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']
def setUpClass(cls):
write_ordered = False
from espressomd.io.writer import h5md # pylint: disable=import-error
h5 = h5md.H5md(filename="test.h5",
write_pos=True,
write_vel=True,
write_force=True,
write_species=True,
write_mass=True,
write_ordered=write_ordered)
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]
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.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.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))
system.integrator.run(steps=0)
h5_file = h5md.H5md(filename="sample.h5",
write_pos=True,
write_vel=True,
write_force=True,
write_species=True,
write_mass=False,
write_charge=True,
write_ordered=True)
for i in range(1):
h5_file.write()
h5_file.flush()
h5_file.close()
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()
system.actors.add(lb_fluid)
print("** Done LB")
print("Equilibrate...", )
system.integrator.run(5000)
print("** Done equilibration")
system.time = 0
if save_h5md:
h5_file = h5md.H5md(filename=h5md_file_name,
write_pos=True,
write_vel=False,
write_force=False,
write_species=True,
write_mass=False,
write_charge=True,
write_ordered=True)
h5_file.write()
h5_file.flush()
print("integrating...")
while (system.time < final_time):
system.integrator.run(500)
if save_h5md:
h5_file.write()
h5_file.flush()
if save_h5md: h5_file.close()
# Warmup loop
for i in range(eq_steps):
print("warmup step", i)
system.integrator.run(steps_per_int)
print("Running at temperature T={:.2f}".format(calc_temperature(system)))
if espresso_release >= (4, 2):
h5_opts = {"file_path": "traj.h5"}
else:
h5_opts = {"filename": "traj.h5"}
h5_file = h5md.H5md(write_pos=True,
write_vel=True,
write_force=True,
write_species=False,
write_mass=True,
write_ordered=False,
**h5_opts)
starttime = time.time()
# Integration loop
for i in range(int_steps):
system.integrator.run(steps_per_int)
E = system.analysis.energy()
e_pot = (E['total'] - E['kinetic']) / len(system.part)
print("time: {:.3f} potential energy: {:.2f}".format(i * time_step, e_pot))
h5_file.write()
system.non_bonded_inter[0, 0].tabulated.set_params(min=min_r,
max=max_r,
energy=p,
force=f)
# Warmup loop
for i in range(eq_steps):
print("warmup step", i)
system.integrator.run(steps_per_int)
print("Running at temperature T={:.2f}".format(calc_temperature(system)))
h5_file = h5md.H5md(filename="traj.h5",
write_pos=True,
write_vel=True,
write_force=True,
write_species=False,
write_mass=True,
write_ordered=False)
starttime = time.time()
# Integration loop
for i in range(int_steps):
system.integrator.run(steps_per_int)
E = system.analysis.energy()
e_pot = (E['total'] - E['kinetic']) / len(system.part)
print("time: {:.3f} potential energy: {:.2f}".format(i * time_step, e_pot))
h5_file.write()
# Take care of the COM movement
system.galilei.galilei_transform()
# Add Lees-Edwards to the script
system.cell_system.node_grid = [1, n_nodes_x, n_nodes_y]
system.cell_system.set_domain_decomposition(
fully_connected=[True, False, False])
system.lees_edwards.protocol = lees_edwards.LinearShear(shear_velocity=vel,
shear_direction=0,
shear_plane_normal=1)
# Open h5md file
h5 = h5md.H5md(filename="./trajectory.h5",
write_pos=True,
write_lees_edwards_offset=True,
write_vel=True,
write_ordered=True)
# Sampling + write h5md files
for i in range(args.samples):
h5.write()
print("Step:", i, flush=True)
system.integrator.run(iterations)
#Close all the files
h5.close()
