def jmesh_to_vtk(infile,
outfile,
infile_dict,
outfile_dict,
reduce=False,
scaling=1.0):
if infile.endswith(".jmsh"):
jmesh = jd.load(infile)
meshElem = jmesh["MeshElem"]
points = jmesh["MeshVertex3"] * scaling
elif infile.endswith(".mat"):
mat_contents = scipy.io.loadmat(infile)
points = mat_contents["node"] * scaling
meshElem = mat_contents["elem"]
subdomains = meshElem[:, 4]
if reduce:
subdomains[subdomains == infile_dict["other"]] = 10
subdomains[subdomains == infile_dict["scalp"]] = 10
subdomains[subdomains == infile_dict["skull"]] = 10
subdomains[subdomains == infile_dict["CSF"]] = outfile_dict["fluid_id"]
subdomains[subdomains == infile_dict["WM"]] = outfile_dict["porous_id"]
subdomains[subdomains == infile_dict["GM"]] = outfile_dict["porous_id"]
n = meshElem.shape[0]
p = 4 # number of points per cell for TETRA
c = np.insert(meshElem[:, :4] - 1, 0, p, axis=1)
cell_type = np.repeat(vtk.VTK_TETRA, n)
offset = np.arange(start=0, stop=n * (p + 1), step=p + 1)
grid = pv.UnstructuredGrid(offset, c, cell_type, points)
grid.cell_arrays["subdomains"] = subdomains.flatten()
if reduce:
grid = grid.threshold(5, scalars="subdomains", invert=True)
pv.save_meshio(outfile, grid)
def test_pathlib_read_write(tmpdir, sphere):
path = pathlib.Path(str(tmpdir.mkdir("tmpdir").join('tmp.vtk')))
pyvista.save_meshio(path, sphere)
assert path.is_file()
mesh = pyvista.read_meshio(path)
assert isinstance(mesh, pyvista.UnstructuredGrid)
assert mesh.points.shape == sphere.points.shape
def test_file_format():
from meshio._exceptions import ReadError, WriteError
with pytest.raises(ReadError):
_ = pyvista.read_meshio(examples.hexbeamfile, file_format="bar")
with pytest.raises((KeyError, WriteError)):
pyvista.save_meshio("foo.bar", beam, file_format="bar")
with pytest.raises((KeyError, WriteError)):
pyvista.save_meshio("foo.npy", beam, file_format="npy")
def test_meshio(mesh_in, tmpdir):
# Save and read reference mesh using meshio
filename = tmpdir.mkdir("tmpdir").join("test_mesh.vtk")
pyvista.save_meshio(filename, mesh_in)
mesh = pyvista.read_meshio(filename)
# Assert mesh is still the same
assert np.allclose(mesh_in.points, mesh.points)
if (mesh_in.celltypes == 11).all():
cells = mesh_in.cells.reshape((mesh_in.n_cells, 9))[:,[0,1,2,4,3,5,6,8,7]].ravel()
assert np.allclose(cells, mesh.cells)
else:
assert np.allclose(mesh_in.cells, mesh.cells)
for k, v in mesh_in.point_arrays.items():
assert np.allclose(v, mesh.point_arrays[k.replace(" ", "_")])
for k, v in mesh_in.cell_arrays.items():
assert np.allclose(v, mesh.cell_arrays[k.replace(" ", "_")])
def generate_mesh(points, name="output.json", alpha=1.):
cloud = pv.PolyData(points)
vol = cloud.delaunay_3d(alpha=alpha)
generated_mesh = vol.extract_geometry()
pv.save_meshio("_temp_mesh.stl", generated_mesh)
stl_to_ffbo_json("_temp_mesh.stl", name)
def cli(rbc, plt, verbose, output, axes, bounding_box, clip, stl):
"""Convert and visualise cell position files used in HemoCell [0].
The script reads from any number of red blood cell position files (RBC.pos)
and allows for direct visualisation with PyVista [1] or conversion to XDMF
for inspection with Paraview through `-o, --output`.
The RBC positions can be provided through `stdin` by specifying a dash
(`-`) as argument and piping the input, e.g. `cat RBC.pos | pos_to_vtk -`.
Optionally, any number of platelets position files (PLT.pos) can be
supplied by the `--plt` argument, which might be repeated any number of
times to specify multiple PLT.pos files.
[0] https://hemocell.eu
[1] https://dev.pyvista.org/index.html
"""
if len(rbc) == 0 and len(plt) == 0:
message = """No input files provided. When passing an RBC through
`stdin`, please provide a dash (`-`) as the argument."""
raise click.UsageError(message)
if (bounding_box is not None) and (stl is not None):
message = """Options `--bounding-box` and `--stl` are exclusive and
cannot be combined. Please provide only one."""
raise click.UsageError(message)
rbcs = Cells(flatten([Cells.from_pos(rbc) for rbc in rbc]))
plts = Cells(flatten([Cells.from_pos(plt) for plt in plt]))
if len(rbcs) == 0:
# The script terminates early when no RBCs are present. This
# most-likely corresponds with users error, e.g. by providing the wrong
# file path or an empty file.
raise click.UsageError("No RBC cells to display." "")
if bounding_box:
bounds = flatten(zip((0, 0, 0), bounding_box))
wireframe = pv.Box(bounds)
if stl:
wireframe = pv.get_reader(stl).read()
wireframe.scale((1e3, 1e3, 1e3))
if clip:
rbcs = rbcs.clip(wireframe, bounding_box)
plts = plts.clip(wireframe, bounding_box)
if len(rbcs) == 0 and len(plts) == 0:
raise click.UsageError("No cells remain after clipping.")
if output:
rbcs = create_glyphs(rbcs, CellType.RBC)
merged_cells = rbcs.merge(plts) if plt else rbcs
pv.save_meshio(output, merged_cells)
if verbose:
click.echo(f"Written to: '{click.format_filename(output)}'")
return 0
plotter = pv.Plotter()
rbcs_glyph = create_glyphs(rbcs, CellType.RBC)
rbcs_actor = plotter.add_mesh(rbcs_glyph, color="red")
if plt:
plts_glyph = create_glyphs(plts, CellType.PLT)
plts_actor = plotter.add_mesh(plts_glyph, color="yellow")
if bounding_box or stl:
plotter.add_mesh(wireframe, style='wireframe')
message = f'RBC: {len(rbcs)}\nPLT: {len(plts)}\n'
if clip:
# Only when the domain is clipped, a bounding domain is known either
# through the given bounding box or by the given STL surface mesh.
# These allow to determine an estimate of the domain's volume and
# thereby estimate the expected hematocrit given the number of RBCs
# left after clipping.
volume = 1e-6 * wireframe.volume
hc_percentage = 100 * rbcs.hematocrit(wireframe)
message += f'Domain volume estimate (µm^3): {volume:.2f}\n'
message += f'Hematocrit (vol%): {hc_percentage:.2f}\n'
plotter.add_text(message, position='lower_right')
# A simple widget illustrating the x-y-z axes orientation of the domain.
if axes:
plotter.add_axes(line_width=5, labels_off=False)
# Two radio buttons are added that enable to show/hide the glyphs
# corresponding to all RBCs or PLTs, where the lambda functions are given
# to implement the callback function toggling the right set of glyphs.
plotter.add_checkbox_button_widget(lambda x: rbcs_actor.SetVisibility(x),
position=(5, 12),
color_on="red",
value=True)
plotter.add_checkbox_button_widget(lambda x: plts_actor.SetVisibility(x),
position=(5, 62),
color_on="yellow",
value=True)
return plotter.show()
def fermi3D(
procar: str = "PROCAR",
outcar: str = "OUTCAR",
poscar: str = "POSCAR",
dirname: str = "",
infile: str = "in.bxsf",
abinit_output: str = None,
fermi: float = None,
bands: List[int] = None,
interpolation_factor: int = 1,
mode: str = "plain",
supercell: List[int] = [1, 1, 1],
extended_zone_directions: List[List[int]] = None,
colors: List[str] or List[Tuple[float, float, float]] = None,
background_color: str = "white",
save_colors: bool = False,
cmap: str = "jet",
atoms: List[int] = None,
orbitals: List[int] = None,
calculate_fermi_speed: bool = False,
calculate_fermi_velocity: bool = False,
calculate_effective_mass: bool = False,
spins: List[int] = None,
spin_texture: bool = False,
arrow_color=None,
arrow_size: float = 0.015,
only_spin: bool = False,
fermi_shift: float = 0,
projection_accuracy: str = "normal",
code: str = "vasp",
vmin: float = 0,
vmax: float = 1,
savegif: str = None,
savemp4: str = None,
save3d: str = None,
save_meshio: bool = False,
perspective: bool = True,
save2d: bool = False,
show_slice: bool = False,
slice_normal: Tuple[float, float, float] = (1, 0, 0),
slice_origin: Tuple[float, float, float] = (0, 0, 0),
show_cross_section_area: bool = False,
iso_slider: bool = False,
iso_range: float = 2,
iso_surfaces: int = 10,
camera_pos: List[float] = [1, 1, 1],
widget: bool = False,
show: bool = True,
repair: bool = True,
):
"""
Parameters
----------
procar : str, optional (default ``'PROCAR'``)
Path to the PROCAR file of the simulation
e.g. ``procar='~/MgB2/fermi/PROCAR'``
outcar : str, optional (default ``'OUTCAR'``)
Path to the OUTCAR file of the simulation
e.g. ``outcar='~/MgB2/fermi/OUTCAR'``
abinit_output : str, optional (default ``None``)
Path to the Abinit output file
e.g. ``outcar='~/MgB2/abinit.out'``
infile : str, optional (default ``infile = in.bxsf'``)
This is the path in the input bxsf file
e.g. ``infile = ni_fs.bxsf'``
fermi : float, optional (default ``None``)
Fermi energy at which the fermi surface is created. In other
words fermi is the isovalue at which the fermi surface is
created. If not defined it is read from the OUTCAR file.
e.g. ``fermi=-5.49``
bands : list int, optional
Which bands are going to be plotted in the fermi surface. The
numbering is based on vasp outputs. If nothing is selected,
this function will iterate over all the bands and plots the
ones that cross fermi.
e.g. ``bands=[14, 15, 16, 17]``
interpolation_factor : int, optional
The kpoints grid will increase by this factor and interpolated
at the new points using Fourier interpolation.
e.g. If the kgrid is 5x5x5, ``interpolation_factor=4`` will
lead to a kgrid of 20x20x20
mode : str, optional (default ``mode='plain'``)
Defines If the fermi surface will have any projection using
colormaps or is a plotted with a uniform plain color.
e.g. ``mode='plain'``, ``mode='parametric'``
supercell : list int, optional (default ``[1, 1, 1]``)
If one wants plot more than the 1st brillouin zone, this
parameter can be used.
e.g. ``supercell=[2, 2, 2]``
extended_zone_directions : list of list of size 3, optional (default ``None``)
If one wants plot more than brillouin zones in a particular direection, this
parameter can be used.
e.g. ``extended_zone_directions=[[1,0,0],[0,1,0],[0,0,1]]``
colors : list str or list tuples of size 4, optional
List of colors for each band. If you use tuple, it represents rgba values
This argument does not work whena 3d file is saved.
The colors for when ``save3d`` is used, we
recomend using qualitative colormaps, as this function will
automatically choose colors from the colormaps.
e.g. ``colors=['red', 'blue', 'green']``
``colors=[(1,0,0,1), (0,1,0,1), (0,0,1,1)]``
background_color : str, optional (default ``white``)
Defines the background color.
e.g. ``background_color='gray'``
save_colors : bool, optional (default ``False``)
In case the plot is saved in 3D and some property of the
material is projected on the fermi surface, this argument
allows the projection to be stored in the 3D file.
e.g. ``save_colors=True``
cmap : str, optional (default ``jet``)
The color map used for color coding the projections. ``cmap``
is only relevant in ``mode='parametric'``. A full list of
color maps in matplotlib are provided in this web
page. `https://matplotlib.org/2.0.1/users/colormaps.html
<https://matplotlib.org/2.0.1/users/colormaps.html>`_
atoms : list int, optional
``atoms`` define the projection of the atoms on the fermi
surfcae . In other words it selects only the contribution of the
atoms provided. Atoms has to be a python list(or numpy array)
containing the atom indices. Atom indices has to be order of
the input files of DFT package. ``atoms`` is only relevant in
``mode='parametric'``. keep in mind that python counting
starts from zero.
e.g. for SrVO\ :sub:`3`\ we are choosing only the oxygen
atoms. ``atoms=[2, 3, 4]``, keep in mind that python counting
starts from zero, for a **POSCAR** similar to following::
Sr1 V1 O3
1.0
3.900891 0.000000 0.000000
0.000000 3.900891 0.000000
0.000000 0.000000 3.900891
Sr V O
1 1 3
direct
0.500000 0.500000 0.500000 Sr atom 0
0.000000 0.000000 0.000000 V atom 1
0.000000 0.500000 0.000000 O atom 2
0.000000 0.000000 0.500000 O atom 3
0.500000 0.000000 0.000000 O atom 4
if nothing is specified this parameter will consider all the
atoms present.
orbitals : list int, optional
``orbitals`` define the projection of orbitals on the fermi
surface. In other words it selects only the contribution of
the orbitals provided. Orbitals has to be a python list(or
numpy array) containing the Orbital indices. Orbitals indices
has to be order of the input files of DFT package. The
following table represents the indecies for different orbitals
in **VASP**.
+-----+-----+----+----+-----+-----+-----+-----+-------+
| s | py | pz | px | dxy | dyz | dz2 | dxz | x2-y2 |
+-----+-----+----+----+-----+-----+-----+-----+-------+
| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
+-----+-----+----+----+-----+-----+-----+-----+-------+
``orbitals`` is only relavent in ``mode='parametric'``
e.g. ``orbitals=[1,2,3]`` will only select the p orbitals
while ``orbitals=[4,5,6,7,8]`` will select the d orbitals.
If nothing is specified pyprocar will select all the present
orbitals.
calculate_fermi_velocity : bool, optional (default False)
Boolean value to calculate fermi velocity vectors on the fermi surface.
Must be used with mode= "property_projection".
e.g. ``fermi_velocity_vector=True``
calculate_fermi_speed : bool, optional (default False)
Boolean value to calculate magnitude of the fermi velocity on the fermi surface.
Must be used with mode= "property_projection".
e.g. ``fermi_velocity=True``
calculate_effective_mass : bool, optional (default False)
Boolean value to calculate the harmonic mean of the effective mass on the fermi surface.
Must be used with mode= "property_projection".
e.g. ``effective_mass=True``
spins : list int, optional
e.g. ``spins=[0]``
spin_texture : bool, optional (default False)
In non collinear calculation one can choose to plot the spin
texture on the fermi surface.
e.g. ``spin_texture=True``
arrow_color : str, optional
Defines the color of the arrows when
``spin_texture=True``. The default will select the colors
based on the color map specified. If arrow_color is selected,
all arrows will have the same color.
e.g. ``arrow_color='red'``
arrow_size : int, optional
As the name suggests defines the size of the arrows, when spin
texture is selected.
e.g. ``arrow_size=3``
only_spin : bool, optional
If ``only_spin=True`` is selected, the fermi surface is not
plotted and only the spins in the spin texture is plotted.
fermi_shift : float, optional
This parameter is useful when one wants to plot the iso-surface
above or belove the fermi level.
e.g. ``fermi_shift=0.6``
projection_accuracy : str, optional (default ``'normal'``)
Selected the accuracy of projected properties. ``'normal'`` and
``'high'`` are the only two options. ``'normal'`` uses the fast
but rather inaccurate nearest neighbor interpolation, while
``'high'`` uses the more accurate linear interpolation for the
projection of the properties.
e.g. ``projection_accuracy='high'``
code : str, optional (default ``'vasp'``)
The DFT code in which the calculation is performed with.
Also, if you want to read a .bxsf file set code ="bxsf"
e.g. ``code='vasp'``
vmin : float, optional
The maximum value in the color bar. cmap is only relevant in
``mode='parametric'``.
e.g. vmin=-1.0
vmax : float, optional
The maximum value in the color bar. cmap is only relevant in
``mode='parametric'``.
e.g. vmax=1.0
savegif : str, optional
pyprocar can save the fermi surface in a gif
format. ``savegif`` is the path to which the gif is saved.
e.g. ``savegif='fermi.gif'`` or ``savegif='~/MgB2/fermi.gif'``
savemp4 : str, optional
pyprocar can save the fermi surface in a mp4 video format.
``savemp4`` is the path to which the video is saved.
e.g. ``savegif='fermi.mp4'`` or ``savegif='~/MgB2/fermi.mp4'``
save3d : str, optional
pyprocar can save the fermi surface in a 3d file format.
pyprocar uses the `trimesh <https://github.com/mikedh/trimesh>`_
to save the 3d file. trimesh can export files with the
following formats STL, binary PLY, ASCII OFF, OBJ, GLTF/GLB
2.0, COLLADA. ``save3d`` is the path to which the file is saved.
e.g. ``save3d='fermi.glb'``
save_meshio : bool, optional
pyprocar can use meshio to save any 3d format supported by it.
perspective : bool, optional
To create the illusion of depth, perspective is used in 2d
graphics. One can turn this feature off by ``perspective=False``
e.g. ``perspective=False``
save2d : str, optional
The fermi surface can be saved as a 2D image. This parameter
turns this feature on and selects the path at which the file
is going to be saved.
e.g. ``save2d='fermi.png'``
show_slice : bool, optional
Creates a widget which slices the fermi surface
slice_origin : tuple, optional
Origin to put the plane widget
slice_normal : bool, optional
Normal of the plane widget
show_cross_section_area : bool, optional
Shows the largest cross sectional area
show_curvature : bool, optional
plots the curvature of the fermi surface
curvature_type : str, optional
If show_curvature is True, this option chooses the type of curvature
availible in Pyvista. ('mean', 'gaussian', 'maximum', 'minimum')
iso_slider : bool, optional
plots a slider widget which controls which iso_energy value viewed
iso_range : float, optional
If iso_slider is True, this specifies the energy range
around the fermi surface to view
iso_surfaces : int, optional
If iso_slider is True, this specifies how many surfaces to
generate in the range specified around the fermi surface
camera_pos : list float, optional (default ``[1, 1, 1]``)
This parameter defines the position of the camera where it is
looking at the fermi surface. This feature is important when
one chooses to use the ``save2d``, ``savegif`` or ``savemp4``
option.
e.g. ``camera_pos=[0.5, 1, -1]``
widget : , optional
.. todo::
show : bool, optional (default ``True``)
If set to ``False`` it will not show the 3D plot.
Returns
-------
s : pyprocar surface object
The whole fermi surface added bands
surfaces : list pyprocar surface objects
list of fermi surface of each band
"""
welcome()
##########################################################################
# Code dependencies
##########################################################################
if code == "vasp" or code == "abinit":
if repair:
repairhandle = UtilsProcar()
repairhandle.ProcarRepair(procar, procar)
print("PROCAR repaired. Run with repair=False next time.")
if code == "vasp":
outcar = io.vasp.Outcar(outcar)
if fermi is None:
e_fermi = outcar.efermi
else:
e_fermi = fermi
poscar = io.vasp.Poscar(poscar)
reciprocal_lattice = poscar.structure.reciprocal_lattice
procarFile = ProcarParser()
procarFile.readFile(procar, False)
data = ProcarSelect(procarFile, deepCopy=True)
elif code == "abinit":
procarFile = ProcarParser()
procarFile.readFile(procar, False)
abinitFile = AbinitParser(abinit_output=abinit_output)
if fermi is None:
e_fermi = abinitFile.fermi
else:
e_fermi = fermi
reciprocal_lattice = abinitFile.reclat
data = ProcarSelect(procarFile, deepCopy=True)
# Converting Ha to eV
data.bands = 27.211396641308 * data.bands
elif code == "qe":
# procarFile = parser
if dirname is None:
dirname = "bands"
procarFile = io.qe.QEParser(scfIn_filename="scf.in",
dirname=dirname,
bandsIn_filename="bands.in",
pdosIn_filename="pdos.in",
kpdosIn_filename="kpdos.in",
atomic_proj_xml="atomic_proj.xml",
dos_interpolation_factor=None)
reciprocal_lattice = procarFile.reciprocal_lattice
data = ProcarSelect(procarFile, deepCopy=True)
if fermi is None:
e_fermi = procarFile.efermi
else:
e_fermi = fermi
# procarFile = QEFermiParser()
# reciprocal_lattice = procarFile.reclat
# data = ProcarSelect(procarFile, deepCopy=True)
# if fermi is None:
# e_fermi = procarFile.efermi
# else:
# e_fermi = fermi
elif code == "lobster":
procarFile = LobsterFermiParser()
reciprocal_lattice = procarFile.reclat
data = ProcarSelect(procarFile, deepCopy=True)
if fermi is None:
e_fermi = 0
else:
e_fermi = fermi
elif code == "bxsf":
e_fermi = fermi
data = BxsfParser(infile=infile)
reciprocal_lattice = data.reclat
elif code == "frmsf":
e_fermi = fermi
data = FrmsfParser(infile=infile)
reciprocal_lattice = data.rec_lattice
bands = np.arange(len(data.bands[0, :]))
##########################################################################
# Data Formating
##########################################################################
bands_to_keep = bands
if bands_to_keep is None:
bands_to_keep = np.arange(len(data.bands[0, :]))
spd = []
if mode == "parametric":
if orbitals is None:
orbitals = [-1]
if atoms is None:
atoms = [-1]
if spins is None:
spins = [0]
data.selectIspin(spins)
data.selectAtoms(atoms, fortran=False)
data.selectOrbital(orbitals)
for iband in bands_to_keep:
spd.append(data.spd[:, iband])
elif mode == "property_projection":
for iband in bands_to_keep:
spd.append(None)
else:
for iband in bands_to_keep:
spd.append(None)
spd_spin = []
if spin_texture:
dataX = ProcarSelect(procarFile, deepCopy=True)
dataY = ProcarSelect(procarFile, deepCopy=True)
dataZ = ProcarSelect(procarFile, deepCopy=True)
dataX.kpoints = data.kpoints
dataY.kpoints = data.kpoints
dataZ.kpoints = data.kpoints
dataX.spd = data.spd
dataY.spd = data.spd
dataZ.spd = data.spd
dataX.bands = data.bands
dataY.bands = data.bands
dataZ.bands = data.bands
dataX.selectIspin([1])
dataY.selectIspin([2])
dataZ.selectIspin([3])
dataX.selectAtoms(atoms, fortran=False)
dataY.selectAtoms(atoms, fortran=False)
dataZ.selectAtoms(atoms, fortran=False)
dataX.selectOrbital(orbitals)
dataY.selectOrbital(orbitals)
dataZ.selectOrbital(orbitals)
for iband in bands_to_keep:
spd_spin.append([
dataX.spd[:, iband], dataY.spd[:, iband], dataZ.spd[:, iband]
])
else:
for iband in bands_to_keep:
spd_spin.append(None)
##########################################################################
# Initialization of the Fermi Surface
##########################################################################
if iso_slider == False:
fermi_surface3D = FermiSurface3D(
kpoints=data.kpoints,
bands=data.bands,
bands_to_keep=bands_to_keep,
spd=spd,
spd_spin=spd_spin,
colors=colors,
calculate_fermi_speed=calculate_fermi_speed,
calculate_fermi_velocity=calculate_fermi_velocity,
calculate_effective_mass=calculate_effective_mass,
fermi=e_fermi,
fermi_shift=fermi_shift,
reciprocal_lattice=reciprocal_lattice,
interpolation_factor=interpolation_factor,
projection_accuracy=projection_accuracy,
supercell=supercell,
cmap=cmap,
vmin=vmin,
vmax=vmax,
extended_zone_directions=extended_zone_directions,
# curvature_type = curvature_type,
)
brillouin_zone = fermi_surface3D.brillouin_zone
# fermi_surface_area = fermi_surface3D.fermi_surface_area
# band_surfaces_area = fermi_surface3D.band_surfaces_area
# fermi_surface_curvature = fermi_surface3D.fermi_surface_curvature
# band_surfaces_curvature = fermi_surface3D.band_surfaces_curvature
elif iso_slider == True:
energy_values = np.linspace(e_fermi - iso_range / 2,
e_fermi + iso_range / 2, iso_surfaces)
e_surfaces = []
for e_value in energy_values:
fermi_surface3D = FermiSurface3D(
kpoints=data.kpoints,
bands_to_keep=bands_to_keep,
bands=data.bands,
spd=spd,
spd_spin=spd_spin,
calculate_fermi_speed=calculate_fermi_speed,
calculate_fermi_velocity=calculate_fermi_velocity,
calculate_effective_mass=calculate_effective_mass,
fermi=e_value,
fermi_shift=fermi_shift,
reciprocal_lattice=reciprocal_lattice,
interpolation_factor=interpolation_factor,
projection_accuracy=projection_accuracy,
supercell=supercell,
cmap=cmap,
vmin=vmin,
vmax=vmax,
extended_zone_directions=extended_zone_directions)
brillouin_zone = fermi_surface3D.brillouin_zone
e_surfaces.append(fermi_surface3D)
##########################################################################
# Plotting the surface
##########################################################################
if show:
p = pyvista.Plotter()
if show or save2d:
# sargs = dict(interactive=True)
p.add_mesh(
brillouin_zone,
style="wireframe",
line_width=3.5,
color="black",
)
if show_slice == True:
text = mode
if show_cross_section_area == True and bands != None:
if len(bands) == 1:
add_mesh_slice_w_cross_sectional_area(plotter=p,
mesh=fermi_surface3D,
normal=slice_normal,
origin=slice_origin,
scalars="scalars")
p.remove_scalar_bar()
else:
print('---------------------------------------------')
print("Can only show area of one band at a time")
print('---------------------------------------------')
else:
if mode == "plain":
text = "Plain"
add_custom_mesh_slice(plotter=p,
mesh=fermi_surface3D,
normal=slice_normal,
origin=slice_origin,
scalars="scalars")
p.remove_scalar_bar()
elif mode == "parametric":
text = "Projection"
add_custom_mesh_slice(plotter=p,
mesh=fermi_surface3D,
normal=slice_normal,
origin=slice_origin,
scalars="scalars")
p.remove_scalar_bar()
elif iso_slider == True:
def create_mesh(value):
res = int(value)
closest_idx = find_nearest(energy_values, res)
if mode == "plain":
scalars = "bands"
elif mode == "parametric":
scalars = "scalars"
elif mode == "property_projection":
if calculate_fermi_speed == True:
scalars = "Fermi Speed"
elif calculate_fermi_velocity == True:
scalars = "Fermi Velocity Vector"
elif calculate_effective_mass == True:
scalars = "Geometric Average Effective Mass"
else:
text = "Spin Texture"
scalars = "spin"
p.add_mesh(e_surfaces[closest_idx],
name='iso_surface',
scalars=scalars)
arrows = e_surfaces[closest_idx].glyph(orient=scalars,
scale=False,
factor=arrow_size)
p.remove_scalar_bar()
if arrow_color is None:
p.add_mesh(arrows,
scalars="Fermi Velocity Vector_magnitude",
cmap=cmap)
else:
p.add_mesh(arrows, color=arrow_color)
p.remove_scalar_bar()
return
if mode == "plain":
text = "Plain"
elif mode == "parametric":
text = "Projection"
elif mode == "property_projection":
if calculate_fermi_speed == True:
text = "Projection"
else:
text = "Spin Texture"
p.add_slider_widget(
create_mesh, [np.amin(energy_values),
np.amax(energy_values)],
title='Energy iso-value',
style='modern',
color='black')
else:
if not spin_texture:
if mode == "plain":
p.add_mesh(fermi_surface3D,
scalars="bands",
cmap=cmap,
rgba=True)
text = "Plain"
elif mode == "parametric":
p.add_mesh(fermi_surface3D, scalars="scalars", cmap=cmap)
p.remove_scalar_bar()
text = "Projection"
elif mode == "property_projection":
if calculate_fermi_speed == True:
text = "Fermi Speed"
p.add_mesh(fermi_surface3D,
scalars="Fermi Speed",
cmap=cmap)
if calculate_effective_mass == True:
text = "Effective Mass"
p.add_mesh(fermi_surface3D,
scalars="Geometric Average Effective Mass",
cmap=cmap)
if calculate_fermi_velocity == True:
text = "Fermi Velocity"
arrows = fermi_surface3D.glyph(
orient="Fermi Velocity Vector",
scale=False,
factor=arrow_size)
p.add_mesh(fermi_surface3D,
scalars="Fermi Velocity Vector_magnitude",
cmap=cmap)
p.remove_scalar_bar()
if arrow_color is None:
p.add_mesh(
arrows,
scalars="Fermi Velocity Vector_magnitude",
cmap=cmap)
else:
p.add_mesh(arrows, color=arrow_color)
p.remove_scalar_bar()
else:
text = "Spin Texture"
# Example dataset with normals
# create a subset of arrows using the glyph filter
arrows = fermi_surface3D.glyph(orient="spin",
scale=False,
factor=arrow_size)
if arrow_color is None:
p.add_mesh(arrows, cmap=cmap, clim=[vmin, vmax])
p.remove_scalar_bar()
else:
p.add_mesh(arrows, color=arrow_color)
if mode != "plain" or spin_texture:
p.add_scalar_bar(
title=text,
n_labels=6,
italic=False,
bold=False,
title_font_size=None,
label_font_size=None,
position_x=0.4,
position_y=0.01,
color="black",
)
p.add_axes(xlabel="Kx",
ylabel="Ky",
zlabel="Kz",
line_width=6,
labels_off=False)
if not perspective:
p.enable_parallel_projection()
p.set_background(background_color)
if not widget:
p.show(cpos=camera_pos, screenshot=save2d)
if savegif is not None:
path = p.generate_orbital_path(n_points=36)
p.open_gif(savegif)
p.orbit_on_path(path)
if savemp4:
path = p.generate_orbital_path(n_points=36)
p.open_movie(savemp4)
p.orbit_on_path(path)
# p.close()
# p.show()
# if iso_slider == False:
# s = boolean_add(fermi_surface3D)
# s.set_color_with_cmap(cmap=cmap, vmin=vmin, vmax=vmax)
# s.pyvista_obj.plot()
# s.trimesh_obj.show()
if save3d is not None:
if save_meshio == True:
pyvista.save_meshio(save3d, fermi_surface3D)
else:
extention = save3d.split(".")[-1]