lx = 10.0
ly = 10.0
lz = 10.0
stokes.stokes_set_l(sys, lx, ly, lz)
ewald_tr = 60.25
xi = stokes.xi_by_tratio(sys, ewald_tr)
ewald_eps = 1.0e-12
stokes.stokes_set_xi(sys, xi, ewald_eps)
print 'xi =', xi
sys.lubmin2 = 4.0000000001
sys.lubmax = 4.0
stokes.stokes_set_iter(sys, "gmres", 2000, 20, 1.0e-6,
1, stokes.get_stdout())
pos = stokes.darray(np*3)
u = stokes.darray(np*3)
f = stokes.darray(np*3)
pos[ 0] = 0.0 # x component
pos[ 1] = 0.0 # y component
pos[ 2] = 0.0 # z component
pos[ 3] = 5.0
pos[ 4] = 0.0
pos[ 5] = 0.0
pos[ 6] = 0.0
pos[ 7] = 5.0
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 ''
