["optcell"])
if "chgcar" in kwargs.keys():
copyorlinkfile(outdir, "CHGCAR", kwargs["chgcar"], "cp")
if "wavecar" in kwargs.keys():
copyorlinkfile(outdir, "WAVECAR", kwargs["wavecar"], "cp")
if "dfile" in kwargs.keys():
if not os.path.exists(os.path.join(outdir, "DFILE")):
with open(os.path.join(outdir, "DFILE"), "w") as f:
f.write(kwargs["dfile"])
if "kpointscell" in kwargs.keys():
import numpy as np
kpoint = "Automatic generation\n0\nMonkhorst\n%d %d %d\n0 0 0"
diag = np.diag(structure.cell)
tmp = np.array(kwargs["kpointscell"]) // diag
tmp[tmp == 0] = 1
vasp.kpoints = kpoint % (tuple(tmp))
else:
if hasattr(vasp, "kspacing"):
vasp.write_kpoints = nowritekpoints
else:
with open(kwargs["kpoints"], "r") as rfile:
vasp.kpoints = rfile.read()
try:
result = vasp(structure, outdir=outdir, comm=common)
except Exception as e:
print("path:" + outdir)
raise e
return result
def vasp(name, incar): """ return a function to set a new vasp form incar @param inputlayer : a function created by front layer @param names : layer name @param incar : path of incar for loading """ from pylada.vasp import read_incar vasp = read_incar(incar) @tools.layer def new(job): @tools.cellcall(job.params["call"]) def func(job): job.params["vasp"] = vasp t_job = job / name t_job.params["call"] = func return [t_job] return new
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_read_from_incar(tmpdir, vasp, structure):
from pylada.vasp import read_incar
vasp.write_incar(path=str(tmpdir.join('INCAR')), structure=structure)
other = read_incar(str(tmpdir.join('INCAR')))
check_vasp(other)
def test_read_from_incar(tmpdir, vasp, structure):
from pylada.vasp import read_incar
vasp.write_incar(path=str(tmpdir.join("INCAR")), structure=structure)
other = read_incar(str(tmpdir.join("INCAR")))
check_vasp(other)