Python Kpoints.automatic方法代码示例

# 需要导入模块: from pymatgen.io.vasp.inputs import Kpoints [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Kpoints import automatic [as 别名]
    def test_static_constructors(self):
        kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
        self.assertEqual(kpoints.kpts, [[3, 3, 3]])
        kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst)
        self.assertEqual(kpoints.kpts, [[2, 2, 2]])
        kpoints = Kpoints.automatic(100)
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Automatic)
        self.assertEqual(kpoints.kpts, [[100]])
        filepath = os.path.join(test_dir, 'POSCAR')
        poscar = Poscar.from_file(filepath)
        kpoints = Kpoints.automatic_density(poscar.structure, 500)
        self.assertEqual(kpoints.kpts, [[1, 3, 3]])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
        kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
        kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
        self.assertEqual(kpoints.kpts, [[6, 10, 13]])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)

        s = poscar.structure
        s.make_supercell(3)
        kpoints = Kpoints.automatic_density(s, 500)
        self.assertEqual(kpoints.kpts, [[1, 1, 1]])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
        kpoints = Kpoints.from_string("""k-point mesh 
0
G
10 10 10
0.5 0.5 0.5
""")
        self.assertArrayAlmostEqual(kpoints.kpts_shift, [0.5, 0.5, 0.5])

# 需要导入模块: from pymatgen.io.vasp.inputs import Kpoints [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Kpoints import automatic [as 别名]
    def test_static_constructors(self):
        kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
        self.assertEqual(kpoints.kpts, [[3, 3, 3]])
        kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst)
        self.assertEqual(kpoints.kpts, [[2, 2, 2]])
        kpoints = Kpoints.automatic(100)
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Automatic)
        self.assertEqual(kpoints.kpts, [[100]])
        filepath = os.path.join(test_dir, "POSCAR")
        poscar = Poscar.from_file(filepath)
        kpoints = Kpoints.automatic_density(poscar.structure, 500)
        self.assertEqual(kpoints.kpts, [[2, 4, 4]])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst)
        kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
        kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
        self.assertEqual(kpoints.kpts, [[6, 11, 13]])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)

        s = poscar.structure
        s.make_supercell(3)
        kpoints = Kpoints.automatic_density(s, 500)
        self.assertEqual(kpoints.kpts, [[1, 1, 1]])
        self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)

# 需要导入模块: from pymatgen.io.vasp.inputs import Kpoints [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Kpoints import automatic [as 别名]
 def set_kpoints(self, kpoint):
     """
     set the kpoint
     """
     if self.Grid_type == 'M':
         self.kpoints = Kpoints.monkhorst_automatic(kpts=kpoint)
     elif self.Grid_type == 'A':
         self.kpoints = Kpoints.automatic(subdivisions=kpoint)
     elif self.Grid_type == 'G':
         self.kpoints = Kpoints.gamma_automatic(kpts=kpoint)
     elif self.Grid_type == '3DD':
         self.kpoints = Kpoints.automatic_density_by_vol(structure= \
                                                             self.poscar.structure, kppvol=kpoint)
     elif self.Grid_type == 'band':
         self.kpoints = Kpoints.automatic_linemode(divisions=kpoint, \
                                                   ibz=HighSymmKpath(self.poscar.structure))

# 需要导入模块: from pymatgen.io.vasp.inputs import Kpoints [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Kpoints import automatic [as 别名]
 def set_kpoints(self, kpoint):
     """
     set the kpoint
     """
     if self.Grid_type == 'M':
         self.kpoints = Kpoints.monkhorst_automatic(kpts = kpoint)
     elif self.Grid_type == 'A':
         self.kpoints = Kpoints.automatic(subdivisions = kpoint)
     elif self.Grid_type == 'G': 
         self.kpoints = Kpoints.gamma_automatic(kpts = kpoint)
     elif self.Grid_type == '3DD':
         self.kpoints = Kpoints.automatic_density_by_vol(structure=\
                        self.poscar.structure, kppvol=kpoint)
     elif self.Grid_type == 'band':
         self.kpoints = Kpoints.automatic_linemode(divisions=kpoint,\
                        ibz=HighSymmKpath(self.poscar.structure))
     name = self.kpoint_to_name(kpoint, self.Grid_type)
     job_dir = self.job_dir +os.sep+ self.key_to_name('KPOINTS') \
       + os.sep + name
     return job_dir

# 需要导入模块: from pymatgen.io.vasp.inputs import Kpoints [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Kpoints import automatic [as 别名]
incar_dict = {
                 'SYSTEM': 'test', 
                 'ENCUT': 500, 
                 'ISIF': 2, 
                 'IBRION': 2, 
                 'ISMEAR': 1, 
                 'EDIFF': 1e-06, 
                 'NPAR': 8, 
                 'SIGMA': 0.1, 
                 'NSW' : 100,
                 'PREC': 'Accurate'
    }
incar = Incar.from_dict(incar_dict)
poscar = Poscar(iface)
potcar = Potcar(poscar.site_symbols)
kpoints = Kpoints.automatic(20)
#set job list. if empty a single job will be run
encut_list = [] #range(400,800,100)
turn_knobs = OrderedDict(
    [
        ('ENCUT', encut_list)
    ])
#job directory
job_dir = 'vasp_job'
# run settings
qadapter = None
job_cmd = None
nprocs = 16
nnodes = 1
walltime = '24:00:00'
mem = 1000

# 需要导入模块: from pymatgen.io.vasp.inputs import Kpoints [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Kpoints import automatic [as 别名]
    def set_kpoints(self, kpoint=None, poscar=None, ibzkpth=None):
        """
        set the kpoint
        """
        # useful to check if a poscar is supplied from setup_poscar_jobs (most often the case)
        # or this is a single poscar use case
        if not poscar:
            poscar = self.poscar

        # splitting into two if elif branches means fewer if statements to check on
        # a run

        # Most general method of setting the k-points for
        # different grid types
        # NOTE: requires that at least one k-points value be passed
        # as a turn - knobs list value
        # this is not true for values that may be caculated out of
        # a database
        # use this part only if this is a non-database run for example
        # for k-points calibration

        if not self.database:

            if self.Grid_type == 'M':
                self.kpoints = Kpoints.monkhorst_automatic(kpts=kpoint)
            elif self.Grid_type == 'A':
                self.kpoints = Kpoints.automatic(subdivisions=kpoint)
            elif self.Grid_type == 'G':
                self.kpoints = Kpoints.gamma_automatic(kpts=kpoint)
            elif self.Grid_type == '3D_vol':
                self.kpoints = Kpoints.automatic_density_by_vol(structure=poscar.structure,
                                                                kppvol=kpoint)
            elif self.Grid_type == 'bulk_bands_pbe':
                self.kpoints = Kpoints.automatic_linemode(divisions=kpoint,
                                                          ibz=HighSymmKpath(
                                                              poscar.structure))

            elif self.Grid_type == 'D':
                self.kpoints = Kpoints.automatic_density(structure=poscar.structure,kppa=kpoint)

            elif self.Grid_type == 'Finer_G_Mesh':
                # kpoint is the scaling factor and self.kpoints is the old kpoint mesh
                self.logger.info('Setting Finer G Mesh for {0} by scale {1}'.format(kpoint, self.finer_kpoint))
                self.kpoints = Kpoints.gamma_automatic(kpts = \
                   [i * self.finer_kpoint for i in kpoint])
                self.logger.info('Finished scaling operation of k-mesh')

        # applicable for database runs
        # future constructs or settinsg can be activated via a yaml file
        # database yaml file or better still the input deck from its speification
        # decides what combination of input calibrate constructor settings to use
        # one of them being the grid_type tag

        elif self.database == 'twod':

            # set of kpoints settings according to the 2D database profile
            # the actual settings of k-points density
            # will in future come from any database input file set

            if self.Grid_type == 'hse_bands_2D_prep':
                kpoint_dict = Kpoints.automatic_gamma_density(poscar.structure,
                                                              200).as_dict()
                kpoint_dict['kpoints'][0][2] = 1  # remove z kpoints
                self.kpoints = Kpoints.from_dict(kpoint_dict)

            elif self.Grid_type == 'hse_bands_2D':
                # can at most return the path to the correct kpoints file
                # needs kpoints to be written out in instrument in a different way
                # not using the Kpoints object
                self.kpoints = get_2D_hse_kpoints(poscar.structure, ibzkpth)

            elif self.Grid_type == 'bands_2D':
                kpoint_dict = Kpoints.automatic_linemode(divisions=20,
                                                         ibz=HighSymmKpath(poscar.structure)).as_dict()
                self.kpoints = Kpoints.from_dict(kpoint_dict)

            elif self.Grid_type == 'relax_2D':
                # general relaxation settings for 2D
                kpoint_dict = Kpoints.automatic_gamma_density(poscar.structure,
                                                              1000).as_dict()
                kpoint_dict['kpoints'][0][2] = 1
                self.kpoints = Kpoints.from_dict(kpoint_dict)

            elif self.Grid_type == 'relax_3D':
                # general relaxation settings for 3D
                kpoint_dict = Kpoints.automatic_gamma_density(
                    poscar.structure, 1000)
                self.kpoints = Kpoints.from_dict(kpoint_dict)