Python Kpoints.automatic_density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 automatic_density [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 automatic_density [as 别名]
    def get_kpoints(self, structure):
        """
        Get a KPOINTS file for NonSCF calculation. In "Line" mode, kpoints are
        generated along high symmetry lines. In "Uniform" mode, kpoints are
        Gamma-centered mesh grid. Kpoints are written explicitly in both cases.

        Args:
            structure (Structure/IStructure): structure to get Kpoints
        """
        if self.mode == "Line":
            kpath = HighSymmKpath(structure)
            cart_k_points, k_points_labels = kpath.get_kpoints()
            frac_k_points = [kpath._prim_rec.get_fractional_coords(k)
                             for k in cart_k_points]
            return Kpoints(comment="Non SCF run along symmetry lines",
                           style="Reciprocal", num_kpts=len(frac_k_points),
                           kpts=frac_k_points, labels=k_points_labels,
                           kpts_weights=[1] * len(cart_k_points))
        else:
            num_kpoints = self.kpoints_settings["kpoints_density"] * \
                structure.lattice.reciprocal_lattice.volume
            kpoints = Kpoints.automatic_density(
                structure, num_kpoints * structure.num_sites)
            mesh = kpoints.kpts[0]
            ir_kpts = SymmetryFinder(structure, symprec=self.sym_prec) \
                .get_ir_reciprocal_mesh(mesh)
            kpts = []
            weights = []
            for k in ir_kpts:
                kpts.append(k[0])
                weights.append(int(k[1]))
            return Kpoints(comment="Non SCF run on uniform grid",
                           style="Reciprocal", num_kpts=len(ir_kpts),
                           kpts=kpts, kpts_weights=weights)

# 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 automatic_density [as 别名]
    def get_kpoints(self, structure):
        """
        Writes out a KPOINTS file using the fully automated grid method. Uses
        Gamma centered meshes  for hexagonal cells and Monk grids otherwise.

        Algorithm:
            Uses a simple approach scaling the number of divisions along each
            reciprocal lattice vector proportional to its length.
        """
        dens = int(self.kpoints_settings['grid_density'])
        return Kpoints.automatic_density(structure, dens)

# 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 automatic_density [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 automatic_density [as 别名]
def vac_antisite_def_struct_gen(mpid, mapi_key, cellmax):
    if not mpid:
        print ("============\nERROR: Provide an mpid\n============")
        return

    if not mapi_key:
        with MPRester() as mp:
            struct = mp.get_structure_by_material_id(mpid)
    else:
        with MPRester(mapi_key) as mp:
            struct = mp.get_structure_by_material_id(mpid)

    prim_struct_sites = len(struct.sites)
    struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
    conv_struct_sites = len(struct.sites)
    conv_prim_rat = int(conv_struct_sites/prim_struct_sites)
    sc_scale = get_sc_scale(struct,cellmax)

    mpvis = MPGGAVaspInputSet()

    # Begin defaults: All default settings.
    blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
    def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6, 
                            'EDIFFG':0.001,'NSW':40,}
    kpoint_den = 6000
    # End defaults
    
    ptcr_flag = True
    try:
        potcar = mpvis.get_potcar(struct)
    except:
        print ("VASP POTCAR folder not detected.\n" \
              "Only INCAR, POSCAR, KPOINTS are generated.\n" \
              "If you have VASP installed on this system, \n" \
              "refer to pymatgen documentation for configuring the settings.")
        ptcr_flag = False


    vac = Vacancy(struct, {}, {})
    scs = vac.make_supercells_with_defects(sc_scale)
    site_no = scs[0].num_sites
    if site_no > cellmax:
        max_sc_dim = max(sc_scale)
        i = sc_scale.index(max_sc_dim)
        sc_scale[i] -= 1
        scs = vac.make_supercells_with_defects(sc_scale)

    for i in range(len(scs)):
        sc = scs[i]
        poscar = mpvis.get_poscar(sc)
        kpoints = Kpoints.automatic_density(sc,kpoint_den)
        incar = mpvis.get_incar(sc)
        if ptcr_flag:
            potcar = mpvis.get_potcar(sc)

        interdir = mpid
        if not i:
            fin_dir = os.path.join(interdir,'bulk')
            try:
                os.makedirs(fin_dir)
            except:
                pass
            incar.update(blk_vasp_incar_param)
            incar.write_file(os.path.join(fin_dir,'INCAR'))
            poscar.write_file(os.path.join(fin_dir,'POSCAR'))
            if ptcr_flag:
                potcar.write_file(os.path.join(fin_dir,'POTCAR'))
            kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
        else:
            blk_str_sites = set(scs[0].sites)
            vac_str_sites = set(sc.sites)
            vac_sites = blk_str_sites - vac_str_sites
            vac_site = list(vac_sites)[0]
            site_mult = int(vac.get_defectsite_multiplicity(i-1)/conv_prim_rat)
            vac_site_specie = vac_site.specie
            vac_symbol = vac_site.specie.symbol

            vac_dir ='vacancy_{}_mult-{}_sitespecie-{}'.format(str(i),
                    site_mult, vac_symbol)
            fin_dir = os.path.join(interdir,vac_dir)
            try:
                os.makedirs(fin_dir)
            except:
                pass
            incar.update(def_vasp_incar_param)
            poscar.write_file(os.path.join(fin_dir,'POSCAR'))
            incar.write_file(os.path.join(fin_dir,'INCAR'))
            if ptcr_flag:
                potcar.write_file(os.path.join(fin_dir,'POTCAR'))
            kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))

            # Antisite generation at all vacancy sites
            struct_species = scs[0].types_of_specie
            for specie in set(struct_species)-set([vac_site_specie]):
                subspecie_symbol = specie.symbol
                anti_struct = sc.copy()
                anti_struct.append(specie, vac_site.frac_coords)
                poscar = mpvis.get_poscar(anti_struct)
                incar = mpvis.get_incar(anti_struct)
                incar.update(def_vasp_incar_param)
#.........这里部分代码省略.........

# 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 automatic_density [as 别名]
def get_VASP_inputs(structure, workdir, job_name, nproc=64, kppa=500, extra_incar_dict = None):

    if os.path.exists(workdir):
        print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
        return -1

    poscar  = Poscar(structure)

    list_potcar_singles, potcar= get_POTCAR(poscar)

    kpoints = Kpoints.automatic_density(structure, kppa=kppa)

    # Default values
    incar_dict = dict(  SYSTEM  =   structure.formula, # Name of job
                        LREAL   =   'Auto',     # Should projections be done in real space? Let VASP decide
                        ENCUT   =   520.,       # 520. eV, just like Ceder
                        IBRION  =   2,          # Controls ionic relataxion: 1-> DISS, 2 -> CG, 3-> MD
                        EDIFF   =   1E-7,       # criterion to stop SCF loop, in eV
                        EDIFFG  =  -1E-3,       # criterion to stop ionic relaxations. Negative means FORCES < |EDIFFG|
                        PREC    =   'HIGH',     # level of precision
                        AMIX    =   0.2,
                        AMIX_MAG=   0.8,
                        BMIX    =   0.001,
                        BMIX_MAG=   0.001,
                        NSW     =   150,        # Maximum number of ionic steps
                        ISMEAR  =   0,          # smearing scheme. Use 0 for insulators, as suggested by VASPWIKI
                        ISPIN   =   2,          # spin polarized 
                        NPAR    =   8,          # VASPWIKI recommends sqrt(ncore)
                        LSCALU  =   False,      # Don't use scalapack. Probably a can of worms.
                        ALGO    =   'NORMAL',   # what ionic relaxation scheme to use? 
                        LORBIT  =   11,         # 11 prints out the DOS
                        ISIF    =   3,          # Controls the computation of stress tensor. 3 computes everything
                        NSIM    =   4,          # how many bands to treat in parallel? Default is 4, probably fine.
                        SIGMA   =   0.025,      # smearing in eV
                        LMAXMIX =   4,          # Description: LMAXMIX controls up to which l-quantum number the one-center PAW charge densities are passed through the charge density mixer. MaterialsProject uses 4.
                        LCHARG  =   False,      # Write charge densities?
                        LWAVE   =   False,      # write out the wavefunctions?
                        LPLANE  =   True,       # Plane distribution of FFT coefficients. Reduces communications in FFT.
                        NELM    =   100,        # maximum number of SCF cycles.
                        NELMDL  =  -10,         # since initial orbitals may be random, fixes hamiltonian for |NELM| SCF cycles to give wf a chance to simmer down.
                        ISTART  =   0,          # begin from scratch!
                        ISYM    =   2)          # use symmetry 

    if extra_incar_dict  != None:
        incar_dict.update( extra_incar_dict  )

    incar   = Incar.from_dict(incar_dict )


    incar.write_file(workdir+'INCAR')
    poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
    kpoints.write_file(workdir+'KPOINTS')
    potcar.write_file(workdir+'POTCAR')


    potcar.sort()
    hack_potcar_file(workdir,list_potcar_singles)
    

    with open(workdir+'job.sh','w') as f:
        f.write(submit_template.format(job_name,nproc))

    with open(workdir+'clean.sh','w') as f:
        f.write(clean_template)

    return 0

# 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 automatic_density [as 别名]
def substitute_def_struct_gen(mpid, solute, mapi_key, cellmax):
    print (mpid, solute, mapi_key, cellmax)
    if not mpid:
        print ("============\nERROR: Provide an mpid\n============")
        return
    if not solute:
        print ("============\nERROR: Provide solute atom\n============")
        return

    if not mapi_key:
        with MPRester() as mp:
            struct = mp.get_structure_by_material_id(mpid)
    else:
        with MPRester(mapi_key) as mp:
            struct = mp.get_structure_by_material_id(mpid)

    print (struct.formula)

    mpvis = MPGGAVaspInputSet()

    # Begin defaults: All default settings.
    blk_vasp_incar_param = {'IBRION':-1,'EDIFF':1e-4,'EDIFFG':0.001,'NSW':0,}
    def_vasp_incar_param = {'ISIF':2,'NELM':99,'IBRION':2,'EDIFF':1e-6, 
                            'EDIFFG':0.001,'NSW':40,}
    kpoint_den = 6000
    # End defaults
    
    # Check if POTCAR file can be geneated
    ptcr_flag = True
    try:
        potcar = mpvis.get_potcar(struct)
    except:
        print ("VASP POTCAR folder not detected.\n" \
              "Only INCAR, POSCAR, KPOINTS are generated.\n" \
              "If you have VASP installed on this system, \n" \
              "refer to pymatgen documentation for configuring the settings.")
        ptcr_flag = False

    print (ptcr_flag)

    vac = Vacancy(struct, {}, {})
    sc_scale = get_sc_scale(struct,cellmax)
    scs = vac.make_supercells_with_defects(sc_scale)
    site_no = scs[0].num_sites
    if site_no > cellmax:
            max_sc_dim = max(sc_scale)
            i = sc_scale.index(max_sc_dim)
            sc_scale[i] -= 1
            scs = vac.make_supercells_with_defects(sc_scale)
    print len(scs)

    interdir = mpid
    blk_str_sites = set(scs[0].sites)
    for i in range(1,len(scs)):
        sc = scs[i]
        vac_str_sites = set(sc.sites)
        vac_sites = blk_str_sites - vac_str_sites
        vac_site = list(vac_sites)[0]
        site_mult = vac.get_defectsite_multiplicity(i-1)
        vac_site_specie = vac_site.specie
        vac_specie = vac_site.specie.symbol

        # Solute substitution defect generation at all vacancy sites
        struct_species = scs[0].types_of_specie
        solute_struct = sc.copy()
        solute_struct.append(solute, vac_site.frac_coords)

        incar = mpvis.get_incar(solute_struct)
        incar.update(def_vasp_incar_param)
        poscar = mpvis.get_poscar(solute_struct)
        kpoints = Kpoints.automatic_density(solute_struct,kpoint_den)
        if ptcr_flag:
            potcar = mpvis.get_potcar(solute_struct)

        sub_def_dir ='solute_{}_mult-{}_sitespecie-{}_subspecie-{}'.format(
                str(i), site_mult, vac_specie, solute)
        fin_dir = os.path.join(interdir,sub_def_dir)
        try:
            os.makedirs(fin_dir)
        except:
            pass
        poscar.write_file(os.path.join(fin_dir,'POSCAR'))
        incar.write_file(os.path.join(fin_dir,'INCAR'))
        kpoints.write_file(os.path.join(fin_dir,'KPOINTS'))
        if ptcr_flag:
            potcar.write_file(os.path.join(fin_dir,'POTCAR'))