def main():
filename = ''
flag_line = 0
step = -1
flag_com = 0
x0 = 0.0
y0 = 0.0
z0 = 0.0
i = 1
while i < len(sys.argv):
if sys.argv[i] == '-f' or sys.argv[i] == '--file':
filename = sys.argv[i+1]
i += 2
elif sys.argv[i] == '-line':
flag_line = 1
i += 1
elif sys.argv[i] == '-step':
step = int(sys.argv[i+1])
step -= 1
i += 2
elif sys.argv[i] == '-com':
flag_com = 1
x0 = float(sys.argv[i+1])
y0 = float(sys.argv[i+2])
z0 = float(sys.argv[i+3])
i += 4
else:
usage()
if filename == '': usage()
nc = stokes.stokes_nc_open (filename)
# pos[] : center of particles
pos = stokes.darray(nc.np * nc.nvec)
# q[] : quaternion
if nc.flag_q != 0:
q = stokes.darray(nc.np * nc.nquat)
else:
q = []
# lattice
lattice = stokes.darray(3)
stokes.stokes_nc_get_array1d (nc, 'l', lattice)
# extract the config at the step
if step >= 0:
if step > nc.ntime:
print 'out of the range %d <= %d'%(step, nc.ntime)
sys.exit(1)
# read the config at the step
t = stokes.stokes_nc_get_time_step (nc, step)
stokes.stokes_nc_get_data (nc, "x", step, pos)
if nc.flag_q != 0:
stokes.stokes_nc_get_data (nc, "q", step, q)
comx = 0.0
comy = 0.0
comz = 0.0
if flag_com != 0:
for i in range(nc.np):
comx += pos[i*3]
comy += pos[i*3+1]
comz += pos[i*3+2]
comx /= float(nc.np)
comy /= float(nc.np)
comz /= float(nc.np)
# print the config
# print arguments as a comment
print '; config at %d step of %s, generated by'%(step+1, filename)
print '; ',
for i in range(len(sys.argv)):
print '%s'%(sys.argv[i]),
print ''
print '; at time %f'%(t)
print '(define x #('
for i in range(nc.np):
print ' %f %f %f ; %d'%(pos[i*3] - comx + x0,
pos[i*3+1] - comy + y0,
pos[i*3+2] - comz + z0,
i)
print '))'
if nc.flag_q != 0:
stokes.stokes_nc_get_data (nc, "q", step, q)
print '(define q #('
for i in range(nc.np):
print ' %f %f %f %f ; %d'\
%(q[i*4],q[i*4+1],q[i*4+2],q[i*4+3],i)
print '))'
sys.exit(1)
# done!
if flag_line == 0:
# print some general informations
stokes.stokes_nc_print_actives(nc, stokes.get_stdout())
print ''
print 'ntime = %d'%(nc.ntime)
print ''
# imposed flows
if nc.flag_ui0 == 1:
ui0 = stokes.darray(3)
stokes.stokes_nc_get_array1d (nc, "Ui0", ui0)
print 'ui0 = %f %f %f'%(ui0[0], ui0[1], ui0[2])
if nc.flag_oi0 == 1:
oi0 = stokes.darray(3)
stokes.stokes_nc_get_array1d (nc, "Oi0", oi0)
print 'oi0 = %f %f %f'%(oi0[0], oi0[1], oi0[2])
if nc.flag_ei0 == 1:
ei0 = stokes.darray(5)
stokes.stokes_nc_get_array1d (nc, "Ei0", ei0)
print 'ei0 = %f %f %f %f %f'\
%(ei0[0], ei0[1], ei0[2], ei0[3], ei0[4])
print ''
print 'lattice %f %f %f\n'%(lattice[0], lattice[1], lattice[2])
# print the infos about the output format
if flag_line == 0:
if nc.flag_q != 0:
print '# t, i, x, y, z, q1, q2, q3, q4'
else:
print '# t, i, x, y, z'
else:
if nc.flag_q != 0:
print '# t, x, y, z, q1, q2, q3, q4 (for particle 0),'\
' ... upto particle %d'%(nc.np)
else:
print '# t, x, y, z (for particle 0), x, y, z (for 1),'\
' ... upto particle %d'%(nc.np)
for i in range(nc.ntime):
t = stokes.stokes_nc_get_time_step (nc, i)
stokes.stokes_nc_get_data (nc, "x", i, pos)
if nc.flag_q != 0:
stokes.stokes_nc_get_data (nc, "q", i, q)
if flag_line == 0:
for j in range(nc.np):
x = pos[j*3]
y = pos[j*3+1]
z = pos[j*3+2]
if nc.flag_q != 0:
print '%f %d %f %f %f %f %f %f %f'\
%(t, j, x, y, z, q[0], q[1], q[2], q[3])
else:
print '%f %d %f %f %f'%(t, j, x, y, z)
else:
print t,
for j in range(nc.np):
x = pos[j*3]
y = pos[j*3+1]
z = pos[j*3+2]
print x, y, z,
if nc.flag_q != 0:
print q[0], q[1], q[2], q[3],
print ''
def main():
filename = ''
nstep = 1
flag_bond = 0
flag_step = 0
flag_bottom = 0
flag_pic = 0
flag_cylinder = 0
flag_sphere = 0
flag_dumbbell = 0
flag_hex2d = 0
i = 1
while i < len(sys.argv):
if sys.argv[i] == '-f' or sys.argv[i] == '--file':
filename = sys.argv[i+1]
i += 2
elif sys.argv[i] == '-step':
nstep = int(sys.argv[i+1])
i += 2
elif sys.argv[i] == '-b' or sys.argv[i] == '--bond':
flag_bond = 1
i += 1
elif sys.argv[i] == '-s':
flag_step = 1
i += 1
elif sys.argv[i] == '-ts':
flag_step = 2
i += 1
elif sys.argv[i] == '-bottom':
flag_bottom = 1
i += 1
elif sys.argv[i] == '-p' or sys.argv[i] == '--pic':
flag_pic = 1
i += 1
elif sys.argv[i] == '-c' or sys.argv[i] == '--cylinder':
flag_cylinder = 1
cylinder_radius = float(sys.argv[i+1])
i += 2
elif sys.argv[i] == '--sphere':
flag_sphere = 1
cavity_radius = float(sys.argv[i+1])
i += 2
elif sys.argv[i] == '-d' or sys.argv[i] == '--dumbbell':
flag_dumbbell = 1
cavity1_radius = float(sys.argv[i+1])
cavity2_radius = float(sys.argv[i+2])
cylinder_length = float(sys.argv[i+3])
cylinder_radius = float(sys.argv[i+4])
i += 5
elif sys.argv[i] == '--hex2d':
flag_hex2d = 1
cavity_radius = float(sys.argv[i+1])
cylinder_radius = float(sys.argv[i+2])
lattice_spacing = float(sys.argv[i+3])
i += 4
else:
usage()
if filename == '' : usage()
nc = stokes.stokes_nc_open (filename)
#stokes.stokes_nc_print_actives(nc, stokes.get_stdout())
print 'ntime = ', nc.ntime
lattice = stokes.darray(3)
stokes.stokes_nc_get_array1d (nc, 'l', lattice)
print 'lattice = ', lattice[0], lattice[1], lattice[2]
# x[] : center of particles
x = stokes.darray(nc.np * nc.nvec)
# q[] : quaternion
if nc.flag_q != 0:
q = stokes.darray(nc.np * nc.nquat)
else:
q = []
# a[] : radius of mobile particles
if nc.flag_a != 0:
a = stokes.darray(nc.np)
stokes.stokes_nc_get_array1d (nc, "a", a)
else:
a = []
# af[] : radius of fixed particles
if nc.flag_af != 0:
af = stokes.darray(nc.npf)
stokes.stokes_nc_get_array1d (nc, "af", af)
else:
af = []
# fixed particles
if nc.npf > 0:
xf0 = stokes.darray(nc.npf * nc.nvec)
stokes.stokes_nc_get_data0 (nc, "xf0", xf0)
if lattice[0] == 0.0 and lattice[1] == 0.0 and lattice[2] == 0.0:
# non-periodic boundary
pfData = ryuon_vtk.make_pData(nc.npf, xf0, af)
(pfActor,pfGlyph) = ryuon_vtk.make_pActor ((1,0,0), 1, 20)
else:
# periodic boundary
pfData = ryuon_vtk.make_pData_periodic(nc.npf, xf0, af,
lattice)
(pfActor,pfGlyph) = ryuon_vtk.make_pActor_periodic ((1,0,0),
1, 20,
lattice)
pfGlyph.SetInput(pfData)
# then, make Actor
if nc.flag_q != 0:
# with quaternion
pActors = []
for i in range (nc.np):
pActors.append(ryuon_vtk.make_pActor_with_quaternion())
else:
# no quaternion in the result
(pActor,pGlyph) = ryuon_vtk.make_pActor((1,1,1), 1, 8)
# pGlyph.SetInput(pData)
# bond Actor
if flag_bond != 0:
(bondActor,bond) = ryuon_vtk.make_bondActor (khaki)
## prepare renderer
ren = vtk.vtkRenderer()
win = vtk.vtkRenderWindow()
win.AddRenderer(ren)
ren.SetBackground (0.1, 0.2, 0.4)
win.SetSize(480,360)
# iren = vtk.vtkRenderWindowInteractor ()
# iren.SetRenderWindow(win)
if nc.flag_q != 0:
for i in range(nc.np):
ren.AddActor(pActors[i])
else:
ren.AddActor(pActor)
if nc.npf > 0:
ren.AddActor(pfActor)
if flag_bond != 0:
ren.AddActor(bondActor)
# periodic box
if lattice[0] != 0.0 or lattice[1] != 0.0 or lattice[2] != 0.0:
CubeEdges = ryuon_vtk.make_cubeActor (lattice)
ren.AddActor(CubeEdges)
# axes
#axesActor = ryuon_vtk.make_axesActor()
#ren.AddActor(axesActor)
# text
textActor = ryuon_vtk.make_textActor()
ren.AddActor(textActor)
# cylinder
if flag_cylinder != 0:
cActor = make_cylinderActor (r=cylinder_radius,
x0=(0.0, 0.0, 0.0),
x1=(200.0, 0.0, 0.0),
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cActor)
# sphere
if flag_sphere != 0:
cavActor = make_sphereActor (x=(0.0, 0.0, 0.0),
r=cavity_radius,
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cavActor)
# dumbbell
if flag_dumbbell != 0:
cActor = make_cylinderActor (r=cylinder_radius,
x0=(-0.5 * cylinder_length, 0.0, 0.0),
x1=(+0.5 * cylinder_length, 0.0, 0.0),
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cActor)
theta1 = math.asin(cylinder_radius / cavity1_radius)
cav1Actor = make_sphereActor (x=(-0.5 * cylinder_length\
-cavity1_radius * math.cos(theta1),
0.0, 0.0),
r=cavity1_radius,
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cav1Actor)
theta2 = math.asin(cylinder_radius / cavity2_radius)
cav2Actor = make_sphereActor (x=(+0.5 * cylinder_length\
+cavity2_radius * math.cos(theta2),
0.0, 0.0),
r=cavity2_radius,
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cav2Actor)
# hex2d
if flag_hex2d != 0:
cav1Actor = make_sphereActor (x=(0.0, 0.0, 0.0),
r=cavity_radius,
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cav1Actor)
cav2Actor = make_sphereActor (x=(lattice_spacing, 0.0, 0.0),
r=cavity_radius,
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cav2Actor)
cav3Actor = make_sphereActor (x=(0.5*lattice_spacing, math.sqrt(3.0) * 0.5 *lattice_spacing, 0.0),
r=cavity_radius,
rgb=(0.0, 0.5, 0.0),
opacity=0.3)
ren.AddActor(cav3Actor)
aCamera = vtk.vtkCamera()
ren.SetActiveCamera (aCamera)
if lattice[0] != 0.0 or lattice[1] != 0.0 or lattice[2] != 0.0:
# periodic boundary
if lattice[0] > lattice[2]:
l = lattice[0]
else:
l = lattice[2]
aCamera.SetFocalPoint (0.5*lattice[0], 0, 0.4*lattice[2])
aCamera.SetPosition (0.5*lattice[0], -1.6*l, 0.5*lattice[2])
# loop
while 1:
i = 0
while i < nc.ntime:
t = stokes.stokes_nc_get_time_step (nc, i)
stokes.stokes_nc_get_data (nc, "x", i, x)
if nc.flag_q != 0:
# with quaternion
for j in range (nc.np):
stokes.stokes_nc_get_data (nc, "q", i, q)
m = ryuon_vtk.Q2M (q[j*4+0],q[j*4+1],q[j*4+2],q[j*4+3])
trans = vtk.vtkTransform()
trans.SetMatrix((m[0],m[3],m[6], x[j*3+0],
m[1],m[4],m[7], x[j*3+1],
m[2],m[5],m[8], x[j*3+2],
0.0, 0.0, 0.0, 1.0));
pActors[j].SetUserTransform(trans)
else:
# no quaternion in the result
pData = ryuon_vtk.make_pData(nc.np, x, a)
pGlyph.SetInput(pData)
# update bond Actor
if flag_bond != 0:
bData = ryuon_vtk.make_bData(nc.np, x)
bond.SetInput(bData)
if lattice[0] == 0.0 and lattice[1] == 0.0 and lattice[2] == 0.0:
# non-periodic boundary
#(cx,cy,cz, lx,ly,lz) = bounding_box (nc.np, x)
(cx,cy,cz, lx0,ly0,lz0, lx1, ly1, lz1)\
= ryuon_vtk.bounding_box_ (nc.np, x)
lx = lx1 - lx0
ly = ly1 - ly0
lz = lz1 - lz0
# centered by COM
if lx > lz:
l = lx
else:
l = lz
# prevent to go far away
#if l > 50: l = 50
if l > 100: l = 100
if flag_bottom == 0:
aCamera.SetFocalPoint (cx, cy, cz)
aCamera.SetPosition (cx, cy-3.0*l, cz+0.1*l)
else:
# bottom align
aCamera.SetFocalPoint (cx, cy, lz0)
aCamera.SetPosition (cx, cy-3.0*l, lz0+0.1*l)
if flag_step == 0:
textActor.SetInput ('time: %f'%(t))
elif flag_step == 1:
textActor.SetInput ('step: %d'%(i))
else:
textActor.SetInput ('time: %f (%d step)'%(t,i))
win.Render()
if flag_pic == 1:
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(win)
wr = vtk.vtkPNGWriter()
wr.SetInput(w2if.GetOutput())
wr.SetFileName('%s-%05d.png'%(filename,i))
wr.Write()
i += nstep
def render_one_step(str_argv, outfile, i,
nc, pos, a, q, xf0, af, lattice,
flag_ball, flag_bonds, bond_radius, bond_color,
flag_lookat, lk_arg, camera_dist, camera_dir,
sphere_radius, cylinder_radius, flag_bb):
file = '%s-%05d.pov'%(outfile, i)
try:
f = open(file, 'w')
except IOError:
print 'cannot open', file
sys.exit()
# write argv[0]
f.write('/* generated for %d step by\n'%(i))
f.write(' * %s\n'%(str_argv))
f.write(' */\n')
stokes.stokes_nc_get_data (nc, "x", i, pos)
# set camera direction
(cx,cy,cz, lx,ly,lz) = bounding_box (nc.np, pos)
if flag_lookat == 0:
if cylinder_radius > 0.0:
# only x is adjustable
lk = [cx, 0, 0]
else:
lk = [cx, cy, cz]
else:
lk = [lk_arg[0], lk_arg[1], lk_arg[2]]
if camera_dir == 'top':
# top view
if camera_dist == 0.0:
if lx > ly:
l = lx
else:
l = ly
# prevent to go too far away
if l > 50: l = 50
camera = [lk[0], lk[1], lk[2]+2*l]
else:
camera = [lk[0], lk[1], lk[2]+camera_dist]
elif camera_dir == 'bottom':
# bottom view
if camera_dist == 0.0:
if lx > ly:
l = lx
else:
l = ly
# prevent to go too far away
if l > 50: l = 50
camera = [lk[0], lk[1], lk[2]-2*l]
else:
camera = [lk[0], lk[1], lk[2]-camera_dist]
else:
# side view
if camera_dist == 0.0:
if lx > lz:
l = lx
else:
l = lz
# prevent to go too far away
if l > 50: l = 50
camera = [lk[0], lk[1]-2*l, lk[2]]
else:
camera = [lk[0], lk[1]-camera_dist, lk[2]]
# write header part
if lattice[0] == 0.0 and lattice[1] == 0.0 and lattice[2] == 0.0:
# non-periodic boundary
write_pov_header_open (f, lattice, camera, lk,
flag_ball, flag_bonds, bond_color)
else:
# periodic boundary
#move_camera (camera, lk)
write_pov_header (f, lattice, camera, lk,
flag_ball, flag_bonds, bond_color)
if flag_bb != 0:
# write bounding box for periodic system
if lattice[0] != 0.0 or lattice[1] != 0.0 or lattice[2] != 0.0:
f.write('box {\n')
f.write(' <0, 0, 0>,\n')
f.write(' <%f, %f, %f>\n'\
%(lattice[0]/100.0, lattice[2]/100.0, lattice[1]/100.0))
f.write(' pigment {\n')
f.write(' rgbf <.9,1,.9, .95>\n')
f.write(' }\n')
f.write(' finish {\n')
f.write(' ambient .2\n')
f.write(' diffuse .6\n')
f.write(' }\n')
f.write('}\n')
# write confinement
if sphere_radius > 0.0:
# draw sphere
f.write('sphere {\n')
f.write(' <0, 0, 0>, %f\n'%(sphere_radius/100.0)) # scale factor 100
f.write(' pigment {\n')
f.write(' rgbf <.9,1,.9, .95>\n')
f.write(' }\n')
f.write(' finish {\n')
f.write(' ambient .2\n')
f.write(' diffuse .6\n')
f.write(' }\n')
f.write('}\n')
if cylinder_radius > 0.0:
# draw cylinder
f.write('cylinder {\n')
f.write(' <%f, 0, 0>,\n'%((cx-lx)*0.01)) # scale factor 0.01
f.write(' <%f, 0, 0>,\n'%((cx+lx)*0.01)) # scale factor 0.01
f.write(' %f\n'%(cylinder_radius*0.01)) # scale factor 0.01
f.write(' pigment {\n')
f.write(' rgbf <.9,1,.9, .95>\n')
f.write(' }\n')
f.write(' finish {\n')
f.write(' ambient .2\n')
f.write(' diffuse .6\n')
f.write(' }\n')
f.write('}\n')
# write mobile particles
if flag_bonds == 0:
# no bond
if nc.flag_q != 0:
# with quaternion
stokes.stokes_nc_get_data (nc, "q", i, q)
for j in range(nc.np):
x = pos[j*3]
y = pos[j*3+1]
z = pos[j*3+2]
if a != []:
rad = a[j]
else:
rad = 1.0
if flag_ball == 0:
write_pov_particle_Q (f, x, y, z, rad,\
[q[j*4+0],q[j*4+1],\
q[j*4+2],q[j*4+3]])
else:
write_pov_particle_Balls_Q (f, x, y, z, rad,\
[q[j*4+0],q[j*4+1],\
q[j*4+2],q[j*4+3]],\
j)
else:
# no quaternion
for j in range(nc.np):
x = pos[j*3]
y = pos[j*3+1]
z = pos[j*3+2]
if a != []:
write_pov_particle (f, x, y, z, a[j])
else:
write_pov_particle (f, x, y, z, 1.0)
else:
# bond
write_pov_particles_with_bonds (f, nc.np, pos, a, bond_radius)
# write fixed particles
for j in range(nc.npf):
x = xf0[j*3]
y = xf0[j*3+1]
z = xf0[j*3+2]
if af != []:
write_pov_particle_fixed (f, x, y, z, af[j])
else:
write_pov_particle_fixed (f, x, y, z, 1.0)
# done
f.close()