Python vasp.Vasp类代码示例

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_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 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(tmpdir, path):
    from numpy import all, abs
    from quantities import kbar, eV, angstrom
    from pylada.crystal import Structure
    from pylada.vasp import Vasp
    from pylada.vasp.relax import Relax
    from pylada import default_comm

    structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
        .add_atom(0, 0, 0, "Si")\
        .add_atom(0.25, 0.25, 0.25, "Si")

    vasp = Vasp()
    vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
    vasp.prec = "accurate"
    vasp.ediff = 1e-5
    vasp.encut = 1
    vasp.ismear = "fermi"
    vasp.sigma = 0.01
    vasp.relaxation = "volume"
    vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)

    functional = Relax(copy=vasp)
    assert abs(functional.ediff - 1e-5) < 1e-8
    assert functional.prec == 'Accurate'
    result = functional(structure, outdir=str(tmpdir), comm=default_comm,
                        relaxation="volume ionic cellshape")
    assert result.success

    assert result.stress.units == kbar and all(abs(result.stress) < 1e0)
    assert result.forces.units == eV / angstrom and all(abs(result.forces) < 1e-1)
    assert result.total_energy.units == eV and all(
        abs(result.total_energy + 10.668652 * eV) < 1e-2)

def test(tmpdir, path):
    from numpy import abs
    from pylada.crystal import Structure
    from pylada.vasp import Vasp
    from pylada.vasp.emass import effective_mass, EMass
    from pylada import default_comm

    structure = Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
        .add_atom(0, 0, 0, "Si")\
        .add_atom(0.25, 0.25, 0.25, "Si")

    vasp = Vasp()
    vasp.kpoints = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
    vasp.prec = "accurate"
    vasp.ediff = 25e-5
    vasp.encut = 1.4
    vasp.ismear = "fermi"
    vasp.sigma = 0.01
    vasp.relaxation = "volume"
    vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
    emass = EMass(copy=vasp)
    assert abs(emass.encut - 1.4) < 1e-8
    assert abs(emass.ediff - 25e-5) < 1e-10
    result = effective_mass(vasp, structure, outdir=str(tmpdir), comm=default_comm,
                            emassparams={'ediff': 1e-8})
    result.emass
    assert result.success
    result = emass(structure, outdir=str(tmpdir), comm=default_comm,
                   emassparams={'ediff': 1e-8})
    assert result.success

def test(path):
  from shutil import rmtree
  from tempfile import mkdtemp
  from pylada.crystal import Structure
  from pylada.vasp import Vasp
  from epirelax import epitaxial
  from pylada import default_comm

  structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.55, name='has a name')\
                       .add_atom(0,0,0, "Si")\
                       .add_atom(0.25,0.25,0.25, "Si")

  vasp = Vasp()
  vasp.kpoints    = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
  vasp.prec       = "accurate"
  vasp.ediff      = 1e-5
  vasp.encut      = 1.4
  vasp.ismear     = "fermi"
  vasp.sigma      = 0.01
  vasp.relaxation = "volume"
  vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
  directory = mkdtemp()
  try: 
    result = epitaxial(vasp, structure, outdir=directory, epiconv=1e-4, comm=default_comm)
    assert result.success
  finally: 
    rmtree(directory)
    pass

def test(path):
  from os import makedirs
  from os.path import exists
  from shutil import rmtree
  from tempfile import mkdtemp
  from pylada.crystal import Structure
  from pylada.vasp import Vasp
  from pylada import default_comm

  structure = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]], scale=5.43, name='has a name')\
                       .add_atom(0,0,0, "Si")\
                       .add_atom(0.25,0.25,0.25, "Si")

  vasp = Vasp()
  vasp.kpoints    = "Automatic generation\n0\nMonkhorst\n2 2 2\n0 0 0"
  vasp.prec       = "accurate"
  vasp.ediff      = 1e-5
  vasp.encut      = 1
  vasp.ismear     = "fermi"
  vasp.sigma      = 0.01
  vasp.relaxation = "volume"
  vasp.add_specie = "Si", "{0}/pseudos/Si".format(path)
  directory = mkdtemp()
  if directory == '/tmp/test' or directory == '/tmp/test/':
    if exists(directory): rmtree(directory)
    makedirs(directory)
  try: 
    result = vasp(structure, outdir=directory, comm=default_comm)
    assert result.success
  finally: 
    if directory != '/tmp/test' and directory != '/tmp/test/':
      rmtree(directory)

    def __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_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 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_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_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)