Python Vasp.add_specie方法代码示例

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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)

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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)

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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)

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import add_specie [as 别名]
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