Python Kpoints.monkhorst_automatic方法代码示例

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
 def test_to_dict_from_dict(self):
     k = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
     d = k.to_dict
     k2 = Kpoints.from_dict(d)
     self.assertEqual(k.kpts, k2.kpts)
     self.assertEqual(k.style, k2.style)
     self.assertEqual(k.kpts_shift, k2.kpts_shift)

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
    def test_static_constructors(self):
        kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
        self.assertEqual(kpoints.style, "Gamma")
        self.assertEqual(kpoints.kpts, [[3, 3, 3]])
        kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
        self.assertEqual(kpoints.style, "Monkhorst")
        self.assertEqual(kpoints.kpts, [[2, 2, 2]])
        kpoints = Kpoints.automatic(100)
        self.assertEqual(kpoints.style, "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, "Monkhorst")
        kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
        self.assertEqual(kpoints.style, "Gamma")
        kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
        self.assertEqual(kpoints.kpts, [[6, 11, 13]])
        self.assertEqual(kpoints.style, "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, "Gamma")

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
 def test_static_constructors(self):
     kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
     self.assertEqual(kpoints.style, "Gamma")
     self.assertEqual(kpoints.kpts, [[3, 3, 3]])
     kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
     self.assertEqual(kpoints.style, "Monkhorst")
     self.assertEqual(kpoints.kpts, [[2, 2, 2]])
     kpoints = Kpoints.automatic(100)
     self.assertEqual(kpoints.style, "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, 3, 4]])

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
    def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
                               user_incar_settings=None,
                               make_dir_if_not_present=True):
        """
        Generate a set of Vasp input files for static calculations from a
        directory of previous Vasp run.

        Args:
            previous_vasp_dir:
                The directory contains the outputs(vasprun.xml and OUTCAR) of
                previous vasp run.
            output_dir:
                The directory to write the VASP input files for the static
                calculations. Default to write in the current directory.
            make_dir_if_not_present:
                Set to True if you want the directory (and the whole path) to
                be created if it is not present.
        """

        try:
            vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
                               parse_dos=False, parse_eigen=None)
            outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
            previous_incar = vasp_run.incar
            previous_kpoints = vasp_run.kpoints
            previous_final_structure = vasp_run.final_structure
        except:
            traceback.format_exc()
            raise RuntimeError("Can't get valid results from previous run")
        structure = MPStaticVaspInputSet.get_structure(vasp_run, outcar)
        mpsvip = MPStaticVaspInputSet()
        mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
        #new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))
        new_incar = mpsvip.get_incar(structure)

        # Use previous run INCAR and override necessary parameters
        previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
                               "LCHARG": True, "LORBIT": 11, "LVHAR": True,
                               "LWAVE": False, "NSW": 0, "ICHARG": 0})

        for incar_key in ["MAGMOM", "NUPDOWN"]:
            if new_incar.get(incar_key, None):
                previous_incar.update({incar_key: new_incar[incar_key]})
            else:
                previous_incar.pop(incar_key, None)

        # use new LDAUU when possible b/c the Poscar might have changed
        # representation
        if previous_incar.get('LDAU'):
            u = previous_incar.get('LDAUU', [])
            j = previous_incar.get('LDAUJ', [])
            if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
                for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
                    previous_incar.update({tag: new_incar[tag]})

        # Compare ediff between previous and staticinputset values,
        # choose the tighter ediff
        previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
                                            new_incar["EDIFF"])})

        # add user settings
        if user_incar_settings:
            previous_incar.update(user_incar_settings)
        previous_incar.write_file(os.path.join(output_dir, "INCAR"))

        # Prefer to use k-point scheme from previous run
        previous_kpoints_density = np.prod(previous_kpoints.kpts[0]) / \
            previous_final_structure.lattice.reciprocal_lattice.volume
        new_kpoints_density = max(previous_kpoints_density, 90)
        new_kpoints = mpsvip.get_kpoints(structure,
                                         kpoints_density=new_kpoints_density)
        if previous_kpoints.style[0] != new_kpoints.style[0]:
            if previous_kpoints.style[0] == "M" and \
                    SymmetryFinder(structure, 0.01).get_lattice_type() != \
                    "hexagonal":
                k_div = (kp + 1 if kp % 2 == 1 else kp
                         for kp in new_kpoints.kpts[0])
                Kpoints.monkhorst_automatic(k_div). \
                    write_file(os.path.join(output_dir, "KPOINTS"))
            else:
                Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
                    write_file(os.path.join(output_dir, "KPOINTS"))
        else:
            new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
slab_potcar.write_file("./Slab_with_vdw/POTCAR")

#set the common INCAR file and KPOINTS
incar_dict = {
                 'SYSTEM': 'ligand_PbS', 
                 'ENCUT': 600, 
                 'ISIF': 2, 
                 'IBRION': 2, 
                 'ALGO': 'Normal', 
                 'ISMEAR': 1, 
                 'ISPIN': 1, 
                 'EDIFF': 1e-06, 
                 'EDIFFG': -0.005, 
                 'NPAR': 8, 
                 'SIGMA': 0.1, 
                 'PREC': 'Accurate',
		 'IVDW': 2,
		 'NSW': 1000
    }

incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts= (8, 8, 1), shift= (0, 0, 0))

#write the files in appropriate directory
incar.write_file("./Interface_with_vdw/INCAR")
incar.write_file("./Slab_with_vdw/INCAR")
kpoints.write_file("./Interface_with_vdw/KPOINTS")
kpoints.write_file("./Slab_with_vdw/KPOINTS")
shu.copy("./submit_job", "./Interface_with_vdw/")
shu.copy("./submit_job", "./Slab_with_vdw")

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
    def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
                               user_incar_settings=None,
                               make_dir_if_not_present=True):
        """
        Generate a set of Vasp input files for static calculations from a
        directory of previous Vasp run.

        Args:
            previous_vasp_dir:
                The directory contains the outputs(vasprun.xml and OUTCAR) of
                previous vasp run.
            output_dir:
                The directory to write the VASP input files for the static
                calculations. Default to write in the current directory.
            make_dir_if_not_present:
                Set to True if you want the directory (and the whole path) to
                be created if it is not present.
        """

        try:
            vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
                               parse_dos=False, parse_eigen=None)
            outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
            previous_incar = Incar.from_file(os.path.join(previous_vasp_dir,
                                                          "INCAR"))
            kpoints = Kpoints.from_file(os.path.join(previous_vasp_dir,
                                                     "KPOINTS"))
        except:
            traceback.format_exc()
            raise RuntimeError("Can't get valid results from previous run")

        structure = MPStaticVaspInputSet.get_structure(
            vasp_run, outcar)
        mpsvip = MPStaticVaspInputSet()
        mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
        new_incar = Incar.from_file(os.path.join(output_dir, "INCAR"))

        # Use previous run INCAR and override necessary parameters
        previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
                               "LCHARG": True, "LORBIT": 11, "LVHAR": True,
                               "LWAVE": False, "NSW": 0, "ICHARG": 0})

        # Compare ediff between previous and staticinputset values,
        # choose the tigher ediff
        previous_incar.update({"EDIFF": min(previous_incar["EDIFF"],
                                            new_incar["EDIFF"])})

        # add user settings
        if user_incar_settings:
            previous_incar.update(user_incar_settings)
        previous_incar.write_file(os.path.join(output_dir, "INCAR"))

        # Prefer to use k-point scheme from previous run
        kpoints_out = Kpoints.from_file(os.path.join(output_dir, "KPOINTS"))
        if kpoints.style != kpoints_out.style and \
                SymmetryFinder(structure, 0.01).get_lattice_type() != \
                "hexagonal":
            k_div = (kp + 1 if kp % 2 == 1 else kp
                     for kp in kpoints_out.kpts[0])
            Kpoints.monkhorst_automatic(k_div).write_file(
                os.path.join(output_dir, "KPOINTS"))

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
def get_calibration_task(structure, phase="CalibrateBulk", \
                         slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
                         turn_knobs={}, incar_params={}, other_params={}):
    """
    returns general calibration task for a structure
    
    Args:
        structure    : pymatgen structure to be calibrated (can be a bulk, ligand, slab
                       or interface)  
        phase        : calibration type, viz. CalibrateBulk, CalibrateMolecule,
                       CalibrateSlab, CalibrateInterface
        hkl          : in case of Slab and Interface miller indices of facet 
        turn_knobs   : specifies the parameters to be calibrated 
        incar_params : dictionary of additional incar parameters, refer defined 
                       incar_dict for defaults 
        other_params : other parameters for calibration, viz. job_dir, is_matrix, etc. 
                       described in the calibrate module
    """
    #structure definition 
    
    poscar = Poscar(structure)
    incar_dict = { 'SYSTEM': 'slab',
                   'ENCUT': 500, 
                   'ISIF': 2, 
                   'IBRION': 2, 
                   'ISMEAR': 1, 
                   'EDIFF': 1e-05, 
                   'NPAR': 4, 
                   'SIGMA': 0.1, 
                   'PREC': 'Accurate'
                 }
    if incar_params: 
        incar_dict.update(incar_params)
    incar = Incar.from_dict(incar_dict)
    kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
    que  = { 'nnodes':1,
             'nprocs':16,
             'walltime':'48:00:00',
             'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'             
            }
    # calibration task: relax hkl
    calparams = {}
    calparams['calibrate'] = phase
    calparams['incar'] = incar.as_dict()
    calparams['poscar'] = poscar.as_dict()
    calparams['kpoints'] = kpoints.as_dict()
    calparams['que_params'] = que
    calparams['turn_knobs'] = turn_knobs
    if phase == 'CalibrateSlab':
         calparams['system'] = {'hkl':slab_interface_params['hkl'],
                                'ligand':slab_interface_params['ligand']
                               }
    elif phase == 'CalibrateInterface':
         calparams['system'] = {'hkl':hkl,
                                'ligand':structure.ligand.reduced_formula
                               }
    calparams['other_params'] = {
        'is_matrix':False,
        'from_ase':True,
        'Grid_type':'M'
        }
    if other_params:
        calparams['other_params'].update(other_params)
    return MPINTCalibrateTask(calparams)

# 需要导入模块: from pymatgen.io.vaspio.vasp_input import Kpoints [as 别名]
# 或者: from pymatgen.io.vaspio.vasp_input.Kpoints import monkhorst_automatic [as 别名]
    def from_previous_vasp_run(previous_vasp_dir, output_dir='.',
                               user_incar_settings=None,
                               make_dir_if_not_present=True,
                               kpoints_density=90, sym_prec=0.1):
        """
        Generate a set of Vasp input files for static calculations from a
        directory of previous Vasp run.

        Args:
            previous_vasp_dir (str): Directory containing the outputs(
                vasprun.xml and OUTCAR) of previous vasp run.
            output_dir (str): Directory to write the VASP input files for
                the static calculations. Defaults to current directory.
            make_dir_if_not_present (bool): Set to True if you want the
                directory (and the whole path) to be created if it is not
                present.
            kpoints_density (int): kpoints density for the reciprocal cell
                of structure. Might need to increase the default value when
                calculating metallic materials.
            sym_prec (float): Tolerance for symmetry finding
        """
        # Read input and output from previous run
        try:
            vasp_run = Vasprun(os.path.join(previous_vasp_dir, "vasprun.xml"),
                               parse_dos=False, parse_eigen=None)
            outcar = Outcar(os.path.join(previous_vasp_dir, "OUTCAR"))
            previous_incar = vasp_run.incar
            previous_kpoints = vasp_run.kpoints
        except:
            traceback.format_exc()
            raise RuntimeError("Can't get valid results from previous run")

        mpsvip = MPStaticVaspInputSet(kpoints_density=kpoints_density,
                                      sym_prec=sym_prec)
        structure = mpsvip.get_structure(vasp_run, outcar)

        mpsvip.write_input(structure, output_dir, make_dir_if_not_present)
        new_incar = mpsvip.get_incar(structure)

        # Use previous run INCAR and override necessary parameters
        previous_incar.update({"IBRION": -1, "ISMEAR": -5, "LAECHG": True,
                               "LCHARG": True, "LORBIT": 11, "LVHAR": True,
                               "LWAVE": False, "NSW": 0, "ICHARG": 0})

        for incar_key in ["MAGMOM", "NUPDOWN"]:
            if new_incar.get(incar_key, None):
                previous_incar.update({incar_key: new_incar[incar_key]})
            else:
                previous_incar.pop(incar_key, None)

        # use new LDAUU when possible b/c the Poscar might have changed
        # representation
        if previous_incar.get('LDAU'):
            u = previous_incar.get('LDAUU', [])
            j = previous_incar.get('LDAUJ', [])
            if sum([u[x] - j[x] for x, y in enumerate(u)]) > 0:
                for tag in ('LDAUU', 'LDAUL', 'LDAUJ'):
                    previous_incar.update({tag: new_incar[tag]})
            # ensure to have LMAXMIX for GGA+U static run
            if "LMAXMIX" not in previous_incar:
                previous_incar.update({"LMAXMIX": new_incar["LMAXMIX"]})

        # Compare ediff between previous and staticinputset values,
        # choose the tighter ediff
        previous_incar.update({"EDIFF": min(previous_incar.get("EDIFF", 1),
                                            new_incar["EDIFF"])})

        # add user settings
        if user_incar_settings:
            previous_incar.update(user_incar_settings)
        previous_incar.write_file(os.path.join(output_dir, "INCAR"))

        # Perform checking on INCAR parameters
        if any([previous_incar.get("NSW", 0) != 0, previous_incar["IBRION"] != -1,
               previous_incar["LCHARG"] != True,
               any([sum(previous_incar["LDAUU"])<=0, previous_incar["LMAXMIX"]<4])
               if previous_incar.get("LDAU") else False]):
            raise ValueError("Incompatible INCAR parameters!")

        # Prefer to use k-point scheme from previous run
        new_kpoints = mpsvip.get_kpoints(structure)
        if previous_kpoints.style[0] != new_kpoints.style[0]:
            if previous_kpoints.style[0] == "M" and \
                    SymmetryFinder(structure, 0.1).get_lattice_type() != \
                    "hexagonal":
                k_div = (kp + 1 if kp % 2 == 1 else kp
                         for kp in new_kpoints.kpts[0])
                Kpoints.monkhorst_automatic(k_div). \
                    write_file(os.path.join(output_dir, "KPOINTS"))
            else:
                Kpoints.gamma_automatic(new_kpoints.kpts[0]). \
                    write_file(os.path.join(output_dir, "KPOINTS"))
        else:
            new_kpoints.write_file(os.path.join(output_dir, "KPOINTS"))