def conf2yap(conf_fname, yap_filename):
print("Yap file : ", yap_filename)
positions, radii, meta = clff.read_conf_file(conf_fname)
positions[:, 0] -= float(meta['lx'])/2
positions[:, 1] -= float(meta['ly'])/2
positions[:, 2] -= float(meta['lz'])/2
if 'np_fixed' in meta:
# for conf with fixed particles
split_line = len(positions) - int(meta['np_fixed'])
pos_mobile, pos_fixed = np.split(positions, [split_line])
rad_mobile, rad_fixed = np.split(radii, [split_line])
yap_out = pyp.layer_switch(3)
yap_out = pyp.add_color_switch(yap_out, 3)
yap_out = np.row_stack((yap_out,
particles_yaparray(pos_mobile, rad_mobile)))
yap_out = pyp.add_layer_switch(yap_out, 4)
yap_out = pyp.add_color_switch(yap_out, 4)
yap_out = np.row_stack((yap_out,
particles_yaparray(pos_fixed, rad_fixed)))
else:
yap_out = pyp.layer_switch(3)
yap_out = pyp.add_color_switch(yap_out, 3)
yap_out = np.row_stack((yap_out,
particles_yaparray(positions, radii)))
pyp.savetxt(yap_filename, yap_out)
def conf2yap(conf_fname, yap_filename):
print("Yap file : ", yap_filename)
positions, radii, meta = clff.read_conf_file(conf_fname)
positions[:, 0] -= float(meta['lx']) / 2
positions[:, 1] -= float(meta['ly']) / 2
positions[:, 2] -= float(meta['lz']) / 2
if 'np_fixed' in meta:
# for conf with fixed particles
split_line = len(positions) - int(meta['np_fixed'])
pos_mobile, pos_fixed = np.split(positions, [split_line])
rad_mobile, rad_fixed = np.split(radii, [split_line])
yap_out = pyp.layer_switch(3)
yap_out = pyp.add_color_switch(yap_out, 3)
yap_out = np.row_stack(
(yap_out, particles_yaparray(pos_mobile, rad_mobile)))
yap_out = pyp.add_layer_switch(yap_out, 4)
yap_out = pyp.add_color_switch(yap_out, 4)
yap_out = np.row_stack(
(yap_out, particles_yaparray(pos_fixed, rad_fixed)))
else:
yap_out = pyp.layer_switch(3)
yap_out = pyp.add_color_switch(yap_out, 3)
yap_out = np.row_stack((yap_out, particles_yaparray(positions, radii)))
pyp.savetxt(yap_filename, yap_out)
def interactions_bonds_yaparray(int_snapshot,
par_snapshot,
icols,
pcols,
f_factor=None,
f_chain_thresh=None,
layer_contacts=1,
layer_noncontacts=2,
color_contacts=1,
color_noncontacts=2):
if f_chain_thresh is None:
f_chain_thresh = 0
r1r2 = lfu.get_interaction_end_points(int_snapshot, par_snapshot,
icols, pcols)
f, r1r2 = filter_interactions_crossing_PBC(int_snapshot, r1r2)
# display a line joining the center of interacting particles
# with a thickness proportional to the normal force
normal_forces = get_normal_force(f, icols)
# convert the force to a thickness. case-by-case.
if f_factor is None:
f_factor = 0.5/np.max(np.abs(normal_forces))
normal_forces = f_factor*np.abs(normal_forces)
avg_force = np.mean(np.abs(normal_forces))
large_forces = normal_forces > f_chain_thresh * avg_force
contact_state = f[:, du.matching_uniq(icols, 'contact state')[1]]
# contacts
keep = np.logical_and(contact_state > 0, large_forces)
yap_out = pyp.layer_switch(layer_contacts)
yap_out = pyp.add_color_switch(yap_out, color_contacts)
contact_bonds = pyp.sticks_yaparray(r1r2[keep], normal_forces[keep])
yap_out = np.row_stack((yap_out, contact_bonds))
# non contacts
keep = np.logical_and(contact_state == 0, large_forces)
yap_out = pyp.add_layer_switch(yap_out, layer_noncontacts)
yap_out = pyp.add_color_switch(yap_out, color_noncontacts)
non_contact_bonds = pyp.sticks_yaparray(r1r2[keep], normal_forces[keep])
yap_out = np.row_stack((yap_out, non_contact_bonds))
return yap_out, f_factor
def interactions_bonds_yaparray(int_snapshot,
par_snapshot,
icols,
pcols,
f_factor=None,
f_chain_thresh=None,
layer_contacts=1,
layer_noncontacts=2,
color_contacts=1,
color_noncontacts=2):
if f_chain_thresh is None:
f_chain_thresh = 0
r1r2 = lfu.get_interaction_end_points(int_snapshot, par_snapshot, icols,
pcols)
f, r1r2 = filter_interactions_crossing_PBC(int_snapshot, r1r2)
# display a line joining the center of interacting particles
# with a thickness proportional to the normal force
normal_forces = get_normal_force(f, icols)
# convert the force to a thickness. case-by-case.
if f_factor is None:
f_factor = 0.5 / np.max(np.abs(normal_forces))
normal_forces = f_factor * np.abs(normal_forces)
avg_force = np.mean(np.abs(normal_forces))
large_forces = normal_forces > f_chain_thresh * avg_force
contact_state = f[:, du.matching_uniq(icols, 'contact state')[1]]
# contacts
keep = np.logical_and(contact_state > 0, large_forces)
yap_out = pyp.layer_switch(layer_contacts)
yap_out = pyp.add_color_switch(yap_out, color_contacts)
contact_bonds = pyp.sticks_yaparray(r1r2[keep], normal_forces[keep])
yap_out = np.row_stack((yap_out, contact_bonds))
# non contacts
keep = np.logical_and(contact_state == 0, large_forces)
yap_out = pyp.add_layer_switch(yap_out, layer_noncontacts)
yap_out = pyp.add_color_switch(yap_out, color_noncontacts)
non_contact_bonds = pyp.sticks_yaparray(r1r2[keep], normal_forces[keep])
yap_out = np.row_stack((yap_out, non_contact_bonds))
return yap_out, f_factor
