Python inputs.Incar类代码示例

    def test_lsorbit_magmom(self):
        magmom1 = [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]]
        magmom2 = [-1, -1, -1, 0, 0, 0, 0, 0]

        ans_string1 = "LSORBIT = True\nMAGMOM = 0.0 0.0 3.0 0 1 0 2 1 2\n"
        ans_string2 = "LSORBIT = True\nMAGMOM = 3*3*-1 3*5*0\n"
        ans_string3 = "LSORBIT = False\nMAGMOM = 2*-1 2*9\n"

        incar = Incar({})
        incar["MAGMOM"] = magmom1
        incar["LSORBIT"] = "T"
        self.assertEqual(ans_string1, str(incar))

        incar["MAGMOM"] = magmom2
        incar["LSORBIT"] = "T"
        self.assertEqual(ans_string2, str(incar))

        incar = Incar.from_string(ans_string1)
        self.assertEqual(incar["MAGMOM"], [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]])

        incar = Incar.from_string(ans_string2)
        self.assertEqual(
            incar["MAGMOM"],
            [[-1, -1, -1], [-1, -1, -1], [-1, -1, -1], [0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 0, 0]],
        )

        incar = Incar.from_string(ans_string3)
        self.assertFalse(incar["LSORBIT"])
        self.assertEqual(incar["MAGMOM"], [-1, -1, 9, 9])

def run_major_axis_anisotropy_calculations(submit=True):
    """
    Perform static calculations with the magnetic axis along
    100, 010, and 001.

    Kwargs:
        submit (bool): Whether or not to submit the job.
    """

    if not os.path.isdir('MAE'):
        os.mkdir('MAE')
    os.chdir('MAE')
    for d in ['100', '010', '001']:
        if not os.path.isdir(d):
            os.path.mkdir(d)
        os.chdir(d)
        os.system('cp ../CONTCAR POSCAR')
        os.system('cp ../POTCAR .')
        axis = [float(char) for char in d]
        # Small positive number, see vasp manual
        if d in ['001', '010']:
            axis[0] = 0.00000001
        else:
            axis[1] = 0.00000001

        saxis = ' '.join(axis)
        incar_dict = INCAR_DICT
        incar_dict.update({'EDIFF': 1e-8, 'GGA_COMPAT': False, 'ISMEAR': -5,
                           'LORBIT': 11, 'LSORBIT': True, 'LWAVE': False,
                           'LCHARG': False, 'LAECHG': False,
                           'MAGMOM': get_magmom_string(), 'SAXIS': saxis})
        Incar.from_dict(incar_dict).write_file('INCAR')

        if submit:
            os.system(submission_command)

 def test_as_dict_and_from_dict(self):
     d = self.incar.as_dict()
     incar2 = Incar.from_dict(d)
     self.assertEqual(self.incar, incar2)
     d["MAGMOM"] = [Magmom([1, 2, 3]).as_dict()]
     incar3 = Incar.from_dict(d)
     self.assertEqual(incar3["MAGMOM"], [Magmom([1, 2, 3])])

def relax(dim=2, submit=True, force_overwrite=False):
    """
    Writes input files and (optionally) submits a self-consistent
    relaxation. Should be run before pretty much anything else, in
    order to get the right energy and structure of the material.

    Args:
        dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
        submit (bool): Whether or not to submit the job.
        force_overwrite (bool): Whether or not to overwrite files
            if an already converged vasprun.xml exists in the
            directory.
    """

    if force_overwrite or not utl.is_converged(os.getcwd()):
        directory = os.getcwd().split('/')[-1]

        # vdw_kernel.bindat file required for VDW calculations.
        if VDW_KERNEL:
            os.system('cp {} .'.format(VDW_KERNEL))
        # KPOINTS
        Kpoints.automatic_density(Structure.from_file('POSCAR'),
                                  1000).write_file('KPOINTS')

        # INCAR
        INCAR_DICT.update(
            {'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))}
        )
        Incar.from_dict(INCAR_DICT).write_file('INCAR')
        # POTCAR
        utl.write_potcar()

        # Special tasks only performed for 2D materials.
        if dim == 2:
            # Ensure 20A interlayer vacuum
            utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
            # Remove all z k-points.
            kpts_lines = open('KPOINTS').readlines()
            with open('KPOINTS', 'w') as kpts:
                for line in kpts_lines[:3]:
                    kpts.write(line)
                kpts.write(kpts_lines[3].split()[0] + ' '
                           + kpts_lines[3].split()[1] + ' 1')

        # Submission script
        if dim == 2:
            binary = VASP_TWOD_BIN
        elif dim == 3:
            binary = VASP_STD_BIN
        if QUEUE_SYSTEM == 'pbs':
            utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary)
            submission_command = 'qsub runjob'

        elif QUEUE_SYSTEM == 'slurm':
            utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary)
            submission_command = 'sbatch runjob'

        if submit:
            os.system(submission_command)

def run_major_axis_anisotropy_calculations(submit=True):
    """
    Perform static calculations with the magnetic axis along
    100, 010, and 001.

    Args:
        submit (bool): Whether or not to submit the job.
    """

    if not os.path.isdir('MAE'):
        os.mkdir('MAE')
    os.chdir('MAE')
    for d in ['100', '010', '001']:
        if not os.path.isdir(d):
            os.mkdir(d)
        os.chdir(d)
        os.system('cp ../CONTCAR POSCAR')
        os.system('cp ../POTCAR .')
        axis = [float(char) for char in d]
        # Small positive number, see vasp manual
        if d in ['001', '010']:
            axis[0] = 0.00000001
        else:
            axis[1] = 0.00000001

        saxis = ' '.join(axis)
        incar_dict = INCAR_DICT
        incar_dict.update({'EDIFF': 1e-8,
                           'GGA_COMPAT': False,
                           'ISMEAR': -5,
                           'LORBIT': 11,
                           'LSORBIT': True,
                           'LWAVE': False,
                           'LCHARG': False,
                           'LAECHG': False,
                           'MAGMOM': get_magmom_string(
                                Structure.from_file('POSCAR')
                            ),
                           'SAXIS': saxis})
        Incar.from_dict(incar_dict).write_file('INCAR')

        if QUEUE_SYSTEM == 'pbs':
            utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
                VASP_TWOD_BIN)
            submission_command = 'qsub runjob'

        elif QUEUE_SYSTEM == 'slurm':
            utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00',
                VASP_TWOD_BIN)
            submission_command = 'sbatch runjob'

        if submit:
            os.system(submission_command)

def run_hse_prep_calculation(dim=2, submit=True):
    """
    Submits a quick static calculation to calculate the IBZKPT
    file using a smaller number of k-points (200/atom instead of
    1000/atom). The other outputs from this calculation are
    essentially useless.

    Args:
        dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
        submit (bool): Whether or not to submit the job.
    """

    if not os.path.isdir('hse_prep'):
        os.mkdir('hse_prep')
    os.chdir('hse_prep')
    os.system('cp ../CONTCAR ./POSCAR')
    if os.path.isfile('../POTCAR'):
        os.system('cp POTCAR .')
    relax(dim=2, submit=False)
    incar_dict = Incar.from_file('INCAR').as_dict()
    incar_dict.update({'NSW': 0, 'NELM': 1, 'LWAVE': False, 'LCHARG': False,
                       'LAECHG': False})
    Incar.from_dict(incar_dict).write_file('INCAR')

    Kpoints.automatic_density(
        Structure.from_file('POSCAR'), 200
    ).write_file('KPOINTS')

    if dim == 2:
        kpts_lines = open('KPOINTS').readlines()

        with open('KPOINTS', 'w') as kpts:
            for line in kpts_lines[:3]:
                kpts.write(line)
            kpts.write(kpts_lines[3].split()[0] + ' '
                       + kpts_lines[3].split()[1] + ' 1')

    if QUEUE == 'pbs':
        write_pbs_runjob('{}_prep'.format(
            os.getcwd().split('/')[-2]), 1, 16, '800mb', '6:00:00', VASP)
        submission_command = 'qsub runjob'

    elif QUEUE == 'slurm':
        write_slurm_runjob('{}_prep'.format(
            os.getcwd().split('/')[-2]), 16, '800mb', '6:00:00', VASP)
        submission_command = 'sbatch runjob'

    if submit:
        os.system(submission_command)

    os.chdir('../')

 def __init__(self, name, incar, poscar, potcar, kpoints,
              qadapter=None, **kwargs ):
     """
     default INCAR from config_dict
     
     """
     self.name = name
     self.incar = Incar.from_dict(incar.as_dict())
     self.poscar = Poscar.from_dict(poscar.as_dict())
     self.potcar = Potcar.from_dict(potcar.as_dict())
     self.kpoints = Kpoints.from_dict(kpoints.as_dict())
     self.extra = kwargs
     if qadapter is not None:
         self.qadapter = qadapter.from_dict(qadapter.to_dict())
     else:
         self.qadapter = None        
     config_dict = {}
     config_dict['INCAR'] = self.incar.as_dict()
     config_dict['POSCAR'] = self.poscar.as_dict() 
     #caution the key and the value are not always the same        
     config_dict['POTCAR'] = self.potcar.as_dict() 
     #dict(zip(self.potcar.as_dict()['symbols'],
     #self.potcar.as_dict()['symbols']))
     config_dict['KPOINTS'] = self.kpoints.as_dict()
     #self.user_incar_settings = self.incar.as_dict()        
     DictVaspInputSet.__init__(self, name, config_dict,
                                ediff_per_atom=False, **kwargs)

 def setup(self):
     """
     setup static jobs for all the calibrate objects
     copies CONTCAR to POSCAR
     sets NSW = 0
     """
     for cal in self.cal_objs:
         for i, jdir in enumerate(cal.old_job_dir_list):
             job_dir = self.job_dir + os.sep \
                 + jdir.replace(os.sep, '_').replace('.', '_') \
                 + os.sep + 'STATIC'
             logger.info('setting up job in {}'.format(job_dir))
             cal.incar = Incar.from_file(jdir + os.sep + 'INCAR')
             cal.incar['EDIFF'] = '1E-6'
             cal.incar['NSW'] = 0
             cal.potcar = Potcar.from_file(jdir + os.sep + 'POTCAR')
             cal.kpoints = Kpoints.from_file(jdir + os.sep + 'KPOINTS')
             contcar_file = jdir + os.sep + 'CONTCAR'
             if os.path.isfile(contcar_file):
                 logger.info('setting poscar file from {}'
                             .format(contcar_file))
                 cal.poscar = Poscar.from_file(contcar_file)
                 cal.add_job(job_dir=job_dir)
             else:
                 logger.critical("""CONTCAR doesnt exist.
                 Setting up job using input set in the old
                 calibration directory""")
                 cal.poscar = Poscar.from_file(jdir + os.sep + 'POSCAR')
                 cal.add_job(job_dir=job_dir)

    def run_task(self, fw_spec):
        chgcar_start = False
        # read the VaspInput from the previous run

        poscar = Poscar.from_file(zpath('POSCAR'))
        incar = Incar.from_file(zpath('INCAR'))

        # figure out what GGA+U values to use and override them
        # LDAU values to use
        mpvis = MPVaspInputSet()
        ggau_incar = mpvis.get_incar(poscar.structure).as_dict()
        incar_updates = {k: ggau_incar[k] for k in ggau_incar.keys() if 'LDAU' in k}

        for k in ggau_incar:
            # update any parameters not set explicitly in previous INCAR
            if k not in incar and k in ggau_incar:
                incar_updates[k] = ggau_incar[k]

        incar.update(incar_updates)  # override the +U keys


        # start from the CHGCAR of previous run
        if os.path.exists('CHGCAR'):
            incar['ICHARG'] = 1
            chgcar_start = True

        # write back the new INCAR to the current directory
        incar.write_file('INCAR')
        return FWAction(stored_data={'chgcar_start': chgcar_start})

def run_pbe_calculation(dim=2, submit=True, force_overwrite=False):
    """
    Setup and submit a normal PBE calculation for band structure along
    high symmetry k-paths.

    Args:
        dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
        submit (bool): Whether or not to submit the job.
        force_overwrite (bool): Whether or not to overwrite files
            if an already converged vasprun.xml exists in the
            directory.
    """

    PBE_INCAR_DICT = {'EDIFF': 1e-6, 'IBRION': 2, 'ISIF': 3,
                      'ISMEAR': 1, 'NSW': 0, 'LVTOT': True, 'LVHAR': True,
                      'LORBIT': 1, 'LREAL': 'Auto', 'NPAR': 4,
                      'PREC': 'Accurate', 'LWAVE': True, 'SIGMA': 0.1,
                      'ENCUT': 500, 'ISPIN': 2}

    directory = os.getcwd().split('/')[-1]

    if not os.path.isdir('pbe_bands'):
        os.mkdir('pbe_bands')
    if force_overwrite or not is_converged('pbe_bands'):
        os.system('cp CONTCAR pbe_bands/POSCAR')
        if os.path.isfile('POTCAR'):
            os.system('cp POTCAR pbe_bands/')
        PBE_INCAR_DICT.update({'MAGMOM': get_magmom_string()})
        Incar.from_dict(PBE_INCAR_DICT).write_file('pbe_bands/INCAR')
        structure = Structure.from_file('POSCAR')
        kpath = HighSymmKpath(structure)
        Kpoints.automatic_linemode(20, kpath).write_file('pbe_bands/KPOINTS')
        os.chdir('pbe_bands')
        if dim == 2:
            remove_z_kpoints()
        if QUEUE == 'pbs':
            write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', VASP)
            submission_command = 'qsub runjob'

        elif QUEUE == 'slurm':
            write_slurm_runjob(directory, 16, '800mb', '6:00:00', VASP)
            submission_command = 'sbatch runjob'

        if submit:
            os.system(submission_command)

        os.chdir('../')

 def test_quad_efg(self):
     incar1 = Incar({})
     incar1["LEFG"] = True
     incar1["QUAD_EFG"] = [0.0, 146.6, -25.58]
     ans_string1 = "LEFG = True\nQUAD_EFG = 0.0 146.6 -25.58\n"
     self.assertEqual(ans_string1, str(incar1))
     incar2 = Incar.from_string(ans_string1)
     self.assertEqual(ans_string1, str(incar2))

    def test_lsorbit_magmom(self):
        magmom1 = [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]]
        magmom2 = [-1, -1, -1, 0, 0, 0, 0, 0]
        magmom4 = [Magmom([1.0, 2.0, 2.0])]

        ans_string1 = "LANGEVIN_GAMMA = 10 10 10\nLSORBIT = True\n" \
                      "MAGMOM = 0.0 0.0 3.0 0 1 0 2 1 2\n"
        ans_string2 = "LANGEVIN_GAMMA = 10\nLSORBIT = True\n" \
                      "MAGMOM = 3*3*-1 3*5*0\n"
        ans_string3 = "LSORBIT = False\nMAGMOM = 2*-1 2*9\n"
        ans_string4_nolsorbit = "LANGEVIN_GAMMA = 10\nLSORBIT = False\nMAGMOM = 1*3.0\n"
        ans_string4_lsorbit = "LANGEVIN_GAMMA = 10\nLSORBIT = True\nMAGMOM = 1.0 2.0 2.0\n"

        incar = Incar({})
        incar["MAGMOM"] = magmom1
        incar["LSORBIT"] = "T"
        incar["LANGEVIN_GAMMA"] = [10, 10, 10]
        self.assertEqual(ans_string1, str(incar))

        incar["MAGMOM"] = magmom2
        incar["LSORBIT"] = "T"
        incar["LANGEVIN_GAMMA"] = 10
        self.assertEqual(ans_string2, str(incar))

        incar["MAGMOM"] = magmom4
        incar["LSORBIT"] = "F"
        self.assertEqual(ans_string4_nolsorbit, str(incar))
        incar["LSORBIT"] = "T"
        self.assertEqual(ans_string4_lsorbit, str(incar))

        incar = Incar.from_string(ans_string1)
        self.assertEqual(incar["MAGMOM"],
                         [[0.0, 0.0, 3.0], [0, 1, 0], [2, 1, 2]])
        self.assertEqual(incar["LANGEVIN_GAMMA"], [10, 10, 10])

        incar = Incar.from_string(ans_string2)
        self.assertEqual(incar["MAGMOM"], [[-1, -1, -1], [-1, -1, -1],
                                           [-1, -1, -1], [0, 0, 0],
                                           [0, 0, 0], [0, 0, 0],
                                           [0, 0, 0], [0, 0, 0]])
        self.assertEqual(incar["LANGEVIN_GAMMA"], [10])

        incar = Incar.from_string(ans_string3)
        self.assertFalse(incar["LSORBIT"])
        self.assertEqual(incar["MAGMOM"], [-1, -1, 9, 9])

 def from_dict(cls, d):
     incar = Incar.from_dict(d["incar"])
     poscar = Poscar.from_dict(d["poscar"])
     potcar = Potcar.from_dict(d["potcar"])
     kpoints = Kpoints.from_dict(d["kpoints"])
     qadapter = None
     if d["qadapter"] is not None:
         qadapter = CommonAdapter.from_dict(d["qadapter"])
     return MPINTVaspInputSet(d["name"], incar, poscar, potcar,
                              kpoints, qadapter, **d["kwargs"])

    def test_optics(self):
        self.mpopticsparamset = MPOpticsNonSCFVaspInputSet.from_previous_vasp_run(
            '{}/static_silicon'.format(test_dir), output_dir='optics_test_dir',
            nedos=1145)
        self.assertTrue(os.path.exists('optics_test_dir/CHGCAR'))
        incar = Incar.from_file('optics_test_dir/INCAR')
        self.assertTrue(incar['LOPTICS'])
        self.assertEqual(incar['NEDOS'], 1145)

        #Remove the directory in which the inputs have been created
        shutil.rmtree('optics_test_dir')

    def test_write(self):
        tmp_dir = "VaspInput.testing"
        self.vinput.write_input(tmp_dir)

        filepath = os.path.join(tmp_dir, "INCAR")
        incar = Incar.from_file(filepath)
        self.assertEqual(incar["NSW"], 99)

        for name in ("INCAR", "POSCAR", "POTCAR", "KPOINTS"):
            os.remove(os.path.join(tmp_dir, name))

        os.rmdir(tmp_dir)