Source code for ase.visualize.vtk.atoms
import numpy as np
from ase import Atoms
from ase.visualize.vtk.sources import vtkAtomSource, vtkForceSource, \
vtkVelocitySource
from ase.visualize.vtk.cell import vtkUnitCellModule, vtkAxesModule
from ase.visualize.vtk.grid import vtkAtomicPositions
from ase.visualize.vtk.module import vtkModuleAnchor, vtkGlyphModule
# -------------------------------------------------------------------
class vtkAtoms(vtkModuleAnchor, vtkAtomicPositions):
[docs] """Provides fundamental representation for ``Atoms``-specific data in VTK.
The ``vtkAtoms`` class plots atoms during simulations, extracting the
relevant information from the list of atoms. It is created using
the list of atoms as an argument to the constructor. Then one or more
visualization modules can be attached using add_module(name, module).
Example:
>>> va = vtkAtoms(atoms)
>>> va.add_forces()
>>> va.add_axes()
>>> XXX va.add_to_renderer(vtk_ren)
"""
def __init__(self, atoms, scale=1):
"""Construct a fundamental VTK-representation of atoms.
atoms: Atoms object or list of Atoms objects
The atoms to be plotted.
scale = 1: float or int
Relative scaling of all Atoms-specific visualization.
"""
assert isinstance(atoms, Atoms)
self.atoms = atoms
self.scale = scale
vtkModuleAnchor.__init__(self)
vtkAtomicPositions.__init__(self, self.atoms.get_positions(),
vtkUnitCellModule(self.atoms))
self.force = None
self.velocity = None
symbols = self.atoms.get_chemical_symbols()
for symbol in np.unique(symbols):
# Construct mask for all atoms with this symbol
mask = np.array(symbols) == symbol
if mask.all():
subset = None
else:
subset = np.argwhere(mask).ravel()
# Get relevant VTK unstructured grid
vtk_ugd = self.get_unstructured_grid(subset)
# Create atomic glyph source for this symbol
glyph_source = vtkAtomSource(symbol, self.scale)
# Create glyph module and anchor it
self.add_module(symbol, vtkGlyphModule(vtk_ugd, glyph_source))
def has_forces(self):
return self.force is not None
def has_velocities(self):
return self.velocity is not None
def add_cell(self):
[docs] """Add a box outline of the cell using atoms.get_cell(). The existing
``vtkUnitCellModule`` is added to the module anchor under ``cell``."""
self.add_module('cell', self.cell)
def add_axes(self):
[docs] """Add an orientation indicator for the cartesian axes. An appropriate
``vtkAxesModule`` is added to the module anchor under ``axes``."""
self.add_module('axes', vtkAxesModule(self.cell))
def add_forces(self):
[docs] """Add force vectors for the atoms using atoms.get_forces(). A
``vtkGlyphModule`` is added to the module anchor under ``force``."""
if self.has_forces():
raise RuntimeError('Forces already present.')
elif self.has_velocities():
raise NotImplementedError('Can\'t add forces due to velocities.')
# Add forces to VTK unstructured grid as vector data
vtk_fda = self.add_vector_property(self.atoms.get_forces(), 'force')
# Calculate max norm of the forces
fmax = vtk_fda.GetMaxNorm()
# Get relevant VTK unstructured grid
vtk_ugd = self.get_unstructured_grid()
self.force = vtkGlyphModule(vtk_ugd, vtkForceSource(fmax, self.scale),
scalemode='vector', colormode=None)
self.add_module('force', self.force)
def add_velocities(self):
[docs] """Add velocity vectors for the atoms using atoms.get_velocities(). A
``vtkGlyphModule`` is added to the module anchor under ``velocity``."""
if self.has_velocities():
raise RuntimeError('Velocities already present.')
elif self.has_forces():
raise NotImplementedError('Can\'t add velocities due to forces.')
# Add velocities to VTK unstructured grid as vector data
vtk_vda = self.add_vector_property(self.atoms.get_velocities(), 'velocity')
# Calculate max norm of the velocities
vmax = vtk_vda.GetMaxNorm()
# Get relevant VTK unstructured grid
vtk_ugd = self.get_unstructured_grid()
self.velocity = vtkGlyphModule(vtk_ugd, vtkVelocitySource(vmax, self.scale),
scalemode='vector', colormode=None)
self.add_module('velocity', self.velocity)