Python Vasp.restart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 restart [as 别名]
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

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

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

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

#.........这里部分代码省略.........

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

# 需要导入模块: from pylada.vasp import Vasp [as 别名]
# 或者: from pylada.vasp.Vasp import restart [as 别名]
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:
#.........这里部分代码省略.........