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
def snaps2yap(pos_fname,
yap_file,
f_factor=None,
f_chain_thresh=None):
forces_fname = pos_fname.replace("par_", "int_")
par_f = clff.snapshot_file(pos_fname)
int_f = clff.snapshot_file(forces_fname)
pcols = par_f.column_def()
icols = int_f.column_def()
is2d = float(par_f.meta_data()['Ly']) == 0
i = 0
for frame_par, frame_int in zip(par_f, int_f):
yap_out, f_factor =\
interactions_bonds_yaparray(frame_int[1], frame_par[1],
icols, pcols,
f_factor=f_factor,
f_chain_thresh=f_chain_thresh,
layer_contacts=1,
layer_noncontacts=2,
color_contacts=4,
color_noncontacts=5)
# display a circle for every particle
yap_out = pyp.add_layer_switch(yap_out, 3)
yap_out = pyp.add_color_switch(yap_out, 3)
if 'position (x, y, z)' in pcols:
pos_slice = pcols['position (x, y, z)']
else:
pos_slice = slice(pcols['position x'], pcols['position z']+1)
pos = frame_par[1][:, pos_slice].astype(np.float)
rad = frame_par[1][:, pcols['radius']].astype(np.float)
if is2d:
angle = frame_par[1][:, pcols['angle']].astype(np.float)
particles, crosses = particles_yaparray(pos, rad, angles=angle)
yap_out = np.row_stack((yap_out, particles))
yap_out = pyp.add_color_switch(yap_out, 1)
yap_out = np.row_stack((yap_out, crosses))
else:
yap_out = np.row_stack((yap_out, particles_yaparray(pos, rad)))
# display bounding box
yap_out = pyp.add_layer_switch(yap_out, 4)
yap_out = pyp.add_color_switch(yap_out, 0)
lx2 = float(par_f.meta_data()['Lx'])/2
ly2 = float(par_f.meta_data()['Ly'])/2
lz2 = float(par_f.meta_data()['Lz'])/2
if not is2d:
yap_out = pyp.add_cmd(yap_out, 'l', cuboid(lx2, ly2, lz2))
else:
yap_out = pyp.add_cmd(yap_out, 'l', rectangle(lx2, lz2))
# display strain
yap_out = pyp.add_layer_switch(yap_out, 5)
yap_out = pyp.add_color_switch(yap_out, 1)
# *cu*rvilinear or *cu*mulated strain depending on LF_DEM version
strain = du.matching_uniq(frame_par[0], ["cu".encode('utf8'), "strain".encode('utf8')])
yap_out = np.row_stack((yap_out,
['t', str(10.), str(0.), str(10.),
'strain='+str(strain), '', '']))
# output
np.savetxt(yap_file, yap_out, fmt="%s "*7)
yap_file.write("\n".encode('utf-8'))
i += 1
out_str = "\r frame " + str(i) +\
" - " + yap_filename + \
" [force factor " + str(f_factor) + "]"
try:
print(out_str, end="", flush=True)
except TypeError:
# to work with Python 2.7.* importing print_function without flush
print(out_str, end="")
print("")
def snaps2yap(pos_fname,
yap_file,
f_factor=None,
f_chain_thresh=None):
forces_fname = pos_fname.replace("par_", "int_")
positions, forces, strains, shear_rates, meta_pos, meta_int =\
read_data(pos_fname, forces_fname)
pcols = lf.convert_columndef_to_indices(meta_pos['column def'])
icols = lf.convert_columndef_to_indices(meta_int['column def'])
nb_of_frames = len(strains)
is2d = meta_pos['Ly'] == 0
i = 0
for f, p, strain, rate in zip(forces, positions, strains, shear_rates):
yap_out, f_factor =\
interactions_bonds_yaparray(f, p, icols, pcols,
f_factor=f_factor,
f_chain_thresh=f_chain_thresh,
layer_contacts=1,
layer_noncontacts=2,
color_contacts=4,
color_noncontacts=5)
# display a circle for every particle
yap_out = pyp.add_layer_switch(yap_out, 3)
yap_out = pyp.add_color_switch(yap_out, 3)
if 'position (x, y, z)' in pcols:
pos_slice = pcols['position (x, y, z)']
else:
pos_slice = slice(pcols['position x'], pcols['position z']+1)
pos = p[:, pos_slice].astype(np.float)
rad = p[:, pcols['radius']].astype(np.float)
if is2d:
angle = p[:, pcols['angle']].astype(np.float)
particles, crosses = particles_yaparray(pos, rad, angles=angle)
yap_out = np.row_stack((yap_out, particles))
yap_out = pyp.add_color_switch(yap_out, 1)
yap_out = np.row_stack((yap_out, crosses))
else:
yap_out = np.row_stack((yap_out, particles_yaparray(pos, rad)))
# display bounding box
yap_out = pyp.add_layer_switch(yap_out, 4)
yap_out = pyp.add_color_switch(yap_out, 0)
lx2 = meta_pos['Lx']/2
ly2 = meta_pos['Ly']/2
lz2 = meta_pos['Lz']/2
if not is2d:
yap_out = pyp.add_cmd(yap_out, 'l', cuboid(lx2, ly2, lz2))
else:
yap_out = pyp.add_cmd(yap_out, 'l', rectangle(lx2, lz2))
# display strain
yap_out = pyp.add_layer_switch(yap_out, 5)
yap_out = pyp.add_color_switch(yap_out, 1)
yap_out = np.row_stack((yap_out,
['t', str(10.), str(0.), str(10.),
'strain='+str(strain), '', '']))
# output
np.savetxt(yap_file, yap_out, fmt="%s "*7)
yap_file.write("\n".encode('utf-8'))
i += 1
out_str = "\r frame " + str(i) + "/"+str(nb_of_frames) +\
" - " + yap_filename + \
" [force factor " + str(f_factor) + "]"
try:
print(out_str, end="", flush=True)
except TypeError:
# to work with Python 2.7.* importing print_function without flush
print(out_str, end="")
print("")
def snaps2yap(pos_fname, yap_file, f_factor=None, f_chain_thresh=None):
forces_fname = pos_fname.replace("par_", "int_")
par_f = clff.snapshot_file(pos_fname)
int_f = clff.snapshot_file(forces_fname)
pcols = par_f.column_def()
icols = int_f.column_def()
is2d = float(par_f.meta_data()['Ly']) == 0
i = 0
for frame_par, frame_int in zip(par_f, int_f):
yap_out, f_factor =\
interactions_bonds_yaparray(frame_int[1], frame_par[1],
icols, pcols,
f_factor=f_factor,
f_chain_thresh=f_chain_thresh,
layer_contacts=1,
layer_noncontacts=2,
color_contacts=4,
color_noncontacts=5)
# display a circle for every particle
yap_out = pyp.add_layer_switch(yap_out, 3)
yap_out = pyp.add_color_switch(yap_out, 3)
if 'position (x, y, z)' in pcols:
pos_slice = pcols['position (x, y, z)']
else:
pos_slice = slice(pcols['position x'], pcols['position z'] + 1)
pos = frame_par[1][:, pos_slice].astype(np.float)
rad = frame_par[1][:, pcols['radius']].astype(np.float)
if is2d:
angle = frame_par[1][:, pcols['angle']].astype(np.float)
particles, crosses = particles_yaparray(pos, rad, angles=angle)
yap_out = np.row_stack((yap_out, particles))
yap_out = pyp.add_color_switch(yap_out, 1)
yap_out = np.row_stack((yap_out, crosses))
else:
yap_out = np.row_stack((yap_out, particles_yaparray(pos, rad)))
# display bounding box
yap_out = pyp.add_layer_switch(yap_out, 4)
yap_out = pyp.add_color_switch(yap_out, 0)
lx2 = float(par_f.meta_data()['Lx']) / 2
ly2 = float(par_f.meta_data()['Ly']) / 2
lz2 = float(par_f.meta_data()['Lz']) / 2
if not is2d:
yap_out = pyp.add_cmd(yap_out, 'l', cuboid(lx2, ly2, lz2))
else:
yap_out = pyp.add_cmd(yap_out, 'l', rectangle(lx2, lz2))
# display strain
yap_out = pyp.add_layer_switch(yap_out, 5)
yap_out = pyp.add_color_switch(yap_out, 1)
# *cu*rvilinear or *cu*mulated strain depending on LF_DEM version
strain = du.matching_uniq(
frame_par[0], ["cu".encode('utf8'), "strain".encode('utf8')])
yap_out = np.row_stack((yap_out, [
't',
str(10.),
str(0.),
str(10.), 'strain=' + str(strain), '', ''
]))
# output
np.savetxt(yap_file, yap_out, fmt="%s " * 7)
yap_file.write("\n".encode('utf-8'))
i += 1
out_str = "\r frame " + str(i) +\
" - " + yap_filename + \
" [force factor " + str(f_factor) + "]"
try:
print(out_str, end="", flush=True)
except TypeError:
# to work with Python 2.7.* importing print_function without flush
print(out_str, end="")
print("")
