#L.fix("thermofix3","clustergr","langevin",Temp,Temp,0.05, 2614,"zero","yes") #L.fix("thermofix3","clustergr","temp/csvr",Temp,Temp,0.1,12345) nodispl = 0 nosputt = 0 displacement = False # save starting coordinates: (startnPart1, startnPart2, nPartsub, startcoords1, startcoords2, coordssub, startindices1, startindices2, indicessub) = getcoords() startcoords = np.append(startcoords1, startcoords2, axis=0) # Output starting geometry: L.dump("Startgeom", "all", "custom", 1, "Startgeom_Full" + ".xyz", "id", "type", "x", "y", "z", "vx", "vy", "vz", "c_K", "c_P", "c_coordno") L.dump_modify("Startgeom", "first", "yes", "pad", 10) # Schreib' beim nullten Schritt ein File raus L.dump_modify("Startgeom", "element", "Au", "Ni", "C") L.dump_modify("Startgeom", "pbc", "yes") # remap atoms via periodic boundary conditions L.run(0) L.undump("Startgeom") L.dump("Startgeom", "all", "xyz", 1, "Startgeom" + ".xyz") L.dump_modify("Startgeom", "first", "yes", "pad", 10) # Schreib' beim nullten Schritt ein File raus L.dump_modify("Startgeom", "element", "Au", "Ni", "C") L.dump_modify("Startgeom", "pbc", "yes") # remap atoms via periodic boundary conditions L.run(0) L.undump("Startgeom")
py_lmp.variable(micelle_group, 'atom', '"type == {:d}"'.format(sol_tip_bead_type)) py_lmp.group(micelle_group, 'dynamic', simulation.rods_group, 'var', micelle_group, 'every', out_freq) micelle_compute = "micelle_ID" if hasattr(run_args, 'micelle_cutoff'): micelle_cutoff = run_args.micelle_cutoff else: SS_tip_int_key = model.eps[(sol_tip_bead_type, sol_tip_bead_type)][1] SS_tip_int_range = model.int_types[SS_tip_int_key][1] micelle_cutoff = 2 * model.rod_radius + SS_tip_int_range py_lmp.compute(micelle_compute, micelle_group, 'aggregate/atom', micelle_cutoff) # OUTPUT dump_elems = "id x y z type mol" try: dump_elems += " c_" + micelle_compute except: pass py_lmp.dump("dump_cmd", "all", "custom", out_freq, '"' + dump_path + '"', dump_elems) py_lmp.dump_modify("dump_cmd", "sort id") py_lmp.thermo_style("custom", "step atoms", "pe temp") py_lmp.thermo(out_freq) # RUN ... py_lmp.run(args.simlen) MPI.Finalize()