def setUpClass(cls):
write_ordered = False
from espressomd.io.writer import h5md
h5_units = h5md.UnitSystem(time='ps', mass='u', length='m', charge='e')
h5 = h5md.H5md(
filename="test.h5",
write_pos=True,
write_vel=True,
write_force=True,
write_species=True,
write_mass=True,
write_charge=True,
write_ordered=write_ordered,
unit_system=h5_units)
h5.write()
h5.flush()
h5.close()
cls.py_file = h5py.File("test.h5", 'r')
cls.py_pos = cls.py_file['particles/atoms/position/value'][0]
cls.py_img = cls.py_file['particles/atoms/image/value'][0]
cls.py_vel = cls.py_file['particles/atoms/velocity/value'][0]
if espressomd.has_features(['ELECTROSTATICS']):
cls.py_crg = cls.py_file['particles/atoms/charge/value'][0]
cls.py_f = cls.py_file['particles/atoms/force/value'][0]
cls.py_id = cls.py_file['particles/atoms/id/value'][0]
cls.py_bonds = cls.py_file['connectivity/atoms']
system = espressomd.System(box_l=[100.0, 100.0, 100.0])
system.time_step = 0.01
system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)
system.cell_system.skin = 0.4
fene = interactions.FeneBond(k=10, d_r_max=2)
system.bonded_inter.add(fene)
positions = polymer.linear_polymer_positions(n_polymers=5,
beads_per_chain=50,
bond_length=1.0,
seed=1234)
for polymer in positions:
for i, pos in enumerate(polymer):
id = len(system.part)
system.part.add(id=id, pos=pos)
if i > 0:
system.part[id].add_bond((fene, id - 1))
h5_units = h5md.UnitSystem(time='ps', mass='u', length='nm', charge='e')
h5_file = h5md.H5md(file_path="sample.h5", unit_system=h5_units)
for i in range(2):
h5_file.write()
system.integrator.run(steps=10)
h5_file.flush()
h5_file.close()