def main():
args = _args().parse_args()
data = h5py.File(args.trj, "r")
idx, box, trj, masses = files_io.prepare_h5md(
data, args.group, args.begin, args.end, no_image=True, step=args.every_frame
)
half_box = 0.5 * box
trj = fix_pbc(trj, box, half_box, args.N, args.molecules)
if args.out_ee:
print ("Calculating end-end distance...")
ee = []
for frame in trj:
ee.extend(compute_ee(args.molecules, args.N, frame))
out_ee = args.out_ee
np.savetxt(out_ee, ee)
print ("Saved to {}".format(out_ee))
if args.out_ee_points:
print ("Save end-to-end points (raw data)...")
ee_points = []
for frame in trj:
for ch in xrange(args.molecules):
b1, b2 = frame[ch * args.N], frame[ch * args.N + args.N - 1]
ee_points.append([b1, b2])
cPickle.dump(ee_points, open(args.out_ee_points, "wb"))
if args.out_rg:
print ("Calculating radius of gyration")
rgs = []
tot_masses = np.sum(masses[: args.N])
for frame in trj:
rg = calculate_rg(args.molecules, args.N, masses, box, half_box, tot_masses, frame)
rgs.extend(rg)
out_rg = args.out_rg
np.savetxt(out_rg, rgs)
print ("Saved Rg^2 to {}".format(out_rg))
if args.out_int:
print ("Calculate internal distances.")
int_distances = []
fidx = 0
for frame in trj:
sys.stdout.write("{}\r".format(fidx))
sys.stdout.flush()
int_distances.append(bonds.calculate_msd_internal_distance(frame, args.molecules, args.N, box, half_box))
fidx += 1
out_int = args.out_int
np.savetxt(out_int, np.average(np.array(int_distances), axis=0))
print ("Saved internal distance to {}".format(out_int))
def _h5_processing(args, q_vector, start_stop_list, pos_cons):
nt = MPI.COMM_WORLD.size
at_group = args.group
if nt > 1:
pid = MPI.COMM_WORLD.rank
if pid >= len(start_stop_list):
return []
start_stop = start_stop_list[pid]
h5file = h5py.File(args.trj, 'r', driver='mpio', comm=MPI.COMM_WORLD)
else:
h5file = h5py.File(args.trj, 'r')
start_stop = start_stop_list[0]
_, box, trj, _ = files_io.prepare_h5md(h5file, at_group, start_stop[0], start_stop[1])
half_box = 0.5*box
vectors = []
process_tuples = [
[vectors, q_vector, bond_libs.calculate_bond_vec],
]
frame_idx = start_stop[0]
for frame in trj:
print('Frame {}'.format(frame_idx))
for output, atom_ids, functor in process_tuples:
if atom_ids is None or atom_ids.size == 0:
continue
atoms = frame[atom_ids]
atom_tuples = []
for d_tuple in atoms:
atom_tuples.append([np.array(x) for x in d_tuple])
output.append(functor(np.array(atom_tuples), box, half_box))
frame_idx += 1
return vectors
