LAMMPS (17 Feb 2022) #===========================================================================# # single particle drag tests # # # # Run consists of a colloidal particle being dragged with a constant force # # through an LB-fluid. The colloidal particle could be single atom or # # be a composite particle. Composite particles could be bonded or just # # rigidly constrained to stay together. You can set flags in the script to # # change these. # # # # Sample output from this run can be found in the files with "log." # # located in the same directory. # #===========================================================================# units nano dimension 3 boundary p p f atom_style molecular region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0 #---------------------------------------------------------------------------- # Set up particles with n_nodes and decide if bonded or rigid #---------------------------------------------------------------------------- variable n_nodes equal 4 # 1, 4, 6 are options with definitions below variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1, # bond parameters set for n_node = 4 case) variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction. variable tstep equal 0.00025 if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain" create_box 1 mydomain Created orthogonal box = (-24 -24 -24) to (24 24 24) 1 by 1 by 1 MPI processor grid if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124" create_atoms 1 single 0.0 0.0 0.204124 Created 1 atoms using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) create_atoms CPU = 0.001 seconds create_atoms 1 single -0.096225 -0.166667 -0.0680414 Created 1 atoms using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) create_atoms CPU = 0.001 seconds create_atoms 1 single -0.096225 0.166667 -0.0680414 Created 1 atoms using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) create_atoms CPU = 0.000 seconds create_atoms 1 single 0.19245 0. -0.0680414 Created 1 atoms using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24) create_atoms CPU = 0.000 seconds #---------------------------------------------------------------------------- # Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing # to ensure that the particles belonging to a given processor remain inside # that processors lattice-Boltzmann grid. # The arguments for neigh_modify have been set to "delay 0 every 1", again # to ensure that the particles belonging to a given processor remain inside # that processors lattice-Boltzmann grid. However, these values can likely # be somewhat increased without issue. If a problem does arise (a particle # is outside of its processors LB grid) an error message is printed and # the simulation is terminated. #---------------------------------------------------------------------------- neighbor 0.3 bin neigh_modify delay 0 every 1 check yes comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx #---------------------------------------------------------------------------- # Implement a hard-sphere interactions between particles & create bonds #---------------------------------------------------------------------------- pair_style lj/cut 5.88 pair_coeff * * 0.0 0.0 5.88 variable total_mass equal 0.002398 # particle mass variable node_mass equal "v_total_mass / v_n_nodes" mass * ${node_mass} mass * 0.0005995 if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35" #velocity all set 0.02 0.0 0.0 #---------------------------------------------------------------------------- # Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes) # to drag particles through the fluid. #---------------------------------------------------------------------------- variable total_force equal 1.0 # total external force on the particle variable node_force equal "v_total_force / v_n_nodes" variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes fix drag all addforce ${node_force} v_oscillateY v_oscillateZ fix drag all addforce 0.25 v_oscillateY v_oscillateZ #--------------------------------------------------------------------------- # Create a lattice-Boltzmann fluid covering the simulation domain. # This fluid feels a force due to the particle (group all here) # (however, this fix does not explicity apply a force back on to these # particles...this is accomplished through the use of the lb/viscous fix). # Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and # lattice spacing dx=1.2. # Different ".log" files in this directory show the output with the stencil # option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's). #---------------------------------------------------------------------------- timestep ${tstep} timestep 0.00025 fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2 Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486) Local Grid Geometry created. (../fix_lb_fluid.cpp:1018) #dumpxdmf 1000 fflow #---------------------------------------------------------------------------- # Apply the force from the fluid to the particles, and integrate their # motion, constraining them to move and rotate together as a single rigid # spherical object or an elastically bonded object #---------------------------------------------------------------------------- fix 2 all lb/viscous if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all" fix 3 all rigid group 1 all 1 rigid bodies with 4 atoms #---------------------------------------------------------------------------- # Create variables containing the positions/velocity of the colloids center # of mass. #---------------------------------------------------------------------------- variable cmx equal xcm(all,x) variable cmy equal xcm(all,y) variable cmz equal xcm(all,z) variable vcmx equal vcm(all,x) variable vcmy equal vcm(all,y) variable vcmz equal vcm(all,z) if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out" variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out variable comdatafile string drag_n4_st3_dt${tstep}.out variable comdatafile string drag_n4_st3_dt0.00025.out #fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no run 10000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - fix lb/fluid command: @Article{Denniston et al., author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead}, title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.}, year = 2022, volume = 275, pages = {108318} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.18 ghost atom cutoff = 6.18 binsize = 3.09, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732) Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 0 0 0 2.1529156e-12 10000 0.021008983 0 0 0.00043509092 1.4149298e-08 Loop time of 185.434 on 1 procs for 10000 steps with 4 atoms Performance: 1164.837 ns/day, 0.021 hours/ns, 53.928 timesteps/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02024 | 0.02024 | 0.02024 | 0.0 | 0.01 Bond | 0.0011585 | 0.0011585 | 0.0011585 | 0.0 | 0.00 Neigh | 8.88e-05 | 8.88e-05 | 8.88e-05 | 0.0 | 0.00 Comm | 0.011615 | 0.011615 | 0.011615 | 0.0 | 0.01 Output | 8.32e-05 | 8.32e-05 | 8.32e-05 | 0.0 | 0.00 Modify | 185.36 | 185.36 | 185.36 | 0.0 | 99.96 Other | | 0.04469 | | | 0.02 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6 ave 6 max 6 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6 Ave neighs/atom = 1.5 Ave special neighs/atom = 0 Neighbor list builds = 9 Dangerous builds = 0 #run 100000 Total wall time: 0:03:05