Python Vasprun.get_vbm方法代码示例

# 需要导入模块: from pymatgen.io.vasp.outputs import Vasprun [as 别名]
# 或者: from pymatgen.io.vasp.outputs.Vasprun import get_vbm [as 别名]
def get_effective_mass():
    """
    This function is in a beta stage, and its results are not
    guaranteed to be useful.

    Finds effective masses from a band structure, using parabolic
    fitting to determine the band curvature at the CBM
    for electrons and at the VBM for holes. This curvature enters
    the equation m* = (hbar)**2 / (d^2E/dk^2).

    To consider anisotropy, the k-space directions to the left and right
    of the CBM/VBM in the band diagram are returned separately.

    *NOTE* Only works for semiconductors and linemode calculations (non-
           spin polarized).
           >30 k-points per string recommended to obtain
           reliable curvatures.

    *NOTE* The parabolic fit can be quite sensitive to the number of
           k-points fit to, so it might be worthwhile adjusting N_KPTS
           to obtain some sense of the error bar.

    TODO: Warn user if CBM/VBM is at the edge of the diagram, and which
          direction (either left or right) was not actually fit to.
          Until fixed, this (most likely) explains any negative masses
          returned.

    Returns:
        Dictionary of the form
            {'electron': {'left': e_m_eff_l, 'right': e_m_eff_r},
             'hole': {'left': h_m_eff_l, 'right': h_m_eff_r}}
            where 'left' and 'right' indicate the reciprocal
            directions to the left and right of the extremum in the
            band structure.
    """

    H_BAR = 6.582119514e-16  # eV*s
    M_0 = 9.10938356e-31  # kg
    N_KPTS = 6  # Number of k-points included in the parabola.

    spin_up = Spin(1)

    band_structure = Vasprun('vasprun.xml').get_band_structure()

    # Locations of CBM and VBM in band_structure.bands
    cbm_band_index = band_structure.get_cbm()['band_index'][spin_up][0]
    cbm_kpoint_index = band_structure.get_cbm()['kpoint_index'][0]

    vbm_band_index = band_structure.get_vbm()['band_index'][spin_up][0]
    vbm_kpoint_index = band_structure.get_vbm()['kpoint_index'][0]

    k = {'electron': {'left': [], 'right': []},
         'hole': {'left': [], 'right': []}}
    E = {'electron': {'left': [], 'right': []},
         'hole': {'left': [], 'right': []}}

    e_ref_coords = band_structure.kpoints[cbm_kpoint_index]._ccoords
    h_ref_coords = band_structure.kpoints[vbm_kpoint_index]._ccoords

    for n in range(-N_KPTS, 1):
        e_coords = band_structure.kpoints[cbm_kpoint_index + n]._ccoords
        h_coords = band_structure.kpoints[vbm_kpoint_index + n]._ccoords

        k['electron']['left'].append(
            ((e_coords[0] - e_ref_coords[0])**2 +
             (e_coords[1] - e_ref_coords[1])**2 +
             (e_coords[2] - e_ref_coords[2])**2)**0.5
            )
        k['hole']['left'].append(
            ((h_coords[0] - h_ref_coords[0])**2 +
             (h_coords[1] - h_ref_coords[1])**2 +
             (h_coords[2] - h_ref_coords[2])**2)**0.5
            )

        e_energy = band_structure.bands[
            spin_up][cbm_band_index][cbm_kpoint_index + n]
        h_energy = band_structure.bands[
            spin_up][vbm_band_index][vbm_kpoint_index + n]

        E['electron']['left'].append(e_energy)
        E['hole']['left'].append(h_energy)

    for n in range(1, 1 + N_KPTS):
        e_coords = band_structure.kpoints[cbm_kpoint_index + n]._ccoords
        h_coords = band_structure.kpoints[vbm_kpoint_index + n]._ccoords

        k['electron']['right'].append(
            ((e_coords[0] - e_ref_coords[0])**2 +
             (e_coords[1] - e_ref_coords[1])**2 +
             (e_coords[2] - e_ref_coords[2])**2)**0.5
            )
        k['hole']['right'].append(
            ((h_coords[0] - h_ref_coords[0])**2 +
             (h_coords[1] - h_ref_coords[1])**2 +
             (h_coords[2] - h_ref_coords[2])**2)**0.5
            )

        e_energy = band_structure.bands[
            spin_up][cbm_band_index][cbm_kpoint_index + n]
        h_energy = band_structure.bands[
#.........这里部分代码省略.........

# 需要导入模块: from pymatgen.io.vasp.outputs import Vasprun [as 别名]
# 或者: from pymatgen.io.vasp.outputs.Vasprun import get_vbm [as 别名]
def plot_band_alignments(directories, run_type='PBE', fmt='pdf'):
    """
    Plot CBM's and VBM's of all compounds together, relative to the band
    edges of H2O.

    Args:
        directories (list): list of the directory paths for materials
            to include in the plot.
        run_type (str): 'PBE' or 'HSE', so that the function knows which
            subdirectory to go into (pbe_bands or hse_bands).
        fmt (str): matplotlib format style. Check the matplotlib
            docs for options.
    """

    if run_type == 'HSE':
        subdirectory = 'hse_bands'
    else:
        subdirectory = 'pbe_bands'

    band_gaps = {}

    for directory in directories:
        sub_dir = os.path.join(directory, subdirectory)
        if is_converged(sub_dir):
            os.chdir(sub_dir)
            band_structure = Vasprun('vasprun.xml').get_band_structure()
            band_gap = band_structure.get_band_gap()

            # Vacuum level energy from LOCPOT.
            locpot = Locpot.from_file('LOCPOT')
            evac = max(locpot.get_average_along_axis(2))

            if not band_structure.is_metal():
                is_direct = band_gap['direct']
                cbm = band_structure.get_cbm()
                vbm = band_structure.get_vbm()

            else:
                cbm = None
                vbm = None
                is_direct = False

            band_gaps[directory] = {'CBM': cbm, 'VBM': vbm,
                                    'Direct': is_direct,
                                    'Metal': band_structure.is_metal(),
                                    'E_vac': evac}

            os.chdir('../../')

    ax = plt.figure(figsize=(16, 10)).gca()

    x_max = len(band_gaps) * 1.315
    ax.set_xlim(0, x_max)

    # Rectangle representing band edges of water.
    ax.add_patch(plt.Rectangle((0, -5.67), height=1.23, width=len(band_gaps),
                 facecolor='#00cc99', linewidth=0))

    ax.text(len(band_gaps) * 1.01, -4.44, r'$\mathrm{H+/H_2}$', size=20,
            verticalalignment='center')
    ax.text(len(band_gaps) * 1.01, -5.67, r'$\mathrm{O_2/H_2O}$', size=20,
            verticalalignment='center')

    x_ticklabels = []

    y_min = -8

    i = 0

    # Nothing but lies.
    are_directs, are_indirects, are_metals = False, False, False

    for compound in [cpd for cpd in directories if cpd in band_gaps]:
        x_ticklabels.append(compound)

        # Plot all energies relative to their vacuum level.
        evac = band_gaps[compound]['E_vac']
        if band_gaps[compound]['Metal']:
            cbm = -8
            vbm = -2
        else:
            cbm = band_gaps[compound]['CBM']['energy'] - evac
            vbm = band_gaps[compound]['VBM']['energy'] - evac

        # Add a box around direct gap compounds to distinguish them.
        if band_gaps[compound]['Direct']:
            are_directs = True
            linewidth = 5
        elif not band_gaps[compound]['Metal']:
            are_indirects = True
            linewidth = 0

        # Metals are grey.
        if band_gaps[compound]['Metal']:
            are_metals = True
            linewidth = 0
            color_code = '#404040'
        else:
            color_code = '#002b80'

#.........这里部分代码省略.........

# 需要导入模块: from pymatgen.io.vasp.outputs import Vasprun [as 别名]
# 或者: from pymatgen.io.vasp.outputs.Vasprun import get_vbm [as 别名]
def plot_band_alignments(directories, run_type="PBE", fmt="pdf"):
    """
    Plot CBM's and VBM's of all compounds together, relative to the band
    edges of H2O.

    Args:
        directories (list): list of the directory paths for materials
            to include in the plot.
        run_type (str): 'PBE' or 'HSE', so that the function knows which
            subdirectory to go into (pbe_bands or hse_bands).
        fmt (str): matplotlib format style. Check the matplotlib
            docs for options.
    """

    if run_type == "HSE":
        subdirectory = "hse_bands"
    else:
        subdirectory = "pbe_bands"

    band_gaps = {}

    for directory in directories:
        if is_converged("{}/{}".format(directory, subdirectory)):
            os.chdir("{}/{}".format(directory, subdirectory))
            band_structure = Vasprun("vasprun.xml").get_band_structure()
            band_gap = band_structure.get_band_gap()

            # Vacuum level energy from LOCPOT.
            locpot = Locpot.from_file("LOCPOT")
            evac = max(locpot.get_average_along_axis(2))

            try:
                is_metal = False
                is_direct = band_gap["direct"]
                cbm = band_structure.get_cbm()
                vbm = band_structure.get_vbm()

            except AttributeError:
                cbm = None
                vbm = None
                is_metal = True
                is_direct = False

            band_gaps[directory] = {"CBM": cbm, "VBM": vbm, "Direct": is_direct, "Metal": is_metal, "E_vac": evac}

            os.chdir("../../")

    ax = plt.figure(figsize=(16, 10)).gca()

    x_max = len(band_gaps) * 1.315
    ax.set_xlim(0, x_max)

    # Rectangle representing band edges of water.
    ax.add_patch(plt.Rectangle((0, -5.67), height=1.23, width=len(band_gaps), facecolor="#00cc99", linewidth=0))
    ax.text(len(band_gaps) * 1.01, -4.44, r"$\mathrm{H+/H_2}$", size=20, verticalalignment="center")
    ax.text(len(band_gaps) * 1.01, -5.67, r"$\mathrm{O_2/H_2O}$", size=20, verticalalignment="center")

    x_ticklabels = []

    y_min = -8

    i = 0

    # Nothing but lies.
    are_directs, are_indirects, are_metals = False, False, False

    for compound in [cpd for cpd in directories if cpd in band_gaps]:
        x_ticklabels.append(compound)

        # Plot all energies relative to their vacuum level.
        evac = band_gaps[compound]["E_vac"]
        if band_gaps[compound]["Metal"]:
            cbm = -8
            vbm = -2
        else:
            cbm = band_gaps[compound]["CBM"]["energy"] - evac
            vbm = band_gaps[compound]["VBM"]["energy"] - evac

        # Add a box around direct gap compounds to distinguish them.
        if band_gaps[compound]["Direct"]:
            are_directs = True
            linewidth = 5
        elif not band_gaps[compound]["Metal"]:
            are_indirects = True
            linewidth = 0

        # Metals are grey.
        if band_gaps[compound]["Metal"]:
            are_metals = True
            linewidth = 0
            color_code = "#404040"
        else:
            color_code = "#002b80"

        # CBM
        ax.add_patch(
            plt.Rectangle(
                (i, cbm), height=-cbm, width=0.8, facecolor=color_code, linewidth=linewidth, edgecolor="#e68a00"
            )
        )
#.........这里部分代码省略.........