Chimie Théorique » QMX

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):

    """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):

        """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):

        """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):

        """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):

        """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)