adsorbed_compute = 'mem_cluster'
py_lmp.compute(adsorbed_compute, adsorbed_group, 'aggregate/atom',
tip_lipid_cutoff)
top_msd_compute = 'mem_top_msd'
py_lmp.compute(top_msd_compute, membrane.top_layer_group, 'msd')
bottom_msd_compute = 'mem_bottom_msd'
py_lmp.compute(bottom_msd_compute, membrane.bottom_layer_group, 'msd')
full_msd_compute = 'mem_full_msd'
py_lmp.compute(full_msd_compute, membrane.main_group, 'msd')
# FIXES & DYNAMICS
mem_dyn_fix = 'mem_dynamics'
press_eq_t = 1000 * run_args.dt
py_lmp.fix(mem_dyn_fix, membrane.main_group, 'nph', 'x 0.0 0.0', press_eq_t,
'y 0.0 0.0', press_eq_t, 'couple xy', 'dilate', 'all')
py_lmp.compute_modify(mem_dyn_fix + '_temp', 'dynamic/dof yes')
py_lmp.neigh_modify('exclude', 'molecule/intra', membrane.main_group)
# -> saves neighbour calculating without consequences (because beads 1 & 3 will
# never be in range anyway & this doesn't affect bonds and angles)
py_lmp.special_bonds(
'fene') # not really necessary because of "neigh_modify exclude"
# MEMBRANE EQUILIBRATION
py_lmp.run(2000) #2 x press_eq_t, for good measure
py_lmp.reset_timestep(0)
# ===== FINAL ===========================================================================
py_lmp.variable('temp_x', 'equal', '"xhi - {:f}"'.format(model.rod_length / 2))
py_lmp.variable('temp_y', 'equal', '"yhi - {:f}"'.format(model.rod_length / 2))
py_lmp.region('gcmc_box', 'block', '-${temp_x}', '${temp_x}', '-${temp_y}',
'${temp_y}', 0.0 + 2 * model.rod_length,
thermo_fix = 'thermostat'
py_lmp.fix(thermo_fix, 'all', 'langevin', run_args.temp, run_args.temp, run_args.damp, seed)#, "zero yes")
simulation.set_rod_dynamics('nve', everything_else=['mol', model.rod_states[0]])
py_lmp.region('gcmc_init', 'block',
membrane.xmin + model.rod_length/2, membrane.xmax - model.rod_length/2,
membrane.ymin + model.rod_length/2, membrane.ymax - model.rod_length/2,
0.0 + model.rod_length/2, run_args.Lz - model.rod_length/2)
rod_gcmc_fix = 'rod_gcmc'
py_lmp.fix(rod_gcmc_fix, simulation.rods_group, 'gcmc', 100, 200, 0,
0, seed, run_args.temp, run_args.mu, 0.0,
'region', 'gcmc_init', 'mol', model.rod_states[0],
'rigid', simulation.rod_dyn_fix, 'tfac_insert', 1.65)
#py_lmp.fix_modify(simulation.rod_dyn_fix, 'dynamic/dof yes') #only for nvt&npt (small)
py_lmp.compute_modify("thermo_temp", "dynamic/dof yes")
# TEST DUMP...
# py_lmp.thermo_style('custom', 'step atoms', 'pe temp')
# py_lmp.variable('thermo_var', 'equal', '"stagger({:d}, 1)"'.format(out_freq))
# py_lmp.thermo('v_thermo_var')
# py_lmp.dump('test_dump', 'all', 'custom', out_freq, dump_path+'_init',
# 'id x y z type mol c_'+cluster_compute)
# py_lmp.dump_modify('test_dump', 'sort id')
# GENERATING INITIAL CONFIGURATION
py_lmp.neigh_modify('every', 1, 'delay', 1)
py_lmp.timestep(run_args.dt)
py_lmp.command('run 2000')
py_lmp.unfix(rod_gcmc_fix)
py_lmp.unfix(zwalls_fix)
