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)

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