import numpy as np
from h5md_module import File, element
import sys
with File(sys.argv[1], 'r') as f:
all_particles = f.particles_group('all')
for loc, name in (
(f['observables'], 'v'),
(all_particles, 'mass'),
(all_particles['box'], 'edges'),
(all_particles, 'id'),
(all_particles, 'position'),
(all_particles, 'force'),
(all_particles, 'velocity'),
):
if name not in loc:
continue
el = element(loc, name)
print '---------------------------------------------------------------'
print '%-10s ----------------------------------------------------' % name
print el.element_type
print el.value.shape, el.step, el.step_offset, el.time, el.time_offset, el.value
import numpy as np
from h5md_module import File, element
N = 32
DT = 0.1
with File('example_for_1.1.h5', 'w',author='Pierre', creator='run.py') as f:
f.observables = f.require_group('observables')
f.connectivity = f.require_group('connectivity')
v_e = element(f.observables, 'v', store='linear', data=1, step=10, step_offset=10, time=5., time_offset=5.)
f.all = f.particles_group('all')
f.all.create_box(dimension=3, boundary=['periodic']*3,
store='time', shape=(0,)+(3,), maxshape=(None,3), dtype=np.float64)
pos = np.zeros((N, 3))
pos_e = element(f.all, 'position', store='time', data=pos, step_from=f.all.box.edges)
vel = np.random.random(pos.shape)-0.5
vel_e = element(f.all, 'velocity', store='time', data=vel, time=5.)
force = np.random.random(pos.shape)-0.5
force_e = element(f.all, 'force', store='time', data=force, time=True)
mass = np.ones((N,))*100.0
element(f.all, 'mass', store='fixed', data=mass)
charge = np.ones((N,))*5.
element(f.all, 'charge', store='fixed', data=charge)
if rank==0:
data = np.arange(N*size, dtype=int)
np.random.shuffle(data)
for i in range(1, size):
comm.Send(data[i*N:(i+1)*N], dest=i, tag=11)
local_ids = data[0:N]
else:
comm.Recv(local_ids, source=0, tag=11)
with File('parallel_example_for_1.1.h5', 'w',author='Pierre', creator='run.py',
driver='mpio', comm=comm) as f:
f.observables = f.require_group('observables')
f.connectivity = f.require_group('connectivity')
v_e = element(f.observables, 'v', store='linear', data=1, step=10, step_offset=10, time=5., time_offset=5.)
f.all = f.particles_group('all')
f.all.create_box(dimension=3, boundary=['periodic']*3,
store='time', shape=(0,)+(3,), maxshape=(None,3), dtype=np.float64)
id_e = element(f.all, 'id', store='time', shape=(0, N*size,), dtype=int, maxshape=(None, N*size))
pos = np.zeros((N, 3))
pos_e = element(f.all, 'position', store='time', shape=(0, N*size, 3), maxshape=(None, N*size, 3), dtype=np.float64, step_from=f.all.box.edges)
vel = np.random.random(pos.shape)-0.5
vel_e = element(f.all, 'velocity', store='time', shape=(0, N*size, 3), maxshape=(None, N*size, 3), dtype=np.float64, time=5.)
force = np.random.random(pos.shape)-0.5