""" import espressomd required_features = ["ELECTROKINETICS", "EK_BOUNDARIES", "EXTERNAL_FORCES"] espressomd.assert_features(required_features) from espressomd import System, shapes, electrokinetics import sys system = System(box_l=[10, 10, 10]) system.set_random_state_PRNG() #system.seed = system.cell_system.get_state()['n_nodes'] * [1234] system.cell_system.skin = 0.4 system.time_step = 0.1 ek = electrokinetics.Electrokinetics(lb_density=1, friction=1, agrid=1, viscosity=1, T=1, prefactor=1) pos = electrokinetics.Species(density=0.05, D=0.1, valency=1, ext_force_density=[0, 0, 1.]) neg = electrokinetics.Species(density=0.05, D=0.1, valency=-1,
This sample simulates planar Poiseuille flow in Espresso. A spherical RBC-like particle is added and advected with and without volume conservation. """ import espressomd required_features = ["LB_BOUNDARIES", "VIRTUAL_SITES_INERTIALESS_TRACERS"] espressomd.assert_features(required_features) from espressomd import System, lb, shapes, lbboundaries import numpy as np from espressomd.virtual_sites import VirtualSitesInertialessTracers # System setup boxZ = 20 system = System(box_l=(20, 20, boxZ)) system.time_step = 1 / 6. system.cell_system.skin = 0.1 system.virtual_sites = VirtualSitesInertialessTracers() print("Parallelization: " + str(system.cell_system.node_grid)) force = 0.001 from addSoft import AddSoft k1 = 0.1 k2 = 1 AddSoft(system, 10, 10, 10, k1, k2) ## case without bending and volCons #outputDir = "outputPure" ## case with bending from addBending import AddBending
def calc(var): # AVB: Create an output directory for this to store the output files outdir = "./Noelle/r01.5kBT4Ads/1000=3.2" if not os.path.exists(outdir): os.makedirs(outdir) # Setup constant time_step = 0.01 loops = 30 step_per_loop = 100 # AVB: the parameters (that I usually use) a = 0.05 r0 = 2.0 * a kBT = 4.0e-6 vwf_type = 0 collagen_type = 1 monomer_mass = 0.01 box_l = 32.0 #print("Shear velocity:") #shear_velocity = float(input()) #vy = box_l*shear_velocity vy = var print(vy) v = [0, vy, 0] # System setup system = 0 system = System(box_l=[box_l, box_l, box_l]) system.set_random_state_PRNG() np.random.seed(seed=system.seed) system.cell_system.skin = 0.4 mpc = 20 # The number of monomers has been set to be 20 as default # Change this value for further simulations # Fene interaction fene = interactions.FeneBond(k=0.04, d_r_max=0.3) system.bonded_inter.add(fene) # Setup polymer of part_id 0 with fene bond # AVB: Notice the mode, max_tries and shield parameters for pruned self-avoiding random walk algorithm polymer.create_polymer(N_P=1, MPC=mpc, bond=fene, bond_length=r0, start_pos=[29.8, 16.0, 16.0], mode=2, max_tries=100, shield=0.6 * r0) # AVB: setting the type of particles and changing mass of each monomer to 0.01 system.part[:].type = vwf_type system.part[:].mass = monomer_mass # AVB: I suggest to add Lennard-Jones interaction between the monomers # AVB: to reproduce hydrophobicity # AVB: parameters for the potential (amplitude and cut-off redius) amplVwfVwf = 4.0 * kBT # sometimes we change this to 2.0*kBT rcutVwfVwf = 1.5 * r0 # AVB: the potential system.non_bonded_inter[vwf_type, vwf_type].lennard_jones.set_params( epsilon=amplVwfVwf, sigma=r0 / 1.122, shift="auto", cutoff=rcutVwfVwf, min=r0 * 0.6) print("Warming up the polymer chain.") ## For longer chains (>100) an extensive ## warmup is neccessary ... system.time_step = 0.002 system.thermostat.set_langevin(kT=4.0e-6, gamma=1.0) # AVB: Here the Langevin thermostat is needed, because we have not yet initialized the LB-fluid. # AVB: And somehow it is necessary so that the polymer adopts the equilibrium conformation of the globule. # AVB: you may skip this step for i in range(100): system.force_cap = float(i) + 1 system.integrator.run(100) print("Warmup finished.") system.force_cap = 0 system.integrator.run(100) system.time_step = time_step system.integrator.run(500) # AVB: the following command turns the Langevin thermostat on in line 49 system.thermostat.turn_off() # AVB: This command sets the velocities of all particles to zero system.part[:].v = [0, 0, 0] # AVB: The density was too small here. I have set 1.0 for now. # AVB: It would be necessary to recalculate, but the density of the liquid should not affect the movements of the polymer (this is how our physical model works). lbf = espressomd.lb.LBFluid(agrid=1, dens=1.0, visc=1.0e2, tau=time_step, fric=0.01) system.actors.add(lbf) system.thermostat.set_lb(kT=4.0e-6) # Setup boundaries walls = [lbboundaries.LBBoundary() for k in range(2)] walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5), velocity=v) walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-30.5)) for wall in walls: system.lbboundaries.add(wall) print("Warming up the system with LB fluid.") system.integrator.run(5000) print("LB fluid warming finished.") # AVB: after this you should have a completely collapsed polymer globule # AVB: If you want to watch the process of globule formation in Paraview, just change 5000 to 0 in line 100 N = 25 x_coord = np.array([30] * N) y_coord = np.arange(14, 24, 5 / N) z_coord = np.arange(14, 24, 5 / N) for i in range(N): for j in range(N): system.part.add(id=i * N + j + 100, pos=np.array([x_coord[i], y_coord[j], z_coord[i]]), v=np.array([0, 0, 0]), type=i * N + j + 100) all_collagen = range(100, (N - 1) * N + (N - 1) + 100) system.comfixed.types = all_collagen for i in range(100, (N - 1) * N + (N - 1) + 100): system.non_bonded_inter[vwf_type, i].lennard_jones.set_params(epsilon=amplVwfVwf, sigma=r0 / 1.122, shift="auto", cutoff=rcutVwfVwf, min=r0 * 0.6) # configure correlators com_pos = ComPosition(ids=(0, )) c = Correlator(obs1=com_pos, tau_lin=16, tau_max=loops * step_per_loop, delta_N=1, corr_operation="square_distance_componentwise", compress1="discard1") system.auto_update_accumulators.add(c) print("Sampling started.") print("lenth after warmup") print( system.analysis.calc_re(chain_start=0, number_of_chains=1, chain_length=mpc - 1)[0]) lengths = [] ylengths = [] for i in range(loops): system.integrator.run(step_per_loop) system.analysis.append() lengths.append( system.analysis.calc_re(chain_start=0, number_of_chains=1, chain_length=mpc - 1)[0]) lbf.print_vtk_velocity(outdir + "/" + str(vy) + "%04i.vtk" % i) system.part.writevtk(outdir + "/" + str(vy) + "vwf_all%04i.vtk" % i, types=all_collagen) system.part.writevtk(outdir + "/" + str(vy) + "vwf_poly%04i.vtk" % i, types=[0]) cor = list(system.part[:].pos) y = [] for l in cor: y.append(l[1]) ylengths.append(max(y) - min(y)) sys.stdout.write("\rSampling: %05i" % i) sys.stdout.flush() walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5)) walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-30.5)) for i in range(100): system.integrator.run(step_per_loop) lengths.append( system.analysis.calc_re(chain_start=0, number_of_chains=1, chain_length=mpc - 1)[0]) system.part.writevtk(outdir + "/" + str(vy) + "vwf_all[r0=2,kBT=4]intheEND.vtk") with open(outdir + "/lengths" + str(vy) + ".dat", "a") as datafile: datafile.write("\n".join(map(str, lengths))) with open(outdir + "/lengthsY" + str(vy) + ".dat", "a") as datafile: datafile.write("\n".join(map(str, ylengths))) mean_vy = [(vy * 10000) / 32, sum(ylengths) / len(ylengths)] print("mean_vy") print(mean_vy) with open(outdir + "/mean_vy" + "2kBT_2r0" + ".dat", "a") as datafile: datafile.write(" ".join(map(str, mean_vy))) c.finalize() corrdata = c.result() corr = zeros((corrdata.shape[0], 2)) corr[:, 0] = corrdata[:, 0] corr[:, 1] = (corrdata[:, 2] + corrdata[:, 3] + corrdata[:, 4]) / 3 savetxt(outdir + "/msd_nom" + str(mpc) + ".dat", corr) with open(outdir + "/rh_out.dat", "a") as datafile: rh = system.analysis.calc_rh(chain_start=0, number_of_chains=1, chain_length=mpc - 1) datafile.write(str(mpc) + " " + str(rh[0]) + "\n")
# AVB: to reproduce hydrophobicity # AVB: parameters for the potential (amplitude and cut-off redius) amplVwfVwf = 4.0 * kBT # sometimes we change this to 2.0*kBT rcutVwfVwf = 2.0 * r0 # AVB: the potential system.non_bonded_inter[vwf_type, vwf_type].lennard_jones.set_params(epsilon=amplVwfVwf, sigma=r0 / 1.122, shift="auto", cutoff=rcutVwfVwf, min=r0 * 0.6) print("Warming up the polymer chain.") ## For longer chains (>100) an extensive ## warmup is neccessary ... system.time_step = 0.002 system.thermostat.set_langevin(kT=4.0e-6, gamma=1.0) # AVB: Here the Langevin thermostat is needed, because we have not yet initialized the LB-fluid. # AVB: And somehow it is necessary so that the polymer adopts the equilibrium conformation of the globule. # AVB: you may skip this step print("Warmup finished.") system.integrator.run(100) system.time_step = time_step system.integrator.run(500) # AVB: the following command turns the Langevin thermostat on in line 49 system.thermostat.turn_off() # AVB: This command sets the velocities of all particles to zero system.part[:].v = [0, 0, 0]