def drawBonds(self, nbonds, start, end, colors=None, bond_radii=None):
bond_positions = start
bond_directions = end - start
bond_lengths = np.linalg.norm(bond_directions, axis=1)
gr3.drawcylindermesh(nbonds, bond_positions, bond_directions, colors,
bond_radii, bond_lengths)
def init_gr3():
def log_callback(message):
print "Log: ", message
gr3.setlogcallback(log_callback)
gr3.init([gr3.GR3_InitAttribute.GR3_IA_FRAMEBUFFER_WIDTH, 1024, gr3.GR3_InitAttribute.GR3_IA_FRAMEBUFFER_HEIGHT, 1024])
print gr3.getrenderpathstring()
# Atome zeichnen
gr3.drawspheremesh(len(atom_data), sphere_positions, sphere_colors, sphere_radii)
# Atombindungen zeichnen
gr3.drawcylindermesh(len(cylinder_positions), cylinder_positions, cylinder_directions, cylinder_colors, cylinder_radii, cylinder_lengths)
def init_gr3():
def log_callback(message):
print("Log: ", message)
gr3.setlogcallback(log_callback)
gr3.init([
gr3.GR3_InitAttribute.GR3_IA_FRAMEBUFFER_WIDTH, 1024,
gr3.GR3_InitAttribute.GR3_IA_FRAMEBUFFER_HEIGHT, 1024
])
print(gr3.getrenderpathstring())
# draw atoms
gr3.drawspheremesh(len(atom_data), sphere_positions, sphere_colors,
sphere_radii)
# draw atomic bonds
gr3.drawcylindermesh(len(cylinder_positions), cylinder_positions,
cylinder_directions, cylinder_colors, cylinder_radii,
cylinder_lengths)
def double_pendulum(theta, length, mass):
gr.clearws()
gr.setviewport(0, 1, 0, 1)
direction = []
position = [(0, 0, 0)]
for i in range(2):
direction.append(
(sin(theta[i]) * length[i] * 2, -cos(theta[i]) * length[i] * 2, 0))
position.append([position[-1][j] + direction[-1][j] for j in range(3)])
gr3.clear()
# draw pivot point
gr3.drawcylindermesh(1, (0, 0.2, 0), (0, 1, 0), (0.4, 0.4, 0.4), 0.4, 0.05)
gr3.drawcylindermesh(1, (0, 0.2, 0), (0, -1, 0), (0.4, 0.4, 0.4), 0.05,
0.2)
gr3.drawspheremesh(1, (0, 0, 0), (0.4, 0.4, 0.4), 0.05)
# draw rods
gr3.drawcylindermesh(2, position, direction, (0.6, 0.6, 0.6) * 2,
(0.05, 0.05), [l * 2 for l in length])
# draw bobs
gr3.drawspheremesh(2, position[1:], (1, 1, 1) * 2, [m * 0.2 for m in mass])
gr3.drawimage(0, 1, 0, 1, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.updatews()
return
def _create_gr3_scene(molecule, show_bonds=True):
"""
Create the GR3 scene from the provided molecule and - if show_bonds is
True (default) - the atomic bonds in the molecule.
"""
gr3.clear()
num_atoms = len(molecule.atomic_numbers)
gr3.drawspheremesh(num_atoms,
molecule.positions,
ATOM_COLORS[molecule.atomic_numbers],
molecule.atomic_radii)
if show_bonds and len(molecule.bonds.index_pairs) > 0:
index_pairs = molecule.bonds.index_pairs
num_bonds = len(molecule.bonds)
bond_positions = molecule.positions[index_pairs[:, 0]]
bond_directions = molecule.positions[index_pairs[:, 1]]-bond_positions
bond_lengths = la.norm(bond_directions, axis=1)
bond_directions /= bond_lengths.reshape(num_bonds, 1)
bond_radii = np.ones(num_bonds, dtype=np.float32)*BOND_RADIUS
bond_colors = np.ones((num_bonds, 3), dtype=np.float32)*0.3
gr3.drawcylindermesh(num_bonds, bond_positions, bond_directions,
bond_colors, bond_radii, bond_lengths)
def _create_gr3_scene(molecule, show_bonds=True):
"""
Create the GR3 scene from the provided molecule and - if show_bonds is
True (default) - the atomic bonds in the molecule.
"""
gr3.clear()
num_atoms = len(molecule.atomic_numbers)
gr3.drawspheremesh(num_atoms,
molecule.positions,
ATOM_COLORS[molecule.atomic_numbers],
molecule.atomic_radii)
if show_bonds and len(molecule.bonds.index_pairs) > 0:
index_pairs = molecule.bonds.index_pairs
num_bonds = len(molecule.bonds)
bond_positions = molecule.positions[index_pairs[:, 0]]
bond_directions = molecule.positions[index_pairs[:, 1]]-bond_positions
bond_lengths = la.norm(bond_directions, axis=1)
bond_directions /= bond_lengths.reshape(num_bonds, 1)
bond_radii = np.ones(num_bonds, dtype=np.float32)*BOND_RADIUS
bond_colors = np.ones((num_bonds, 3), dtype=np.float32)*0.3
gr3.drawcylindermesh(num_bonds, bond_positions, bond_directions,
bond_colors, bond_radii, bond_lengths)
def pendulum(t, theta, omega, acceleration):
gr.clearws()
gr.setviewport(0, 1, 0, 1)
x, y = (sin(theta) * 3.0, -cos(theta) * 3.0)
gr3.clear()
# draw pivot point
gr3.drawspheremesh(1, (0, 0, 0), (0.4, 0.4, 0.4), 0.1)
# draw rod
gr3.drawcylindermesh(1, (0, 0, 0), (x, y, 0), (0.6, 0.6, 0.6), 0.05, 3.0)
# draw sphere
gr3.drawspheremesh(1, (x, y, 0), (1, 1, 1), 0.25)
# show angular velocity
V = 0.3 * omega - sign(omega) * 0.15
gr3.drawcylindermesh(1, (x, y, 0), (cos(theta), sin(theta), 0), (0, 0, 1),
0.05, V)
gr3.drawconemesh(1, (x + cos(theta) * V, y + sin(theta) * V, 0),
(-y, x, 0), (0, 0, 1), 0.1,
sign(omega) * 0.25)
# show angular acceleration
A = 0.3 * acceleration
gr3.drawcylindermesh(1, (x, y, 0), (sin(theta), cos(theta), 0), (1, 0, 0),
0.05, A)
gr3.drawconemesh(1, (x + sin(theta) * A, y + cos(theta) * A, 0),
(x, -y, 0), (1, 0, 0), 0.1, 0.25)
# draw GR3 objects
gr3.drawimage(0, 1, 0.15, 0.85, 500, 350,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.settextfontprec(2, gr.TEXT_PRECISION_STRING)
gr.setcharheight(0.024)
gr.settextcolorind(1)
gr.textext(0.05, 0.96, 'Damped Pendulum')
gr.mathtex(0.05, 0.9, '\\omega=\\dot{\\theta}')
gr.mathtex(0.05, 0.83,
'\\dot{\\omega}=-\\gamma\\omega-\\frac{g}{l}sin(\\theta)')
gr.setcharheight(0.020)
gr.textext(0.05, 0.20, 't:%7.2f' % t)
gr.textext(0.05, 0.16, '\\theta:%7.2f' % (theta / pi * 180))
gr.settextcolorind(4)
gr.textext(0.05, 0.12, '\\omega:%7.2f' % omega)
gr.settextcolorind(2)
gr.textext(0.05, 0.08, 'y_{A}:%6.2f' % acceleration)
gr.updatews()
return
def pendulum(t, theta, omega, acceleration):
gr.clearws()
gr.setviewport(0, 1, 0, 1)
x, y = (sin(theta) * 3.0, -cos(theta) * 3.0)
gr3.clear()
# draw pivot point
gr3.drawspheremesh(1, (0, 0, 0), (0.4, 0.4, 0.4), 0.1)
# draw rod
gr3.drawcylindermesh(1, (0, 0, 0), (x, y, 0), (0.6, 0.6, 0.6), 0.05, 3.0)
# draw sphere
gr3.drawspheremesh(1, (x, y, 0), (1, 1, 1), 0.25)
# show angular velocity
V = 0.3 * omega - sign(omega) * 0.15
gr3.drawcylindermesh(1, (x, y, 0), (cos(theta), sin(theta), 0), (0, 0, 1),
0.05, V)
gr3.drawconemesh(1, (x + cos(theta) * V, y + sin(theta) * V, 0),
(-y, x, 0), (0, 0, 1), 0.1, sign(omega) * 0.25)
# show angular acceleration
A = 0.3 * acceleration
gr3.drawcylindermesh(1, (x, y, 0), (sin(theta), cos(theta), 0), (1, 0, 0),
0.05, A)
gr3.drawconemesh(1, (x + sin(theta) * A, y + cos(theta) * A, 0),
(x, -y, 0), (1, 0, 0), 0.1, 0.25)
# draw GR3 objects
gr3.drawimage(0, 1, 0.15, 0.85, 500, 350, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.settextfontprec(2, gr.TEXT_PRECISION_STRING)
gr.setcharheight(0.024)
gr.settextcolorind(1)
gr.textext(0.05, 0.96, 'Damped Pendulum')
gr.mathtex(0.05, 0.9, '\\omega=\\dot{\\theta}')
gr.mathtex(0.05, 0.83, '\\dot{\\omega}=-\\gamma\\omega-\\frac{g}{l}sin(\\theta)')
gr.setcharheight(0.020)
gr.textext(0.05, 0.20, 't:%7.2f' % t)
gr.textext(0.05, 0.16, '\\theta:%7.2f' % (theta / pi * 180))
gr.settextcolorind(4)
gr.textext(0.05, 0.12, '\\omega:%7.2f' % omega)
gr.settextcolorind(2)
gr.textext(0.05, 0.08, 'y_{A}:%6.2f' % acceleration)
gr.updatews()
return
def create_scene(self):
"""
Create GR3 meshes. ``self.results`` contains the mesh data
and in ``self.settings`` is specified which meshes shound be rendered.
"""
c = config.Colors.background
gr3.setbackgroundcolor(c[0], c[1], c[2], 1.0)
gr3.clear()
if self.results is None:
return
show_domains = self.settings.show_domains
show_surface_cavities = self.settings.show_surface_cavities
show_center_cavities = self.settings.show_center_cavities
if show_center_cavities and self.results.center_cavities is not None:
show_surface_cavities = False
elif show_surface_cavities and self.results.surface_cavities is not None:
show_domains = False
self.objectids = [None]
edges = self.results.atoms.volume.edges
num_edges = len(edges)
edge_positions = [edge[0] for edge in edges]
edge_directions = [[edge[1][i]-edge[0][i] for i in range(3)] for edge in edges]
edge_lengths = [sum([c*c for c in edge])**0.5 for edge in edge_directions]
edge_radius = min(edge_lengths)/200
if self.settings.show_bounding_box:
gr3.drawcylindermesh(num_edges, edge_positions, edge_directions,
[config.Colors.bounding_box]*num_edges,
[edge_radius]*num_edges, edge_lengths)
corners = list(set([tuple(edge[0]) for edge in edges] + [tuple(edge[1]) for edge in edges]))
num_corners = len(corners)
gr3.drawspheremesh(num_corners, corners,
[config.Colors.bounding_box]*num_corners,
[edge_radius]*num_corners)
if self.settings.show_atoms and self.results.atoms is not None:
visible_atom_indices = self.settings.visible_atom_indices
if visible_atom_indices is not None:
visible_atom_indices = [comp for comp in visible_atom_indices if 0 <= comp < self.results.atoms.number]
else:
visible_atom_indices = range(self.results.atoms.number)
if len(visible_atom_indices) == 0:
visible_atom_indices = None
if visible_atom_indices is not None:
visible_atom_indices = np.array(visible_atom_indices)
gr3.drawspheremesh(len(visible_atom_indices),
self.results.atoms.positions[visible_atom_indices],
self.results.atoms.colors[visible_atom_indices],
np.ones(len(visible_atom_indices))*config.OpenGL.atom_radius)
if self.settings.show_bonds:
bonds = self.results.atoms.bonds
for start_index, target_indices in enumerate(bonds):
if start_index not in visible_atom_indices:
continue
target_indices = np.array([i for i in target_indices if i in visible_atom_indices])
if len(target_indices) == 0:
continue
start_position = self.results.atoms.positions[start_index]
target_positions = self.results.atoms.positions[target_indices]
directions = target_positions - start_position
bond_lengths = la.norm(directions, axis=1)
directions /= bond_lengths.reshape(len(directions), 1)
gr3.drawcylindermesh(len(target_indices),
target_positions,
-directions,
[config.Colors.bonds] * self.results.atoms.number,
np.ones(bond_lengths.shape)*config.OpenGL.bond_radius,
bond_lengths)
if self.results is None:
return
if show_domains and self.results.domains is not None:
self.draw_cavities(self.results.domains,
config.Colors.domain, 'domain',
self.settings.visible_domain_indices)
if show_surface_cavities and self.results.surface_cavities is not None:
self.draw_cavities(self.results.surface_cavities,
config.Colors.surface_cavity, 'surface cavity',
self.settings.visible_surface_cavity_indices)
if show_center_cavities and self.results.center_cavities is not None:
self.draw_cavities(self.results.center_cavities,
config.Colors.center_cavity, 'center cavity',
self.settings.visible_center_cavity_indices)