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_system(): from pylada.crystal.cppwrappers import Structure from pylada.vasp import Vasp a = Vasp() b = Structure() assert a.system is None assert a._input['system'].keyword == 'system' assert a._input['system'].output_map(vasp=a, structure=b) is None a.system = 'system' assert a.system == 'system' assert 'system' in a._input['system'].output_map(vasp=a, structure=b) assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'system' b.name = 'hello' assert 'system' in a._input['system'].output_map(vasp=a, structure=b) assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'system: hello' a.system = None assert a.system is None assert 'system' in a._input['system'].output_map(vasp=a, structure=b) assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'hello' a.system = None assert a.system is None assert 'system' in a._input['system'].output_map(vasp=a, structure=b) assert a._input['system'].output_map(vasp=a, structure=b)['system'] == 'hello'
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_system():
from pylada.crystal import Structure
from pylada.vasp import Vasp
a = Vasp()
b = Structure()
assert a.system is None
assert a._input['system'].keyword == 'system'
assert a._input['system'].output_map(vasp=a, structure=b) is None
a.system = 'system'
assert a.system == 'system'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'system'
b.name = 'hello'
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(
vasp=a, structure=b)['system'] == 'system: hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'hello'
a.system = None
assert a.system is None
assert 'system' in a._input['system'].output_map(vasp=a, structure=b)
assert a._input['system'].output_map(vasp=a,
structure=b)['system'] == 'hello'
def test_alias():
from pylada.vasp import Vasp
from pylada.error import ValueError
a = Vasp()
assert a.ismear is None
assert a._input['ismear'].keyword == 'ismear'
assert a._input['ismear'].output_map() is None
map = a._input['ismear'].aliases
assert len(map) != 0
for i, items in map.items():
for item in items:
a.ismear = item
assert a.ismear == items[0]
assert 'ismear' in a._input['ismear'].output_map()
assert a._input['ismear'].output_map()['ismear'] == str(i)
a.ismear = i
assert a.ismear == items[0]
a.ismear = str(i)
assert a.ismear == items[0]
try:
a.lmaxmix = 'a'
except ValueError:
pass
else:
raise Exception()
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 vasp(Specie):
from pylada.vasp import Vasp
from pylada.vasp.specie import U, nlep
vasp = Vasp()
vasp.species = {'A': Specie([]), 'B': Specie([]), 'X': Specie([])}
for key in list(vasp._input.keys()):
if key not in ['ldau']:
del vasp._input[key]
return vasp
def vasp(Specie):
from pylada.vasp import Vasp
from pylada.vasp.specie import U, nlep
vasp = Vasp()
vasp.species = {'A': Specie([]), 'B': Specie([]), 'X': Specie([])}
for key in list(vasp._input.keys()):
if key not in ['ldau']:
del vasp._input[key]
return vasp
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.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(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 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_choice():
from pickle import loads, dumps
from pylada.vasp import Vasp
a = Vasp()
assert a.ispin is None
assert a._input['ispin'].keyword == 'ispin'
assert a._input['ispin'].output_map() is None
a.ispin = 1
assert a.ispin == 1
assert 'ispin' in a._input['ispin'].output_map()
assert a._input['ispin'].output_map()['ispin'] == '1'
a.ispin = 2
assert a.ispin == 2
assert 'ispin' in a._input['ispin'].output_map()
assert a._input['ispin'].output_map()['ispin'] == '2'
a.ispin = None
assert a.ispin is None
assert a._input['ispin'].keyword == 'ispin'
assert a._input['ispin'].output_map() is None
try:
a.ispin = 5
except:
pass
else:
raise RuntimeError()
a.ispin = '1'
assert a.ispin == 1
a.ispin = '2'
assert a.ispin == 2
try:
a.ispin = '3'
except:
pass
else:
raise RuntimeError()
a.ispin = None
o = a._input['ispin']
d = {'ChoiceKeyword': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map() is None
assert repr(loads(dumps(o))) == repr(o)
a.ispin = 2
o = a._input['ispin']
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map()['ispin'] == '2'
assert repr(loads(dumps(o))) == repr(o)
def test_nelect():
from os.path import dirname
from pickle import loads, dumps
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__))
assert a.extraelectron is None
assert a._input['extraelectron'].output_map() is None
assert a._input['nelect'].output_map() is None
a.extraelectron = 0
assert a.extraelectron == 0
assert a.nelect is None
assert a._input['extraelectron'].output_map() is None
assert a._input['nelect'].output_map() is None
a.extraelectron = 1
assert a.extraelectron == 1
assert a.nelect is None
assert 'nelect' in a._input['extraelectron'].output_map(
vasp=a, structure=structure)
assert abs(
float(a._input['extraelectron'].output_map(vasp=a, structure=structure)
['nelect']) - 9.0) < 1e-8
assert a._input['nelect'].output_map() is None
a.nelect = 1
a.extraelectron = -1
assert a.extraelectron == -1
assert a.nelect is None
assert 'nelect' in a._input['extraelectron'].output_map(
vasp=a, structure=structure)
assert abs(
float(a._input['extraelectron'].output_map(vasp=a, structure=structure)
['nelect']) - 7.0) < 1e-8
assert a._input['nelect'].output_map() is None
o = a._input['extraelectron']
d = {'ExtraElectron': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert abs(
float(
eval(repr(o), d).output_map(vasp=a, structure=structure)['nelect'])
- 7.0) < 1e-8
assert repr(loads(dumps(o))) == repr(o)
a.nelect = 8
assert a.nelect == 8
assert a.extraelectron is None
assert 'nelect' in a._input['nelect'].output_map()
assert abs(float(a._input['nelect'].output_map()['nelect']) - 8.0) < 1e-8
assert a._input['extraelectron'].output_map() is None
o = a._input['nelect']
d = {'NElect': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert abs(float(eval(repr(o), d).output_map()['nelect']) - 8.0) < 1e-8
assert repr(loads(dumps(o))) == repr(o)
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 vasp():
from pylada.vasp import Vasp
vasp = Vasp()
for key in list(vasp._input.keys()):
if key not in ['isif', 'nsw', 'ibrion', 'relaxation']:
del vasp._input[key]
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 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_alias():
from pylada.vasp import Vasp
from pylada.error import ValueError
a = Vasp()
assert a.ismear is None
assert a._input['ismear'].keyword == 'ismear'
assert a._input['ismear'].output_map() is None
map = a._input['ismear'].aliases
assert len(map) != 0
for i, items in map.items():
for item in items:
a.ismear = item
assert a.ismear == items[0]
assert 'ismear' in a._input['ismear'].output_map()
assert a._input['ismear'].output_map()['ismear'] == str(i)
a.ismear = i
assert a.ismear == items[0]
a.ismear = str(i)
assert a.ismear == items[0]
try:
a.lmaxmix = 'a'
except ValueError:
pass
else:
raise Exception()
def test_nelect():
from os.path import dirname
from pickle import loads, dumps
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__))
assert a.extraelectron is None
assert a._input['extraelectron'].output_map() is None
assert a._input['nelect'].output_map() is None
a.extraelectron = 0
assert a.extraelectron == 0
assert a.nelect is None
assert a._input['extraelectron'].output_map() is None
assert a._input['nelect'].output_map() is None
a.extraelectron = 1
assert a.extraelectron == 1
assert a.nelect is None
assert 'nelect' in a._input['extraelectron'].output_map(vasp=a, structure=structure)
assert abs(float(a._input['extraelectron'].output_map(
vasp=a, structure=structure)['nelect']) - 9.0) < 1e-8
assert a._input['nelect'].output_map() is None
a.nelect = 1
a.extraelectron = -1
assert a.extraelectron == -1
assert a.nelect is None
assert 'nelect' in a._input['extraelectron'].output_map(vasp=a, structure=structure)
assert abs(float(a._input['extraelectron'].output_map(
vasp=a, structure=structure)['nelect']) - 7.0) < 1e-8
assert a._input['nelect'].output_map() is None
o = a._input['extraelectron']
d = {'ExtraElectron': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert abs(float(eval(repr(o), d).output_map(
vasp=a, structure=structure)['nelect']) - 7.0) < 1e-8
assert repr(loads(dumps(o))) == repr(o)
a.nelect = 8
assert a.nelect == 8
assert a.extraelectron is None
assert 'nelect' in a._input['nelect'].output_map()
assert abs(float(a._input['nelect'].output_map()['nelect']) - 8.0) < 1e-8
assert a._input['extraelectron'].output_map() is None
o = a._input['nelect']
d = {'NElect': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert abs(float(eval(repr(o), d).output_map()['nelect']) - 8.0) < 1e-8
assert repr(loads(dumps(o))) == repr(o)
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 __call__(self, structure, outdir=None, **kwargs ):
from copy import deepcopy
from os import getcwd
from os.path import join
from pylada.misc import RelativePath
from pylada.error import ExternalRunFailed
from pylada.vasp.extract import Extract
from pylada.vasp import Vasp
from pylada.vasp.relax import Relax
# make this function stateless.
structure_ = structure.copy()
outdir = getcwd() if outdir is None else RelativePath(outdir).path
############ Calc 1 ###############
name = self.names[0]
## functional for Calc 1
relax = Relax(copy=deepcopy(self.vasp))
relax.relaxation = "volume ionic cellshape"
relax.maxiter = 10
relax.keep_steps = True
relax.first_trial = { "kpoints": "\n0\nAuto\n10", "encut": 0.9 }
## end of the functional
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done run it
output = relax(structure_, outdir=fulldir, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
############ Calc 2 ###############
name = self.names[1]
## functional for Calc 2
wfn = Vasp(copy=deepcopy(self.vasp))
wfn.isym = 1
wfn.ismear = -5
wfn.nbands=24*len(structure_)
wfn.kpoints="\n0\nGamma\n4 4 4\n0. 0. 0.\n"
## end of the functional
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done, run it
output = wfn(structure_, outdir=fulldir, restart=output, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
return self.Extract(fulldir)
def test_bool():
from pickle import loads, dumps
from pylada.vasp import Vasp
a = Vasp()
assert a._input['addgrid'].keyword == 'addgrid'
assert a._input['addgrid'].output_map() is None
assert a.addgrid is None
a.addgrid = False
assert a.addgrid is False
assert 'addgrid' in a._input['addgrid'].output_map()
assert a._input['addgrid'].output_map()['addgrid'] == '.FALSE.'
a.addgrid = True
assert a.addgrid is True
assert 'addgrid' in a._input['addgrid'].output_map()
assert a._input['addgrid'].output_map()['addgrid'] == '.TRUE.'
a.addgrid = None
assert a._input['addgrid'].keyword == 'addgrid'
assert a._input['addgrid'].output_map() is None
a.addgrid = 0
assert a.addgrid is False
a.addgrid = False
o = a._input['addgrid']
d = {'BoolKeyword': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map()['addgrid'] == '.FALSE.'
assert repr(loads(dumps(o))) == repr(o)
a.addgrid = True
o = a._input['addgrid']
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map()['addgrid'] == '.TRUE.'
assert repr(loads(dumps(o))) == repr(o)
a.addgrid = None
o = a._input['addgrid']
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map() is None
assert repr(loads(dumps(o))) == repr(o)
def test():
from collections import namedtuple
from pickle import loads, dumps
from pylada.vasp import Vasp
Restart = namedtuple('Restart', ['success', 'lmaxmix', 'lvhar'])
a = Vasp()
o = a._input['lsorbit']
d = {'LSorbit': o.__class__}
assert a.lsorbit is None
assert a.nonscf == False
assert a._input['lsorbit'].keyword == 'lsorbit'
assert a._input['nonscf'].keyword is None
assert o.output_map(vasp=a) is None
assert eval(repr(o), d).output_map(vasp=a) is None
assert eval(repr(o), d).value is None
assert loads(dumps(o)).value is None
a.lsorbit = True
assert a.nonscf
assert a.lsorbit
try:
a._input['lsorbit'].output_map(vasp=a)
except ValueError:
pass
else:
raise Exception()
a.restart = Restart(False, 7, False)
try:
a._input['lsorbit'].output_map(vasp=a)
except ValueError:
pass
else:
raise Exception()
a.restart = Restart(True, 7, False)
assert 'lsorbit' in o.output_map(vasp=a)
assert o.output_map(vasp=a)['lsorbit'] == '.TRUE.'
assert a.lmaxmix == 7
a.lmaxmix = 5
a.restart = Restart(True, 6, False)
assert 'lsorbit' in o.output_map(vasp=a)
assert o.output_map(vasp=a)['lsorbit'] == '.TRUE.'
assert a.lmaxmix == 6
assert loads(dumps(o)).value is True
assert eval(repr(o), d).value is True
def test_bool():
from pickle import loads, dumps
from pylada.vasp import Vasp
a = Vasp()
assert a._input['addgrid'].keyword == 'addgrid'
assert a._input['addgrid'].output_map() is None
assert a.addgrid is None
a.addgrid = False
assert a.addgrid is False
assert 'addgrid' in a._input['addgrid'].output_map()
assert a._input['addgrid'].output_map()['addgrid'] == '.FALSE.'
a.addgrid = True
assert a.addgrid is True
assert 'addgrid' in a._input['addgrid'].output_map()
assert a._input['addgrid'].output_map()['addgrid'] == '.TRUE.'
a.addgrid = None
assert a._input['addgrid'].keyword == 'addgrid'
assert a._input['addgrid'].output_map() is None
a.addgrid = 0
assert a.addgrid is False
a.addgrid = False
o = a._input['addgrid']
d = {'BoolKeyword': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map()['addgrid'] == '.FALSE.'
assert repr(loads(dumps(o))) == repr(o)
a.addgrid = True
o = a._input['addgrid']
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map()['addgrid'] == '.TRUE.'
assert repr(loads(dumps(o))) == repr(o)
a.addgrid = None
o = a._input['addgrid']
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map() is None
assert repr(loads(dumps(o))) == repr(o)
def test_lsorbit():
from collections import namedtuple
from pickle import loads, dumps
from pylada.vasp import Vasp
Restart = namedtuple('Restart', ['success', 'lmaxmix', 'lvhar'])
a = Vasp()
o = a._input['lsorbit']
d = {'LSorbit': o.__class__}
assert a.lsorbit is None
assert a.nonscf == False
assert a._input['lsorbit'].keyword == 'lsorbit'
assert a._input['nonscf'].keyword is None
assert o.output_map(vasp=a) is None
assert eval(repr(o), d).output_map(vasp=a) is None
assert eval(repr(o), d).value is None
assert loads(dumps(o)).value is None
a.lsorbit = True
assert a.nonscf
assert a.lsorbit
try:
a._input['lsorbit'].output_map(vasp=a)
except ValueError:
pass
else:
raise Exception()
a.restart = Restart(False, 7, False)
try:
a._input['lsorbit'].output_map(vasp=a)
except ValueError:
pass
else:
raise Exception()
a.restart = Restart(True, 7, False)
assert 'lsorbit' in o.output_map(vasp=a)
assert o.output_map(vasp=a)['lsorbit'] == '.TRUE.'
assert a.lmaxmix == 7
a.lmaxmix = 5
a.restart = Restart(True, 6, False)
assert 'lsorbit' in o.output_map(vasp=a)
assert o.output_map(vasp=a)['lsorbit'] == '.TRUE.'
assert a.lmaxmix == 6
assert loads(dumps(o)).value is True
assert eval(repr(o), d).value is True
def test_copy_files():
from tempfile import mkdtemp
from shutil import rmtree
from os import makedirs
from os.path import exists, join
from pylada.vasp import Vasp
directory = mkdtemp()
if exists(directory):
rmtree(directory)
makedirs(directory)
makedirs(join(directory, 'indir'))
with open(join(directory, 'indir', 'infile'), 'w') as file:
file.write('hello')
with open(join(directory, 'indir', 'this'), 'w') as file:
file.write('hello')
with open(join(directory, 'indir', 'that'), 'w') as file:
file.write('hello')
try:
vasp = Vasp()
# Shouldn't copy yet
vasp._copy_additional_files(outdir=join(directory, 'outdir'))
assert not exists(join(directory, 'outdir', 'infile'))
assert not exists(join(directory, 'outdir', 'this'))
assert not exists(join(directory, 'outdir', 'that'))
# Now should copy
vasp.files = join(directory, 'indir', 'infile')
vasp._copy_additional_files(outdir=join(directory, 'outdir'))
assert exists(join(directory, 'outdir', 'infile'))
assert not exists(join(directory, 'outdir', 'this'))
assert not exists(join(directory, 'outdir', 'that'))
# Do it again, should be fine
vasp._copy_additional_files(outdir=join(directory, 'outdir'))
assert exists(join(directory, 'outdir', 'infile'))
# Copy mutliple files
vasp.files = [
join(directory, 'indir', u) for u in ['infile', 'this', 'that']
]
vasp._copy_additional_files(outdir=join(directory, 'outdir'))
assert exists(join(directory, 'outdir', 'infile'))
assert exists(join(directory, 'outdir', 'this'))
assert exists(join(directory, 'outdir', 'that'))
finally:
if directory != '/tmp/test':
rmtree(directory)
def test():
from collections import namedtuple
from pickle import loads, dumps
from numpy import all, abs, array
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.specie import U, nlep
import pylada
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, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
a = Vasp()
Specie = namedtuple('Specie', ['U'])
a.species = {'A': Specie([]), 'B': Specie([]), 'X': Specie([])}
pylada.vasp_has_nlep = False
o = a._input['ldau']
d = {'LDAU': o.__class__}
assert a.ldau == True
assert o.output_map(vasp=a, structure=structure) is None
assert eval(repr(o), d)._value == True
assert eval(repr(o), d).keyword == 'LDAU'
assert loads(dumps(o)).keyword == 'LDAU'
assert loads(dumps(o))._value
# now disables U.
a.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([]), 'X': Specie([])}
a.ldau = False
assert a.ldau == False
print o
assert o.output_map(vasp=a) is None
# now prints U
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(
abs(array(map['LDUU'].split(), dtype='float64') - [0.5, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUL'].split(), dtype='float64') - [0, -1, -1]) < 1e-8)
a.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 1, 0.6)]),
'X': Specie([])
}
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(
abs(array(map['LDUU'].split(), dtype='float64') -
[0.5, 0, 0.6]) < 1e-8)
assert all(
abs(array(map['LDUL'].split(), dtype='float64') - [0, -1, 1]) < 1e-8)
# now tries NLEP
pylada.vasp_has_nlep = True
a.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 1, -1.0)]),
'X': Specie([])
}
a.ldau = False
assert a.ldau == False
assert o.output_map(vasp=a) is None
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(
abs(array(map['LDUL1'].split(), dtype='float64') - [0, -1, 0]) < 1e-8)
assert all(
abs(array(map['LDUU1'].split(), dtype='float64') -
[0.5, 0, -0.5]) < 1e-8)
assert all(
abs(array(map['LDUJ1'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO1'].split(), dtype='float64') - [1, 1, 1]) < 1e-8)
assert all(
abs(array(map['LDUL2'].split(), dtype='float64') - [-1, -1, 1]) < 1e-8)
assert all(
abs(array(map['LDUU2'].split(), dtype='float64') -
[0, 0, -1.0]) < 1e-8)
assert all(
abs(array(map['LDUJ2'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO2'].split(), dtype='float64') - [1, 1, 2]) < 1e-8)
a.species = {
'A': Specie([U(2, 0, 0.5)]),
'B': Specie([U(2, 0, -0.5), nlep(2, 2, -1.0, -3.0)]),
'X': Specie([])
}
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(
abs(array(map['LDUL1'].split(), dtype='float64') - [0, -1, 0]) < 1e-8)
assert all(
abs(array(map['LDUU1'].split(), dtype='float64') -
[0.5, 0, -0.5]) < 1e-8)
assert all(
abs(array(map['LDUJ1'].split(), dtype='float64') - [0, 0, 0]) < 1e-8)
assert all(
abs(array(map['LDUO1'].split(), dtype='float64') - [1, 1, 1]) < 1e-8)
assert all(
abs(array(map['LDUL2'].split(), dtype='float64') - [-1, -1, 2]) < 1e-8)
assert all(
abs(array(map['LDUU2'].split(), dtype='float64') -
[0, 0, -1.0]) < 1e-8)
assert all(
abs(array(map['LDUJ2'].split(), dtype='float64') -
[0, 0, -3.0]) < 1e-8)
assert all(
abs(array(map['LDUO2'].split(), dtype='float64') - [1, 1, 3]) < 1e-8)
def test():
from pickle import loads, dumps
from pylada.vasp import Vasp
from pylada.error import ValueError
a = Vasp()
for key in a._input.keys():
if key not in ['isif', 'nsw', 'ibrion', 'relaxation']:
del a._input[key]
assert a.relaxation == 'static'
assert len(a.output_map(vasp=a)) == 1
assert a.output_map(vasp=a)['ibrion'] == str(-1)
a.relaxation = 'cellshape'
assert a.relaxation == 'cellshape'
assert a.isif == 5
assert a.nsw == 50
assert a.ibrion == 2
assert len(a.output_map(vasp=a)) == 3
assert a.output_map(vasp=a)['ibrion'] == str(2)
assert a.output_map(vasp=a)['isif'] == str(5)
assert a.output_map(vasp=a)['nsw'] == str(50)
a = loads(dumps(a))
assert len(a.output_map(vasp=a)) == 3
assert a.output_map(vasp=a)['ibrion'] == str(2)
assert a.output_map(vasp=a)['isif'] == str(5)
assert a.output_map(vasp=a)['nsw'] == str(50)
a.relaxation = 'cellshape volume'
a.nsw = 25
assert a.relaxation == 'cellshape volume'
assert a.isif == 6
assert a.nsw == 25
assert a.ibrion == 2
assert len(a.output_map(vasp=a)) == 3
assert a.output_map(vasp=a)['ibrion'] == str(2)
assert a.output_map(vasp=a)['isif'] == str(6)
assert a.output_map(vasp=a)['nsw'] == str(25)
a.relaxation = 'ions'
assert a.relaxation == 'ionic'
assert a.isif == 2
a.relaxation = 'ionic'
assert a.relaxation == 'ionic'
assert a.isif == 2
a.relaxation = 'cellshape, volume ions'
print a.relaxation
assert a.relaxation == 'cellshape ionic volume'
assert a.isif == 3
a.relaxation = 'cellshape, ionic'
assert a.relaxation == 'cellshape ionic'
assert a.isif == 4
a.relaxation = 'volume'
assert a.relaxation == 'volume'
assert a.isif == 7
a.relaxation = 'static'
assert a.ibrion == -1
assert a.nsw == 0
assert a.isif == 2
try: a.relaxation = 'ions, volume'
except ValueError: pass
else: raise Exception
def test_magmom():
from pickle import loads, dumps
from pylada.crystal.cppwrappers import Structure
from pylada.vasp import 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")
for atom in structure:
if atom.type == 'Mg': atom.magmom = -1e0
vasp = Vasp()
vasp.magmom = None
assert vasp.magmom is None
assert vasp._input['magmom'].keyword == 'MAGMOM'
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure) is None
# ispin == 1
vasp.magmom = True
vasp.ispin = 1
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure) is None
# ispins == 2, magmom == False
vasp.ispin = 2
vasp.magmom = None
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure) is None
vasp.magmom = False
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure) is None
# now for real print
vasp.magmom = True
assert 'MAGMOM' in vasp._input['magmom'].output_map(vasp=vasp, structure=structure)
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure)['MAGMOM'] == '4*-1.00 2*0.00 8*0.00'
# now print a string directly.
vasp.magmom = 'hello'
assert vasp.magmom == 'hello'
assert 'MAGMOM' in vasp._input['magmom'].output_map(vasp=vasp, structure=structure)
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure)['MAGMOM'] == 'hello'
# check repr
assert repr(vasp._input['magmom']) == "Magmom(value='hello')"
# check pickling
assert repr(loads(dumps(vasp._input['magmom']))) == "Magmom(value='hello')"
# more tests.
for atom, mag in zip(structure, [1, -1, 1, 1]):
if atom.type == 'Mg': atom.magmom = mag
for atom, mag in zip(structure, [0.5, 0.5]):
if atom.type == 'Al': atom.magmom = mag
vasp.magmom = True
assert 'MAGMOM' in vasp._input['magmom'].output_map(vasp=vasp, structure=structure)
assert vasp._input['magmom'].output_map(vasp=vasp, structure=structure)['MAGMOM'] == '1.00 -1.00 2*1.00 2*0.00 8*0.00'
def __call__(self, structure, outdir=None, vasp=None, **kwargs):
from copy import deepcopy
from os import getcwd
from os.path import join
from pylada.misc import RelativePath
from pylada.error import ExternalRunFailed
from pylada.vasp.extract import Extract, MassExtract
from pylada.vasp import Vasp
from pylada.vasp.relax import Relax
# make this function stateless.
structure_ = structure.copy()
outdir = getcwd() if outdir is None else RelativePath(outdir).path
############ Calc 1 ###############
name = self.names[0]
## functional for Calc 1
relax = Relax(copy=vasp)
relax.relaxation = "volume ionic cellshape"
relax.maxiter = 10
relax.keep_steps = True
relax.first_trial = {"kpoints": "\n0\nAuto\n10", "encut": 0.9}
## end of the functional
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done run it
output = relax(structure_, outdir=fulldir, restart=None, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
############ Calc 2 ###############
name = self.names[1]
## functional for Calc 2
final = Vasp(copy=vasp)
final.nbands = 24 * len(structure_)
final.kpoints = "\n0\nGamma\n2 2 2\n0. 0. 0.\n"
final.loptics = True
final.relaxation = "static"
## end of the functional
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done, run it
output = final(structure_, outdir=fulldir, restart=output, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
############## GW Loop ########################
for name in self.names[2:]:
gw = Vasp(copy=vasp)
gw.kpoints = "\n0\nGamma\n2 2 2\n0. 0. 0.\n"
gw.nbands = 24 * len(structure_)
gw.lcharg = True
gw.add_keyword('nelm', 1)
gw.add_keyword('algo', 'gw')
gw.add_keyword('LMAXFOCKAE', 4)
gw.add_keyword('nomega', 64)
gw.add_keyword('precfock', 'fast')
gw.add_keyword('encutgw', 50)
gw.add_keyword('encutlf', 50)
gw.add_keyword('lrpa', False)
gw.add_keyword('nkred', 2)
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done, run it
output = gw(structure_, outdir=fulldir, restart=output, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
#########################
return self.Extract(fulldir)
def test_typed():
from pylada.vasp import Vasp
from pylada.error import ValueError
a = Vasp()
assert a.nbands is None
assert a._input['nbands'].keyword == 'nbands'
assert a._input['nbands'].output_map() is None
a.nbands = 50
assert a.nbands == 50
assert 'nbands' in a._input['nbands'].output_map()
assert a._input['nbands'].output_map()['nbands'] == str(a.nbands)
a.nbands = '51'
assert a.nbands == 51
assert 'nbands' in a._input['nbands'].output_map()
assert a._input['nbands'].output_map()['nbands'] == str(a.nbands)
a.nbands = None
assert a.nbands is None
assert a._input['nbands'].output_map() is None
try:
a.nbands = 'a'
except ValueError:
pass
else:
raise Exception()
assert a.smearings is None
assert a._input['smearings'].keyword == 'smearings'
assert a._input['smearings'].output_map() is None
a.smearings = [1.5, 1.0, 0.5]
assert len(a.smearings) == 3
assert all(abs(i - v) < 1e-8 for i, v in zip(a.smearings, [1.5, 1.0, 0.5]))
assert 'smearings' in a._input['smearings'].output_map()
assert all(
abs(float(i) - v) < 1e-8 for i, v in zip(
a._input['smearings'].output_map()['smearings'].split(),
[1.5, 1.0, 0.5]))
a.smearings = ['1.2', '0.2']
assert len(a.smearings) == 2
assert all(abs(i - v) < 1e-8 for i, v in zip(a.smearings, [1.2, 0.2]))
assert 'smearings' in a._input['smearings'].output_map()
assert all(
abs(float(i) - v) < 1e-8 for i, v in zip(
a._input['smearings'].output_map()['smearings'].split(),
[1.2, 0.2]))
a.smearings = '1.3 0.3'
assert len(a.smearings) == 2
assert all(abs(i - v) < 1e-8 for i, v in zip(a.smearings, [1.3, 0.3]))
assert 'smearings' in a._input['smearings'].output_map()
assert all(
abs(float(i) - v) < 1e-8 for i, v in zip(
a._input['smearings'].output_map()['smearings'].split(),
[1.3, 0.3]))
a.smearings = '1.3, 0.3'
assert len(a.smearings) == 2
assert all(abs(i - v) < 1e-8 for i, v in zip(a.smearings, [1.3, 0.3]))
a.smearings = '1.3; 0.3'
assert len(a.smearings) == 2
assert all(abs(i - v) < 1e-8 for i, v in zip(a.smearings, [1.3, 0.3]))
a.smearings = None
assert a.smearings is None
assert a._input['smearings'].output_map() is None
try:
a.smearings = 5.5
except ValueError:
pass
else:
raise Exception()
try:
a.smearings = [5.5, 'a']
except ValueError:
pass
else:
raise Exception()
def test_ediffg():
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['ediffg']
d = {'Ediffg': o.__class__}
assert a.ediffg is None
assert a.ediffg_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 == 'ediffg'
assert loads(dumps(o)).output_map() is None
a.ediffg_per_atom = 1e-5
a.ediffg = 2e-4
assert abs(a.ediffg - 2e-4) < 1e-8
assert a.ediffg_per_atom is None
assert abs(float(o.output_map(structure=structure)['ediffg']) - a.ediffg) < a.ediffg * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediffg']) - a.ediffg) < a.ediffg * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediffg']) - a.ediffg) < a.ediffg * 1e-2
a.ediffg_per_atom = 1e-5
a.ediffg = -2e-4
assert abs(a.ediffg + 2e-4) < 1e-8
assert a.ediffg_per_atom is None
assert abs(float(o.output_map(structure=structure)['ediffg']) - a.ediffg) < -a.ediffg * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediffg']) - a.ediffg) < -a.ediffg * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediffg']) - a.ediffg) < -a.ediffg * 1e-2
a.ediffg = 2e-4
a.ediffg_per_atom = 2e-4
o = a._input['ediffg_per_atom']
d = {'EdiffgPerAtom': o.__class__}
assert a.ediffg is None
assert abs(a.ediffg_per_atom - 2e-4) < 1e-8
assert abs(float(o.output_map(structure=structure)['ediffg']) - 2e-4*N) < 2e-4 * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediffg']) - 2e-4*N) < 2e-4 * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediffg']) - 2e-4*N) < 2e-4 * 1e-2
a.ediffg = 2e-4
a.ediffg_per_atom = -2e-4
assert a.ediffg is None
assert abs(a.ediffg_per_atom + 2e-4) < 1e-8
assert abs(float(o.output_map(structure=structure)['ediffg']) + 2e-4) < 2e-4 * 1e-2
assert abs(float(eval(repr(o), d).output_map(structure=structure)['ediffg']) + 2e-4) < 2e-4 * 1e-2
assert abs(float(loads(dumps(o)).output_map(structure=structure)['ediffg']) + 2e-4) < 2e-4 * 1e-2
a.ediffg_per_atom = None
assert a.ediffg is None
assert a.ediffg_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 == 'ediffg'
assert loads(dumps(o)).output_map() is None
a.ediffg = 1e-4
a.ediffg_per_atom = None
assert abs(a.ediffg-1e-4) < 1e-8
assert a.ediffg_per_atom is None
a.ediffg_per_atom = 1e-4
a.ediffg = None
assert abs(a.ediffg_per_atom-1e-4) < 1e-8
assert a.ediffg is None
def test_typed(): from pylada.vasp import Vasp from pylada.error import ValueError a = Vasp() assert a.nbands is None assert a._input['nbands'].keyword == 'nbands' assert a._input['nbands'].output_map() is None a.nbands = 50 assert a.nbands == 50 assert 'nbands' in a._input['nbands'].output_map() assert a._input['nbands'].output_map()['nbands'] == str(a.nbands) a.nbands = '51' assert a.nbands == 51 assert 'nbands' in a._input['nbands'].output_map() assert a._input['nbands'].output_map()['nbands'] == str(a.nbands) a.nbands = None assert a.nbands is None assert a._input['nbands'].output_map() is None try: a.nbands = 'a' except ValueError: pass else: raise Exception() assert a.smearings is None assert a._input['smearings'].keyword == 'smearings' assert a._input['smearings'].output_map() is None a.smearings = [1.5, 1.0, 0.5] assert len(a.smearings) == 3 assert all(abs(i-v) < 1e-8 for i, v in zip(a.smearings, [1.5, 1.0, 0.5])) assert 'smearings' in a._input['smearings'].output_map() assert all(abs(float(i)-v) < 1e-8 for i, v in zip(a._input['smearings'].output_map()['smearings'].split(), [1.5, 1.0, 0.5])) a.smearings = ['1.2', '0.2'] assert len(a.smearings) == 2 assert all(abs(i-v) < 1e-8 for i, v in zip(a.smearings, [1.2, 0.2])) assert 'smearings' in a._input['smearings'].output_map() assert all(abs(float(i)-v) < 1e-8 for i, v in zip(a._input['smearings'].output_map()['smearings'].split(), [1.2, 0.2])) a.smearings = '1.3 0.3' assert len(a.smearings) == 2 assert all(abs(i-v) < 1e-8 for i, v in zip(a.smearings, [1.3, 0.3])) assert 'smearings' in a._input['smearings'].output_map() assert all(abs(float(i)-v) < 1e-8 for i, v in zip(a._input['smearings'].output_map()['smearings'].split(), [1.3, 0.3])) a.smearings = '1.3, 0.3' assert len(a.smearings) == 2 assert all(abs(i-v) < 1e-8 for i, v in zip(a.smearings, [1.3, 0.3])) a.smearings = '1.3; 0.3' assert len(a.smearings) == 2 assert all(abs(i-v) < 1e-8 for i, v in zip(a.smearings, [1.3, 0.3])) a.smearings = None assert a.smearings is None assert a._input['smearings'].output_map() is None try: a.smearings = 5.5 except ValueError: pass else: raise Exception() try: a.smearings = [5.5, 'a'] except ValueError: pass else: raise Exception()
def test():
from collections import namedtuple
from pickle import loads, dumps
from numpy import all, abs, array
from pylada.crystal import Structure
from pylada.vasp import Vasp
from pylada.vasp.specie import U, nlep
import pylada
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, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
a = Vasp()
Specie = namedtuple('Specie', ['U'])
a.species = {'A': Specie([]), 'B': Specie([]), 'X': Specie([])}
pylada.vasp_has_nlep = False
o = a._input['ldau']
d = {'LDAU': o.__class__}
assert a.ldau == True
assert o.output_map(vasp=a, structure=structure) is None
assert eval(repr(o), d)._value == True
assert eval(repr(o), d).keyword == 'LDAU'
assert loads(dumps(o)).keyword == 'LDAU'
assert loads(dumps(o))._value
# now disables U.
a.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([]), 'X': Specie([])}
a.ldau = False
assert a.ldau == False
print o
assert o.output_map(vasp=a) is None
# now prints U
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(abs(array(map['LDUU'].split(), dtype='float64')-[0.5, 0, 0]) < 1e-8)
assert all(abs(array(map['LDUL'].split(), dtype='float64')-[0, -1, -1]) < 1e-8)
a.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([U(2, 1, 0.6)]), 'X': Specie([])}
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUJ'].split(), dtype='float64')) < 1e-8)
assert all(abs(array(map['LDUU'].split(), dtype='float64')-[0.5, 0, 0.6]) < 1e-8)
assert all(abs(array(map['LDUL'].split(), dtype='float64')-[0, -1, 1]) < 1e-8)
# now tries NLEP
pylada.vasp_has_nlep = True
a.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([U(2, 0, -0.5), nlep(2, 1, -1.0)]), 'X': Specie([])}
a.ldau = False
assert a.ldau == False
assert o.output_map(vasp=a) is None
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUL1'].split(), dtype='float64')-[0, -1, 0]) < 1e-8)
assert all(abs(array(map['LDUU1'].split(), dtype='float64')-[0.5, 0, -0.5]) < 1e-8)
assert all(abs(array(map['LDUJ1'].split(), dtype='float64')-[0, 0, 0]) < 1e-8)
assert all(abs(array(map['LDUO1'].split(), dtype='float64')-[1, 1, 1]) < 1e-8)
assert all(abs(array(map['LDUL2'].split(), dtype='float64')-[-1, -1, 1]) < 1e-8)
assert all(abs(array(map['LDUU2'].split(), dtype='float64')-[0, 0, -1.0]) < 1e-8)
assert all(abs(array(map['LDUJ2'].split(), dtype='float64')-[0, 0, 0]) < 1e-8)
assert all(abs(array(map['LDUO2'].split(), dtype='float64')-[1, 1, 2]) < 1e-8)
a.species = {'A': Specie([U(2, 0, 0.5)]), 'B': Specie([U(2, 0, -0.5), nlep(2, 2, -1.0, -3.0)]), 'X': Specie([])}
a.ldau = True
map = o.output_map(vasp=a, structure=structure)
assert map['LDAU'] == '.TRUE.'
assert map['LDAUTYPE'] == '2'
assert all(abs(array(map['LDUL1'].split(), dtype='float64')-[0, -1, 0]) < 1e-8)
assert all(abs(array(map['LDUU1'].split(), dtype='float64')-[0.5, 0, -0.5]) < 1e-8)
assert all(abs(array(map['LDUJ1'].split(), dtype='float64')-[0, 0, 0]) < 1e-8)
assert all(abs(array(map['LDUO1'].split(), dtype='float64')-[1, 1, 1]) < 1e-8)
assert all(abs(array(map['LDUL2'].split(), dtype='float64')-[-1, -1, 2]) < 1e-8)
assert all(abs(array(map['LDUU2'].split(), dtype='float64')-[0, 0, -1.0]) < 1e-8)
assert all(abs(array(map['LDUJ2'].split(), dtype='float64')-[0, 0, -3.0]) < 1e-8)
assert all(abs(array(map['LDUO2'].split(), dtype='float64')-[1, 1, 3]) < 1e-8)
def main():
from boost.mpi import world
from scipy.optimize import fmin as scipy_simplex
from pylada.vasp import Extract, ExtractGW, Vasp, Specie
from pylada.vasp.specie import nlep as nlep_parameters, U as u_parameters
from pylada.vasp.incar import Standard, NBands
from sys import exit
indir = "SnO2"
dft_in = Extract(directory=indir, comm=world)
dft_in.OUTCAR = "OUTCAR_pbe"
dft_in.CONTCAR = "POSCAR"
gw_in = ExtractGW(directory=indir, comm=world)
gw_in.OUTCAR = "OUTCAR_gw"
gw_in.CONTCAR = "POSCAR"
# Creates species with nlep parameters to optimize
species = Specie\
(
"Sn",
path="pseudos/Sn",
U=[nlep_parameters(type="Dudarev", l=i, U0=0e0) for i in ["s", "p", "d"]]
),\
Specie\
(
"O",
path="pseudos/O",
U=[nlep_parameters(type="Dudarev", l=i, U0=0e0) for i in ["s", "p"]]
)
# add U to Sn atoms.
species[0].U.append( u_parameters(type="Dudarev", U=2e0, l=2) )
# creates vasp launcher
vasp = Vasp\
(
kpoints = lambda x: "Automatic generation\n0\ngamma\n6 6 10\n0 0 0",
precision = "accurate",
smearing = "bloechl",
ediff = 1e-5,
relaxation = "ionic",
encut = 1, # uses ENMAX * 1, which is VASP default
species = species
)
# adds some extra parameters.
vasp.nbands = Standard("NBANDS", 64)
vasp.lorbit = Standard("LORBIT", 10)
vasp.npar = Standard("NPAR", 2)
vasp.lplane = Standard("LPLANE", ".TRUE.")
vasp.addgrid = Standard("ADDGRID", ".TRUE.")
del vasp.fftgrid
# creates objective function.
objective = Objective(vasp, dft_in, gw_in)
x0, f0, iter, funcalls, warnflag = scipy_simplex(objective, objective.x, maxfun=150, full_output=1, xtol=0.2)
world.barrier()
if world.rank == 0:
print "minimum value:", f0
print "for: ", x0 * units
print "after %i iterations and %i function calls." % (iter, funcalls)
print "with warning flag: ", warnflag
print final(x0)
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
def __call__(self, structure, outdir=None, vasp=None, **kwargs ):
from copy import deepcopy
from os import getcwd
from os.path import join
from pylada.misc import RelativePath
from pylada.error import ExternalRunFailed
from pylada.vasp.extract import Extract, MassExtract
from pylada.vasp import Vasp
from pylada.vasp.relax import Relax
# make this function stateless.
structure_ = structure.copy()
outdir = getcwd() if outdir is None else RelativePath(outdir).path
############ Calc 1 ###############
name = self.names[0]
## functional for Calc 1
relax = Relax(copy=vasp)
relax.relaxation = "volume ionic cellshape"
relax.maxiter = 10
relax.keep_steps = True
relax.first_trial = { "kpoints": "\n0\nAuto\n10", "encut": 0.9 }
## end of the functional
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done run it
output = relax(structure_, outdir=fulldir, restart=None, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
############ Calc 2 ###############
name = self.names[1]
## functional for Calc 2
final = Vasp(copy=vasp)
final.nbands=24*len(structure_)
final.kpoints="\n0\nGamma\n2 2 2\n0. 0. 0.\n"
final.loptics=True
final.relaxation="static"
## end of the functional
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done, run it
output = final(structure_, outdir=fulldir, restart=output, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
############## GW Loop ########################
for name in self.names[2:]:
gw = Vasp(copy=vasp)
gw.kpoints ="\n0\nGamma\n2 2 2\n0. 0. 0.\n"
gw.nbands =24*len(structure_)
gw.lcharg = True
gw.add_keyword('nelm',1)
gw.add_keyword('algo','gw')
gw.add_keyword('LMAXFOCKAE',4)
gw.add_keyword('nomega',64)
gw.add_keyword('precfock','fast')
gw.add_keyword('encutgw',50)
gw.add_keyword('encutlf',50)
gw.add_keyword('lrpa',False)
gw.add_keyword('nkred',2)
params = deepcopy(kwargs)
fulldir = join(outdir, name)
## if this calculation has not been done, run it
output = gw(structure_, outdir=fulldir, restart=output, **params)
if not output.success:
raise ExternalRunFailed("VASP calculation did not succeed.")
#########################
return self.Extract(fulldir)
def vasp():
from pylada.vasp import Vasp
return Vasp()
def test_choice():
from pickle import loads, dumps
from pylada.vasp import Vasp
a = Vasp()
assert a.ispin is None
assert a._input['ispin'].keyword == 'ispin'
assert a._input['ispin'].output_map() is None
a.ispin = 1
assert a.ispin == 1
assert 'ispin' in a._input['ispin'].output_map()
assert a._input['ispin'].output_map()['ispin'] == '1'
a.ispin = 2
assert a.ispin == 2
assert 'ispin' in a._input['ispin'].output_map()
assert a._input['ispin'].output_map()['ispin'] == '2'
a.ispin = None
assert a.ispin is None
assert a._input['ispin'].keyword == 'ispin'
assert a._input['ispin'].output_map() is None
try:
a.ispin = 5
except:
pass
else:
raise RuntimeError()
a.ispin = '1'
assert a.ispin == 1
a.ispin = '2'
assert a.ispin == 2
try:
a.ispin = '3'
except:
pass
else:
raise RuntimeError()
a.ispin = None
o = a._input['ispin']
d = {'ChoiceKeyword': o.__class__}
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map() is None
assert repr(loads(dumps(o))) == repr(o)
a.ispin = 2
o = a._input['ispin']
assert repr(eval(repr(o), d)) == repr(o)
assert eval(repr(o), d).output_map()['ispin'] == '2'
assert repr(loads(dumps(o))) == repr(o)
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_icharg():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR, CHGCAR
from pylada.vasp import Vasp
from pylada.misc import local_path
from pylada.error import ValueError
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['icharg']
d = {'ICharg': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.icharg == 'auto'
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
local_path(restartdir).ensure(dir=True)
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# do not copy if empty
with open(join(restartdir, CHGCAR), 'w') as file:
pass
with open(join(restartdir, WAVECAR), 'w') as file:
pass
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# now copy only CHGCAR
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy only CHGCAR with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '11'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy both
a.nonscf = False
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now copy both with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '10'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now check that latest is copied
remove(join(restartdir, CHGCAR))
remove(join(directory, CHGCAR))
sleep(1.2)
with open(join(directory, WAVECAR), 'w') as file:
file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file:
pass # Buffering issues..
a.nonscf = False
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello'
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello world'
# makes sure requests are honored
# tries request. Should fail since CHGCAR does not exist.
remove(join(directory, WAVECAR))
a.icharg = 'chgcar'
assert a.icharg == 'chgcar'
try:
o.output_map(vasp=a, outdir=directory)
except ValueError:
pass
else:
raise Exception()
# now try for gold.
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
assert eval(repr(o), d).value == 'chgcar'
assert loads(dumps(o)).value == 'chgcar'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
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
def test_istart():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR
from pylada.vasp import Vasp
from pylada.misc import Changedir
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['istart']
d = {'IStart': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory): rmtree(directory)
makedirs(directory)
try:
assert a.istart == 'auto'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
with Changedir(restartdir) as pwd: pass
with open(join(restartdir, WAVECAR), 'w') as file: file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# do not copy if file is empty
a.restart = Extract(restartdir, True)
with open(join(restartdir, WAVECAR), 'w') as file: pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# now should copy
assert a.istart == 'auto'
with open(join(restartdir, WAVECAR), 'w') as file: file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
# check it copies only latest file.
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
file.flush()
with open(join(restartdir, WAVECAR), 'r') as file: pass
sleep(1.5)
with open(join(directory, WAVECAR), 'w') as file: file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file: pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
sleep(0.2)
with open(join(restartdir, WAVECAR), 'w') as file: file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
# check if scratch is required
remove(join(directory, WAVECAR))
a.istart = 'scratch'
assert a.istart == 'scratch'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'scratch'
assert loads(dumps(o)).value == 'scratch'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
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_istart():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR
from pylada.vasp import Vasp
from pylada.misc import local_path
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['istart']
d = {'IStart': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.istart == 'auto'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
local_path(restartdir).ensure(dir=True)
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# do not copy if file is empty
a.restart = Extract(restartdir, True)
with open(join(restartdir, WAVECAR), 'w') as file:
pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# now should copy
assert a.istart == 'auto'
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
# check it copies only latest file.
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
file.flush()
with open(join(restartdir, WAVECAR), 'r') as file:
pass
sleep(1.5)
with open(join(directory, WAVECAR), 'w') as file:
file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file:
pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
sleep(0.2)
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
# check if scratch is required
remove(join(directory, WAVECAR))
a.istart = 'scratch'
assert a.istart == 'scratch'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'scratch'
assert loads(dumps(o)).value == 'scratch'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
def test():
from pickle import loads, dumps
from pylada.vasp import Vasp
import pylada
pylada.is_vasp_4 = True
a = Vasp()
# default.
assert a.algo == 'Fast'
# wrong argument.
try:
a.algo = 0
except:
pass
else:
raise RuntimeError()
try:
a.algo = "WTF"
except:
pass
else:
raise RuntimeError()
# possible inputs and some.
d = {
'Very_Fast': ['very fast', 'VERY-fAst', 'very_FAST', 'v'],
'VeryFast': ['very fast', 'VERY-fAst', 'very_FAST', 'v'],
'Fast': ['fast', 'f'],
'Normal': ['normal', 'n'],
'Damped': ['damped', 'd'],
'Diag': ['diag'],
'All': ['all', 'a'],
'Nothing': ['nothing'],
'chi': ['chi'],
'GW': ['gw'],
'GW0': ['gw0'],
'scGW': ['scgw'],
'scGW0': ['scgw0'],
'Conjugate': ['conjugate', 'c'],
'Subrot': ['subrot', 's'],
'Eigenval': ['eigenval', 'e']
}
vasp5 = 'Subrot', 'chi', 'GW', 'GW0', 'scGW', 'scGW0', 'Conjugate', 'Eigenval', 'Exact', 'Nothing'
dictionary = {'Algo': a._input['algo'].__class__}
for isvasp4 in [True, False]:
pylada.is_vasp_4 = isvasp4
for key, items in d.iteritems():
for value in items:
if key in vasp5 and isvasp4:
try:
a.algo = value
except:
pass
else:
raise RuntimeError((value, key))
continue
a.algo = value
o = a._input['algo']
if key == 'VeryFast' and isvasp4:
assert a.algo == 'Very_Fast'
assert o.output_map()['algo'] == 'Very_Fast'
assert loads(dumps(o)).output_map()["algo"] == 'Very_Fast'
assert eval(repr(o),
dictionary).output_map()["algo"] == 'Very_Fast'
elif key == 'Very_Fast' and not isvasp4:
assert a.algo == 'VeryFast'
assert o.output_map()['algo'] == 'VeryFast'
assert loads(dumps(o)).output_map()["algo"] == 'VeryFast'
assert eval(repr(o),
dictionary).output_map()["algo"] == 'VeryFast'
else:
assert a.algo == key
assert o.output_map()['algo'] == key
assert loads(dumps(o)).output_map()["algo"] == key
assert eval(repr(o),
dictionary).output_map()["algo"] == key
a.algo = None
assert a.algo is None
assert o.output_map() is None
assert loads(dumps(o)).output_map() is None
assert eval(repr(o), dictionary).output_map() is None
n1=int(round(b1/step))
if np.mod(n1,2)!=0: n1=n1-1
n2=int(round(b2/step))
if np.mod(n2,2)!=0: n2=n2-1
n3=int(round(b3/step))
if np.mod(n3,2)!=0: n3=n3-1
print n1,n2,n3
if n1==0:n1=1
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
def test_icharg():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR, CHGCAR
from pylada.vasp import Vasp
from pylada.misc import Changedir
from pylada.error import ValueError
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['icharg']
d = {'ICharg': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory): rmtree(directory)
makedirs(directory)
try:
assert a.icharg == 'auto'
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
with Changedir(restartdir) as pwd: pass
with open(join(restartdir, CHGCAR), 'w') as file: file.write('hello')
with open(join(restartdir, WAVECAR), 'w') as file: file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# do not copy if empty
with open(join(restartdir, CHGCAR), 'w') as file: pass
with open(join(restartdir, WAVECAR), 'w') as file: pass
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# now copy only CHGCAR
with open(join(restartdir, CHGCAR), 'w') as file: file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy only CHGCAR with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '11'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy both
a.nonscf = False
with open(join(restartdir, WAVECAR), 'w') as file: file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now copy both with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '10'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now check that latest is copied
remove(join(restartdir, CHGCAR))
remove(join(directory, CHGCAR))
sleep(1.2)
with open(join(directory, WAVECAR), 'w') as file: file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file: pass # Buffering issues..
a.nonscf = False
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello'
with open(join(restartdir, WAVECAR), 'w') as file: file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello world'
# makes sure requests are honored
# tries request. Should fail since CHGCAR does not exist.
remove(join(directory, WAVECAR))
a.icharg = 'chgcar'
assert a.icharg == 'chgcar'
try: o.output_map(vasp=a, outdir=directory)
except ValueError: pass
else: raise Exception()
# now try for gold.
with open(join(restartdir, CHGCAR), 'w') as file: file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
assert eval(repr(o), d).value == 'chgcar'
assert loads(dumps(o)).value == 'chgcar'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
def test_magmom():
from pickle import loads, dumps
from pylada.crystal.cppwrappers import Structure
from pylada.vasp import 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")
for atom in structure:
if atom.type == 'Mg': atom.magmom = -1e0
vasp = Vasp()
vasp.magmom = None
assert vasp.magmom is None
assert vasp._input['magmom'].keyword == 'MAGMOM'
assert vasp._input['magmom'].output_map(vasp=vasp,
structure=structure) is None
# ispin == 1
vasp.magmom = True
vasp.ispin = 1
assert vasp._input['magmom'].output_map(vasp=vasp,
structure=structure) is None
# ispins == 2, magmom == False
vasp.ispin = 2
vasp.magmom = None
assert vasp._input['magmom'].output_map(vasp=vasp,
structure=structure) is None
vasp.magmom = False
assert vasp._input['magmom'].output_map(vasp=vasp,
structure=structure) is None
# now for real print
vasp.magmom = True
assert 'MAGMOM' in vasp._input['magmom'].output_map(vasp=vasp,
structure=structure)
print vasp._input['magmom'].output_map(vasp=vasp,
structure=structure)['MAGMOM']
assert vasp._input['magmom'].output_map(
vasp=vasp, structure=structure)['MAGMOM'] == '4*-1.0 2*0.0 8*0.0'
# now print a string directly.
vasp.magmom = 'hello'
assert vasp.magmom == 'hello'
assert 'MAGMOM' in vasp._input['magmom'].output_map(vasp=vasp,
structure=structure)
assert vasp._input['magmom'].output_map(
vasp=vasp, structure=structure)['MAGMOM'] == 'hello'
# check repr
assert repr(vasp._input['magmom']) == "Magmom(value='hello')"
# check pickling
assert repr(loads(dumps(vasp._input['magmom']))) == "Magmom(value='hello')"
# more tests.
for atom, mag in zip(structure, [1, -1, 1, 1]):
if atom.type == 'Mg': atom.magmom = mag
for atom, mag in zip(structure, [0.5, 0.5]):
if atom.type == 'Al': atom.magmom = mag
vasp.magmom = True
assert 'MAGMOM' in vasp._input['magmom'].output_map(vasp=vasp,
structure=structure)
assert vasp._input['magmom'].output_map(
vasp=vasp,
structure=structure)['MAGMOM'] == '1.0 -1.0 2*1.0 2*0.0 8*0.0'
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_istart():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR
from pylada.vasp import Vasp
from pylada.misc import Changedir
Extract = namedtuple("Extract", ["directory", "success"])
a = Vasp()
o = a._input["istart"]
d = {"IStart": o.__class__}
directory = mkdtemp()
if directory in ["/tmp/test", "/tmp/test/"]:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.istart == "auto"
assert o.output_map(vasp=a, outdir=directory)["istart"] == "0"
assert eval(repr(o), d).value == "auto"
assert loads(dumps(o)).value == "auto"
restartdir = join(directory, "restart")
with Changedir(restartdir) as pwd:
pass
with open(join(restartdir, WAVECAR), "w") as file:
file.write("hello")
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)["istart"] == "0"
assert not exists(join(directory, "WAVECAR"))
# do not copy if file is empty
a.restart = Extract(restartdir, True)
with open(join(restartdir, WAVECAR), "w") as file:
pass
assert o.output_map(vasp=a, outdir=directory)["istart"] == "0"
assert not exists(join(directory, "WAVECAR"))
# now should copy
assert a.istart == "auto"
with open(join(restartdir, WAVECAR), "w") as file:
file.write("hello")
assert o.output_map(vasp=a, outdir=directory)["istart"] == "1"
assert exists(join(directory, "WAVECAR"))
# check it copies only latest file.
with open(join(restartdir, WAVECAR), "w") as file:
file.write("hello")
file.flush()
with open(join(restartdir, WAVECAR), "r") as file:
pass
sleep(1.5)
with open(join(directory, WAVECAR), "w") as file:
file.write("hello world")
with open(join(directory, WAVECAR), "r") as file:
pass
assert o.output_map(vasp=a, outdir=directory)["istart"] == "1"
assert exists(join(directory, "WAVECAR"))
with open(join(directory, WAVECAR), "r") as file:
assert file.read().rstrip().lstrip() == "hello world"
sleep(0.2)
with open(join(restartdir, WAVECAR), "w") as file:
file.write("hello")
assert o.output_map(vasp=a, outdir=directory)["istart"] == "1"
assert exists(join(directory, "WAVECAR"))
with open(join(directory, WAVECAR), "r") as file:
assert file.read().rstrip().lstrip() == "hello"
# check if scratch is required
remove(join(directory, WAVECAR))
a.istart = "scratch"
assert a.istart == "scratch"
assert o.output_map(vasp=a, outdir=directory)["istart"] == "0"
assert eval(repr(o), d).value == "scratch"
assert loads(dumps(o)).value == "scratch"
finally:
if directory not in ["/tmp/test", "/tmp/test/"] and exists(directory):
rmtree(directory)
def test_algo_keyword():
from pickle import loads, dumps
from pylada.vasp import Vasp
import pylada
pylada.is_vasp_4 = True
a = Vasp()
# default.
assert a.algo == 'Fast'
# wrong argument.
try:
a.algo = 0
except:
pass
else:
raise RuntimeError()
try:
a.algo = "WTF"
except:
pass
else:
raise RuntimeError()
# possible inputs and some.
d = {
'Very_Fast': ['very fast', 'VERY-fAst', 'very_FAST', 'v'],
'VeryFast': ['very fast', 'VERY-fAst', 'very_FAST', 'v'],
'Fast': ['fast', 'f'],
'Normal': ['normal', 'n'],
'Damped': ['damped', 'd'],
'Diag': ['diag'],
'All': ['all', 'a'],
'None': ['none'],
'Nothing': ['nothing'],
'chi': ['chi'],
'GW': ['gw'],
'GW0': ['gw0'],
'scGW': ['scgw'],
'scGW0': ['scgw0'],
'Conjugate': ['conjugate', 'c'],
'Subrot': ['subrot', 's'],
'Eigenval': ['eigenval', 'e']
}
vasp5 = 'Subrot', 'chi', 'GW', 'GW0', 'scGW', 'scGW0', 'Conjugate', 'Eigenval', 'Exact', 'Nothing'
dictionary = {'Algo': a._input['algo'].__class__}
for isvasp4 in [True, False]:
pylada.is_vasp_4 = isvasp4
for key, items in d.items():
for value in items:
if key in vasp5 and isvasp4:
try:
a.algo = value
except:
pass
else:
raise RuntimeError((value, key))
continue
a.algo = value
o = a._input['algo']
if key == 'VeryFast' and isvasp4:
assert a.algo == 'Very_Fast'
assert o.output_map()['algo'] == 'Very_Fast'
assert loads(dumps(o)).output_map()["algo"] == 'Very_Fast'
assert eval(repr(o), dictionary).output_map()["algo"] == 'Very_Fast'
elif key == 'Very_Fast' and not isvasp4:
assert a.algo == 'VeryFast'
assert o.output_map()['algo'] == 'VeryFast'
assert loads(dumps(o)).output_map()["algo"] == 'VeryFast'
assert eval(repr(o), dictionary).output_map()["algo"] == 'VeryFast'
else:
assert a.algo == key
assert o.output_map()['algo'] == key
assert loads(dumps(o)).output_map()["algo"] == key
assert eval(repr(o), dictionary).output_map()["algo"] == key
a.algo = None
assert a.algo is None
assert o.output_map() is None
assert loads(dumps(o)).output_map() is None
assert eval(repr(o), dictionary).output_map() is None
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