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Fix bond visualization; data handling. #4502

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merged 2 commits into from
May 9, 2022
Merged

Fix bond visualization; data handling. #4502

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e4e5d24
Fix bond visualization; data handling.
pkreissl Apr 19, 2022
7a972ba
Merge branch 'python' into visualizer_opengl_bonds
kodiakhq[bot] May 9, 2022
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108 changes: 72 additions & 36 deletions src/python/espressomd/visualization_opengl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -663,7 +663,7 @@ def update(self):
self.specs['update_fps']:
# ES UPDATES WHEN SYSTEM HAS PROPAGATED. ALSO UPDATE ON PAUSE
# FOR PARTICLE INFO
self._update_particles()
self._update_particles_and_bonds()

# LB UPDATE
if self.specs['LB_draw_velocity_plane']:
Expand Down Expand Up @@ -701,45 +701,64 @@ def update(self):

# FETCH DATA ON STARTUP
def _initial_espresso_updates(self):
self._update_particles()
self._update_particles_and_bonds()
if self.has_particle_data['charge']:
self._update_charge_color_range()
self._update_bonds()
if self.specs['draw_constraints']:
self._update_constraints()
if self.specs['draw_cells'] or self.specs['draw_nodes']:
self._update_nodes()
if self.specs['draw_cells']:
self._update_cells()

def _update_particles_and_bonds(self):
"""Fetch particle data from core and put it in the data dicts
used by the visualizer.

"""
parts_from_core = self.system.part.all()
self._update_particles(parts_from_core)
self._update_bonds(parts_from_core)

# GET THE PARTICLE DATA
def _update_particles(self):
def _update_particles(self, particle_data):
"""Updates particle data used for drawing particles.
Do not call directly but use _update_particles_and_bonds()!

self.particles['pos'] = self.system.part.all().pos_folded
self.particles['type'] = self.system.part.all().type
"""
self.particles['pos'] = particle_data.pos_folded
self.particles['type'] = particle_data.type
# particle ids can be discontiguous, therefore create a dict that maps
# particle ids to respective index in data arrays (used by
# _draw_bonds())
self.index_from_id = {
id: ndx for ndx, id in enumerate(
particle_data.id)}

if self.has_particle_data['velocity']:
self.particles['velocity'] = self.system.part.all().v
self.particles['velocity'] = particle_data.v

if self.has_particle_data['force']:
self.particles['force'] = self.system.part.all().f
self.particles['force'] = particle_data.f

if self.has_particle_data['ext_force']:
self.particles['ext_force'] = self.system.part.all().ext_force
self.particles['ext_force'] = particle_data.ext_force

if self.has_particle_data['charge']:
self.particles['charge'] = self.system.part.all().q
self.particles['charge'] = particle_data.q

if self.has_particle_data['director']:
self.particles['director'] = self.system.part.all().director
self.particles['director'] = particle_data.director

if self.has_particle_data['node']:
self.particles['node'] = self.system.part.all().node
self.particles['node'] = particle_data.node

if self.info_id != -1:
# data array index of particle with id info_id
info_index = self.index_from_id[self.info_id]
for attr in self.particle_attributes:
self.highlighted_particle[attr] = getattr(
self.system.part.by_id(self.info_id), attr)
self.highlighted_particle[attr] = \
getattr(particle_data, attr)[info_index]

def _update_lb_velocity_plane(self):
if self.lb_is_cpu:
Expand Down Expand Up @@ -881,20 +900,31 @@ def shape_arguments(shape, part_type):
self.shapes.append(Shape(*arguments))

# GET THE BOND DATA, SO FAR CALLED ONCE UPON INITIALIZATION
def _update_bonds(self):
def _update_bonds(self, particle_data):
"""Update bond data used for drawing bonds.
Do not call directily but use _update_particles_and_bonds()!

Updates data array self.bonds[]; structure of elements is:
[<id of first bond partner>,
<id of second bond partner>,
<bond type]

"""
if self.specs['draw_bonds']:
self.bonds = []
for i, particle in enumerate(self.system.part):
for particle in particle_data:
for bond in particle.bonds:
# b[0]: Bond, b[1:] Partners
# input data:
# bond[0]: bond type, bond[1:] bond partners
bond_type = bond[0].type_number()
if len(bond) == 4:
self.bonds.append([i, bond[1], bond_type])
self.bonds.append([i, bond[2], bond_type])
self.bonds.append([particle.id, bond[1], bond_type])
self.bonds.append([particle.id, bond[2], bond_type])
self.bonds.append([bond[2], bond[3], bond_type])
else:
for bond_partner in bond[1:]:
self.bonds.append([i, bond_partner, bond_type])
self.bonds.append(
[particle.id, bond_partner, bond_type])

def _draw_text(self, x, y, text, color,
font=OpenGL.GLUT.GLUT_BITMAP_9_BY_15):
Expand Down Expand Up @@ -1008,13 +1038,12 @@ def radius_by_lj(part_type):
return radius

def _draw_system_particles(self, color_by_id=False):
part_ids = range(len(self.particles['pos']))
part_type = -1
reset_material = False

for part_id in part_ids:
for part_id, index in self.index_from_id.items():
part_type_last = part_type
part_type = int(self.particles['type'][part_id])
part_type = int(self.particles['type'][index])

# Only change material if type/charge has changed, color_by_id or
# material was reset by arrows
Expand All @@ -1034,23 +1063,23 @@ def _draw_system_particles(self, color_by_id=False):
else:
if self.specs['particle_coloring'] == 'auto':
# Color auto: Charge then Type
if self.has_particle_data['charge'] and self.particles['charge'][part_id] != 0:
if self.has_particle_data['charge'] and self.particles['charge'][index] != 0:
color = self._color_by_charge(
self.particles['charge'][part_id])
self.particles['charge'][index])
reset_material = True
else:
color = self._modulo_indexing(
self.specs['particle_type_colors'], part_type)
elif self.specs['particle_coloring'] == 'charge':
color = self._color_by_charge(
self.particles['charge'][part_id])
self.particles['charge'][index])
reset_material = True
elif self.specs['particle_coloring'] == 'type':
color = self._modulo_indexing(
self.specs['particle_type_colors'], part_type)
elif self.specs['particle_coloring'] == 'node':
color = self._modulo_indexing(
self.specs['particle_type_colors'], self.particles['node'][part_id])
self.specs['particle_type_colors'], self.particles['node'][index])

# Invert color of highlighted particle
if part_id == self.drag_id or part_id == self.info_id:
Expand All @@ -1067,7 +1096,7 @@ def _draw_system_particles(self, color_by_id=False):
radius, self.specs['quality_particles'], self.specs['quality_particles'])
OpenGL.GL.glEndList()

self._redraw_sphere(self.particles['pos'][part_id])
self._redraw_sphere(self.particles['pos'][index])

if self.has_images:
for imx in self.image_vectors[0]:
Expand All @@ -1076,12 +1105,12 @@ def _draw_system_particles(self, color_by_id=False):
if imx != 0 or imy != 0 or imz != 0:
offset = [imx, imy, imz] * self.system.box_l
self._redraw_sphere(
self.particles['pos'][part_id] + offset)
self.particles['pos'][index] + offset)

if espressomd.has_features('EXTERNAL_FORCES'):
if self.specs['ext_force_arrows'] or part_id == self.drag_id:
if any(
v != 0 for v in self.particles['ext_force'][part_id]):
v != 0 for v in self.particles['ext_force'][index]):
if part_id == self.drag_id:
sc = 1
else:
Expand All @@ -1092,8 +1121,8 @@ def _draw_system_particles(self, color_by_id=False):
self.specs['ext_force_arrows_type_colors'], part_type)
arrow_radius = self._modulo_indexing(
self.specs['ext_force_arrows_type_radii'], part_type)
draw_arrow(self.particles['pos'][part_id], np.array(
self.particles['ext_force'][part_id]) * sc, arrow_radius, arrow_col,
draw_arrow(self.particles['pos'][index], np.array(
self.particles['ext_force'][index]) * sc, arrow_radius, arrow_col,
self.materials['chrome'], self.specs['quality_arrows'])
reset_material = True

Expand Down Expand Up @@ -1122,11 +1151,12 @@ def _draw_arrow_property(self, part_id, part_type,
type_scale, type_colors, type_radii, prop):
sc = self._modulo_indexing(type_scale, part_type)
if sc > 0:
v = self.particles[prop][part_id]
v = self.particles[prop][self.index_from_id[part_id]]
col = self._modulo_indexing(type_colors, part_type)
radius = self._modulo_indexing(type_radii, part_type)
draw_arrow(
self.particles['pos'][part_id], np.array(v, dtype=float) * sc,
self.particles['pos'][self.index_from_id[part_id]
], np.array(v, dtype=float) * sc,
radius, col, self.materials['chrome'], self.specs['quality_arrows'])

def _draw_bonds(self):
Expand All @@ -1137,8 +1167,14 @@ def _draw_bonds(self):
self.specs['bond_type_materials'], b[2])]
radius = self._modulo_indexing(
self.specs['bond_type_radius'], b[2])
x_a = self.particles['pos'][b[0]]
x_b = self.particles['pos'][b[1]]
# if particles are deleted in the core, index_from_id might
# throw a KeyError -- e. g. when deleting a bond created by
# collision_detection (using virtual site particles)
try:
x_a = self.particles['pos'][self.index_from_id[b[0]]]
x_b = self.particles['pos'][self.index_from_id[b[1]]]
except BaseException:
pass
dx = x_b - x_a

if abs(dx[0]) < box_l_2[0] and abs(
Expand Down