def read_h5_file(folder, bending=False):
""" read data from hdf5 file"""
### file path
fpath = folder + 'out.h5'
assert os.path.exists(fpath), "The out.h5 file does NOT exist for " + fpath
fl = h5py.File(fpath, 'r')
### positions of beads
xu = np.array(fl['/beads/xu'], dtype=np.float32)
cid = np.array(fl['/beads/cid'], dtype=np.float32)
### cell information
comu = np.array(fl['/cells/comu'], dtype=np.float32)
pol = np.array(fl['/cells/pol'], dtype=np.float32)
nbpc = np.array(fl['/cells/nbpc'], dtype=np.float32)
### simulation information
lx = fl['/info/box/x'][...]
ly = fl['/info/box/y'][...]
dt = fl['/info/dt'][...]
nsteps = fl['/info/nsteps'][...]
ncells = fl['/info/ncells'][...]
nbeads = fl['/info/nbeads'][...]
nsamp = fl['/info/nsamp'][...]
### simulation parameters
eps = fl['/param/eps'][...]
rho = fl['/param/rho'][...]
fp = fl['/param/fp'][...]
areak = fl['/param/areak'][...]
bl = fl['/param/bl'][...]
sigma = fl['/param/sigma'][...]
kappa = 100.0
if bending:
kappa = fl['/param/kappa'][...]
fl.close()
### generate classes to submerge data
sim = misc_tools.Simulation(lx, ly, dt, nsteps, ncells, nbeads, nsamp, nbpc, \
eps, rho, fp, areak, bl, sigma, kappa)
cells = misc_tools.Cells(comu, pol, nbpc, sim)
beads = misc_tools.Beads(xu, cid)
return sim, cells, beads
def read_h5_file_beads(folder, filen):
""" read data from hdf5 file for filament information"""
### file path
fpath = folder + filen + '.h5'
assert os.path.exists(fpath), "The out.h5 file does NOT exist for " + fpath
fl = h5py.File(fpath, 'r')
### bead information
xu = np.array(fl['/beads/xu'], dtype=np.float32)
#pol = np.array(fl['/beads/pol'], dtype=np.float32)
cid = np.array(fl['/beads/cid'], dtype=np.int32)
### simulation information
lx = fl['/info/box/x'][...]
ly = fl['/info/box/y'][...]
dt = fl['/info/dt'][...]
nsteps = fl['/info/nsteps'][...]
nfils = fl['/info/nfils'][...]
nbeads = fl['/info/nbeads'][...]
nsamp = fl['/info/nsamp'][...]
nbpf = fl['/info/nbpf'][...]
### simulation parameters
density = fl['/param/density'][...]
kappa = fl['/param/kappa'][...]
km = fl['/param/km'][...]
pa = fl['/param/pa'][...]
pp = fl['/param/pp'][...]
bl = fl['/param/bl'][...]
sigma = fl['/param/sigma'][...]
fl.close()
### generate classes to submerge data
sim = misc_tools.Simulation(lx, ly, dt, nsteps, nfils, nbeads, nsamp, nbpf, \
density, kappa, km, pa, pp, bl, sigma)
beads = misc_tools.Beads(xu, cid)
return sim, beads
def read_sim_info_arvind_format(folder, filen):
""" read simulation info from hdf5 file in arvind style"""
### file path
fpath = folder + filen + '.h5'
assert os.path.exists(fpath), "The out.h5 file does NOT exist for " + fpath
fl = h5py.File(fpath, 'r')
### simulation information
lx = fl['/info/box/x'][...]
ly = fl['/info/box/y'][...]
dt = fl['/info/dt'][...]
nsteps = fl['/info/nsteps'][...]
nfils = fl['/info/nfils'][...]
nbeads = fl['/info/nbeads'][...]
nsamp = fl['/info/nsamp'][...]
nbpf = fl['/info/nbpf'][...]
### simulation parameters
density = fl['/param/density'][...]
kappa = fl['/param/kappa'][...]
km = fl['/param/km'][...]
pa = fl['/param/pa'][...]
pp = fl['/param/pp'][...]
bl = fl['/param/bl'][...]
sigma = fl['/param/sigma'][...]
fl.close()
### generate classes to submerge data
sim = misc_tools.Simulation(lx, ly, dt, nsteps, nfils, nbeads, nsamp, nbpf, \
density, kappa, km, pa, pp, bl, sigma)
return sim