Merge branch 'master' into prepare-clang-format
# Conflicts: # src/KOKKOS/nbin_kokkos.h # src/KOKKOS/nbin_ssa_kokkos.h # src/MOLECULE/bond_fene_expand.h # src/USER-DPD/nbin_ssa.h # src/USER-DPD/nstencil_half_bin_2d_ssa.h # src/USER-DPD/nstencil_half_bin_3d_ssa.h # src/USER-INTEL/nbin_intel.h # src/USER-MISC/fix_propel_self.cpp # src/USER-OMP/npair_full_multi_old_omp.h # src/USER-OMP/npair_half_multi_old_newton_omp.h # src/USER-OMP/npair_half_size_multi_newtoff_omp.h # src/USER-OMP/npair_halffull_newtoff_omp.h # src/USER-OMP/npair_halffull_newton_omp.h # src/USER-OMP/npair_skip_omp.h # src/main.cpp # src/nbin_standard.h # src/npair_full_multi_old.h # src/npair_halffull_newtoff.h # src/npair_halffull_newton.h # src/npair_skip.h # src/npair_skip_respa.h # src/npair_skip_size.h # src/npair_skip_size_off2on.h # src/npair_skip_size_off2on_oneside.h # src/nstencil_full_bin_2d.h # src/nstencil_full_bin_3d.h # src/nstencil_full_ghost_bin_2d.h # src/nstencil_full_ghost_bin_3d.h # src/nstencil_full_multi_2d.h # src/nstencil_full_multi_3d.h # src/nstencil_full_multi_old_2d.h # src/nstencil_full_multi_old_3d.h # src/nstencil_half_bin_2d_newtoff.cpp # src/nstencil_half_bin_3d_newtoff.cpp # src/nstencil_half_bin_3d_newton_tri.h # src/nstencil_half_ghost_bin_2d_newtoff.cpp # src/nstencil_half_ghost_bin_2d_newtoff.h # src/nstencil_half_ghost_bin_3d_newtoff.cpp # src/nstencil_half_ghost_bin_3d_newtoff.h # src/nstencil_half_multi_2d.h # src/nstencil_half_multi_2d_newtoff.h # src/nstencil_half_multi_2d_newton_tri.h # src/nstencil_half_multi_2d_tri.h # src/nstencil_half_multi_3d_newtoff.h # src/nstencil_half_multi_3d_newton_tri.h
This commit is contained in:
Axel Kohlmeyer
53
examples/USER/brownian/2d_velocity/in2d.velocity
Normal file
53
examples/USER/brownian/2d_velocity/in2d.velocity
Normal file
@ -0,0 +1,53 @@
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||||
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
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variable gamma_t equal 1.0
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variable temp equal 1.0
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variable seed equal 1974019
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variable fp equal 4.0
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variable params string ${gamma_t}_${temp}_${fp}
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units lj
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dimension 2
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newton off
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lattice sq 0.4
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region box block -16 16 -16 16 -0.2 0.2
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create_box 1 box
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create_atoms 1 box
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mass * 1.0
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velocity all create 1.0 1 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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pair_style none
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fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
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fix vel all propel/self velocity ${fp}
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fix 2 all enforce2d
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fix_modify vel virial yes
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compute press all pressure NULL virial
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thermo_style custom step temp epair c_press
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#equilibration
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timestep 0.0000000001
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thermo 500
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run 5000
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reset_timestep 0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*] c_press
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timestep 0.00001
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thermo 1000
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# main run
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run 12000
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@ -0,0 +1,151 @@
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LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
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variable gamma_t equal 1.0
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variable temp equal 1.0
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variable seed equal 1974019
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variable fp equal 4.0
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variable params string ${gamma_t}_${temp}_${fp}
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variable params string 1_${temp}_${fp}
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variable params string 1_1_${fp}
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variable params string 1_1_4
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units lj
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dimension 2
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newton off
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lattice sq 0.4
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Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
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region box block -16 16 -16 16 -0.2 0.2
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create_box 1 box
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Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 1024 atoms
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create_atoms CPU = 0.001 seconds
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mass * 1.0
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velocity all create 1.0 1 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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pair_style none
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fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
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fix step all brownian 1 ${seed} gamma_t ${gamma_t}
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fix step all brownian 1 1974019 gamma_t ${gamma_t}
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fix step all brownian 1 1974019 gamma_t 1
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fix vel all propel/self velocity ${fp}
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fix vel all propel/self velocity 4
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fix 2 all enforce2d
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fix_modify vel virial yes
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compute press all pressure NULL virial
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thermo_style custom step temp epair c_press
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#equilibration
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timestep 0.0000000001
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thermo 500
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run 5000
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WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
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Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
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Step Temp E_pair c_press
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0 1 0 -0.18336111
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500 2.0519273e+10 0 -0.048238222
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1000 1.9821717e+10 0 -0.4711053
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1500 1.9697609e+10 0 -0.13539588
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2000 2.0209443e+10 0 0.0094958039
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2500 1.9591299e+10 0 0.40117118
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3000 2.089566e+10 0 -0.036548251
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3500 1.978692e+10 0 0.28282578
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4000 2.0657848e+10 0 0.17618064
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4500 2.0837353e+10 0 -0.080724651
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5000 2.0348316e+10 0 -0.17471195
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Loop time of 0.575164 on 1 procs for 5000 steps with 1024 atoms
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Performance: 0.075 tau/day, 8693.168 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0036819 | 0.0036819 | 0.0036819 | 0.0 | 0.64
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Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
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Modify | 0.51999 | 0.51999 | 0.51999 | 0.0 | 90.41
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Other | | 0.05121 | | | 8.90
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 65.0000 ave 65 max 65 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
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|
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Total # of neighbors = 0
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Ave neighs/atom = 0.0000000
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Neighbor list builds = 0
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Dangerous builds = 0
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reset_timestep 0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*] c_press
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timestep 0.00001
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thermo 1000
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# main run
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run 12000
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
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Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
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Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
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0 2.0328444e+10 0 0 0 0 0 -0.17471195
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1000 197017.59 0 0.018147562 0.019839233 0 0.037986796 -0.71897807
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2000 197030.23 0 0.03909867 0.041721342 0 0.080820011 -0.30051929
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3000 201997.2 0 0.065694399 0.06235257 0 0.12804697 -0.85167039
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4000 199927.76 0 0.085698715 0.080328815 0 0.16602753 0.18493117
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5000 198665.7 0 0.10896054 0.097021266 0 0.2059818 -0.090735406
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6000 199277.78 0 0.13081111 0.11724814 0 0.24805925 -0.18189034
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7000 199850.54 0 0.14721838 0.13806858 0 0.28528696 0.11334674
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8000 191577.11 0 0.16582149 0.15935853 0 0.32518002 -0.73284569
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9000 197331.29 0 0.17995704 0.18652927 0 0.3664863 -0.015558407
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10000 197048.17 0 0.2034106 0.20329856 0 0.40670916 0.36985211
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11000 200105.54 0 0.21809835 0.21966463 0 0.43776298 0.36437
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12000 203180.39 0 0.23810386 0.23666184 0 0.47476569 -0.072006034
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Loop time of 1.37465 on 1 procs for 12000 steps with 1024 atoms
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Performance: 7542.303 tau/day, 8729.517 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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||||
---------------------------------------------------------------
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||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.01
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||||
Comm | 0.0024607 | 0.0024607 | 0.0024607 | 0.0 | 0.18
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Output | 0.00068665 | 0.00068665 | 0.00068665 | 0.0 | 0.05
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Modify | 1.2479 | 1.2479 | 1.2479 | 0.0 | 90.78
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Other | | 0.1235 | | | 8.98
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Nlocal: 1024.00 ave 1024 max 1024 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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|
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Total # of neighbors = 0
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Ave neighs/atom = 0.0000000
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Neighbor list builds = 15
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Dangerous builds = 0
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Total wall time: 0:00:01
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@ -0,0 +1,151 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
|
||||
|
||||
variable gamma_t equal 1.0
|
||||
variable temp equal 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp equal 4.0
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||||
variable params string ${gamma_t}_${temp}_${fp}
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||||
variable params string 1_${temp}_${fp}
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||||
variable params string 1_1_${fp}
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variable params string 1_1_4
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||||
|
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units lj
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||||
dimension 2
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newton off
|
||||
|
||||
lattice sq 0.4
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Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
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region box block -16 16 -16 16 -0.2 0.2
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create_box 1 box
|
||||
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
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2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
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||||
Created 1024 atoms
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||||
create_atoms CPU = 0.001 seconds
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mass * 1.0
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velocity all create 1.0 1 loop geom
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||||
|
||||
neighbor 1.0 bin
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||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
|
||||
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
|
||||
fix step all brownian 1 1974019 gamma_t ${gamma_t}
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||||
fix step all brownian 1 1974019 gamma_t 1
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fix vel all propel/self velocity ${fp}
|
||||
fix vel all propel/self velocity 4
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||||
fix 2 all enforce2d
|
||||
fix_modify vel virial yes
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step temp epair c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 500
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||||
run 5000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
|
||||
Step Temp E_pair c_press
|
||||
0 1 0 -0.18336111
|
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500 1.9862591e+10 0 -0.32013566
|
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1000 2.0093184e+10 0 -0.36609742
|
||||
1500 1.9562283e+10 0 -0.53349351
|
||||
2000 1.9903977e+10 0 0.63783249
|
||||
2500 2.0260128e+10 0 0.30046413
|
||||
3000 1.9948065e+10 0 -0.63093105
|
||||
3500 1.9507486e+10 0 0.48762848
|
||||
4000 2.0049087e+10 0 0.40289309
|
||||
4500 1.9975813e+10 0 0.57649363
|
||||
5000 2.0129291e+10 0 -0.41288352
|
||||
Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms
|
||||
|
||||
Performance: 0.181 tau/day, 20924.952 timesteps/s
|
||||
92.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34
|
||||
Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13
|
||||
Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27
|
||||
Other | | 0.06992 | | | 29.26
|
||||
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 33.0000 ave 33 max 33 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*] c_press
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 12000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||
0 2.0109634e+10 0 0 0 0 0 -0.41288352
|
||||
1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126
|
||||
2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705
|
||||
3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601
|
||||
4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473
|
||||
5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791
|
||||
6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467
|
||||
7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646
|
||||
8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452
|
||||
9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228
|
||||
10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262
|
||||
11000 202911.93 0 0.21569236 0.22221715 0 0.43790952 -0.38430031
|
||||
12000 192590.04 0 0.24041439 0.24114487 0 0.48155926 -0.1677052
|
||||
Loop time of 0.443026 on 4 procs for 12000 steps with 1024 atoms
|
||||
|
||||
Performance: 23402.683 tau/day, 27086.439 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.2663e-05 | 3.3855e-05 | 3.4809e-05 | 0.0 | 0.01
|
||||
Comm | 0.0030291 | 0.0030628 | 0.0030825 | 0.0 | 0.69
|
||||
Output | 0.00027895 | 0.00051624 | 0.001184 | 0.0 | 0.12
|
||||
Modify | 0.31607 | 0.33372 | 0.37391 | 4.0 | 75.33
|
||||
Other | | 0.1057 | | | 23.86
|
||||
|
||||
Nlocal: 256.000 ave 259 max 253 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
54
examples/USER/brownian/asphere/in2d.ellipsoid
Normal file
54
examples/USER/brownian/asphere/in2d.ellipsoid
Normal file
@ -0,0 +1,54 @@
|
||||
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_r_1 string inf
|
||||
variable gamma_r_2 string inf
|
||||
variable gamma_r_3 string 0.1
|
||||
variable gamma_t_1 string 5.0
|
||||
variable gamma_t_2 string 7.0
|
||||
variable gamma_t_3 string inf
|
||||
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole ellipsoid
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * shape 3.0 1.0 1.0
|
||||
set type * quat/random ${seed}
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
||||
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
||||
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
||||
dipole 1.0 0.0 0.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||
# x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
54
examples/USER/brownian/asphere/in3d.ellipsoid
Normal file
54
examples/USER/brownian/asphere/in3d.ellipsoid
Normal file
@ -0,0 +1,54 @@
|
||||
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_r_1 string 2.0
|
||||
variable gamma_r_2 string 0.25
|
||||
variable gamma_r_3 string 0.1
|
||||
variable gamma_t_1 string 5.0
|
||||
variable gamma_t_2 string 7.0
|
||||
variable gamma_t_3 string 9.0
|
||||
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole ellipsoid
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * shape 3.0 1.0 1.0
|
||||
set type * quat/random ${seed}
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
||||
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
||||
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
||||
dipole 1.0 0.0 0.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||
# x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_r_1 string inf
|
||||
variable gamma_r_2 string inf
|
||||
variable gamma_r_3 string 0.1
|
||||
variable gamma_t_1 string 5.0
|
||||
variable gamma_t_2 string 7.0
|
||||
variable gamma_t_3 string inf
|
||||
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole ellipsoid
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.005 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
3600 settings made for dipole/random
|
||||
set type * shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
3600 settings made for shape
|
||||
set type * quat/random ${seed}
|
||||
set type * quat/random 198098
|
||||
Setting atom values ...
|
||||
3600 settings made for quat/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.114 | 5.114 | 5.114 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 0.99972222 0 0 0 0 0
|
||||
100 34376.187 0 0.00034728749 0.00034318997 0 0.00069047747
|
||||
200 36135.708 0 0.00067452936 0.0006818928 0 0.0013564222
|
||||
300 34444.929 0 0.0010189319 0.00099849203 0 0.002017424
|
||||
400 35668.312 0 0.0013648699 0.0013311884 0 0.0026960583
|
||||
500 35388.615 0 0.0017330203 0.0016077184 0 0.0033407387
|
||||
600 35180.065 0 0.002052223 0.0019394635 0 0.0039916865
|
||||
700 34035.38 0 0.0024329956 0.0022664905 0 0.0046994861
|
||||
800 34581.664 0 0.002783885 0.0025794872 0 0.0053633723
|
||||
900 34579.945 0 0.003163442 0.0029351952 0 0.0060986372
|
||||
1000 34158.066 0 0.0035589034 0.0032627605 0 0.0068216639
|
||||
1100 33453.827 0 0.0038861895 0.003565372 0 0.0074515615
|
||||
1200 33608.06 0 0.0041325698 0.0038943268 0 0.0080268966
|
||||
1300 34381.633 0 0.004405682 0.0043294156 0 0.0087350976
|
||||
1400 32925.746 0 0.0047383547 0.0046803517 0 0.0094187065
|
||||
1500 34809.764 0 0.0051149571 0.0049309746 0 0.010045932
|
||||
1600 33580.096 0 0.0054893472 0.0052465377 0 0.010735885
|
||||
1700 34596.275 0 0.00581894 0.0056500316 0 0.011468972
|
||||
1800 33926.736 0 0.0062129617 0.0059796125 0 0.012192574
|
||||
1900 35577.131 0 0.0065668637 0.0062530163 0 0.01281988
|
||||
2000 34224.967 0 0.0070005917 0.006598912 0 0.013599504
|
||||
2100 33991.406 0 0.0073134826 0.0069119252 0 0.014225408
|
||||
2200 34647.054 0 0.007659301 0.0073434715 0 0.015002772
|
||||
2300 33956.835 0 0.007965191 0.0076318537 0 0.015597045
|
||||
2400 35272.549 0 0.0082467116 0.007929202 0 0.016175914
|
||||
2500 33901.494 0 0.0086251299 0.0082790757 0 0.016904206
|
||||
2600 34138.227 0 0.0089419364 0.0086639744 0 0.017605911
|
||||
2700 33691.013 0 0.0093083376 0.0090219118 0 0.018330249
|
||||
2800 34716.817 0 0.0095840095 0.0094118945 0 0.018995904
|
||||
2900 34473.982 0 0.0099773501 0.0098167668 0 0.019794117
|
||||
3000 33406.776 0 0.010391969 0.010098625 0 0.020490594
|
||||
Loop time of 3.67112 on 1 procs for 3000 steps with 3600 atoms
|
||||
|
||||
Performance: 706.051 tau/day, 817.189 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.037973 | 0.037973 | 0.037973 | 0.0 | 1.03
|
||||
Output | 0.0040674 | 0.0040674 | 0.0040674 | 0.0 | 0.11
|
||||
Modify | 3.515 | 3.515 | 3.515 | 0.0 | 95.75
|
||||
Other | | 0.1141 | | | 3.11
|
||||
|
||||
Nlocal: 3600.00 ave 3600 max 3600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 121.000 ave 121 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_r_1 string inf
|
||||
variable gamma_r_2 string inf
|
||||
variable gamma_r_3 string 0.1
|
||||
variable gamma_t_1 string 5.0
|
||||
variable gamma_t_2 string 7.0
|
||||
variable gamma_t_3 string inf
|
||||
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
|
||||
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole ellipsoid
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.007 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
3600 settings made for dipole/random
|
||||
set type * shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
3600 settings made for shape
|
||||
set type * quat/random ${seed}
|
||||
set type * quat/random 198098
|
||||
Setting atom values ...
|
||||
3600 settings made for quat/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.102 | 5.102 | 5.102 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 0.99972222 0 0 0 0 0
|
||||
100 33874.438 0 0.0003458147 0.00033165629 0 0.00067747099
|
||||
200 34893.188 0 0.00066290209 0.00068146332 0 0.0013443654
|
||||
300 34494.226 0 0.0010064902 0.0010276646 0 0.0020341548
|
||||
400 34537.887 0 0.0013457339 0.0014057042 0 0.0027514381
|
||||
500 34458.46 0 0.0017006949 0.0017120083 0 0.0034127033
|
||||
600 33229.977 0 0.0020841613 0.0020485346 0 0.0041326959
|
||||
700 33288.631 0 0.0024270272 0.0023673304 0 0.0047943576
|
||||
800 35317.512 0 0.0027924435 0.0026950912 0 0.0054875347
|
||||
900 33094.299 0 0.0031503627 0.0030789319 0 0.0062292946
|
||||
1000 35801.751 0 0.003489398 0.0034594626 0 0.0069488607
|
||||
1100 33427.701 0 0.0038547506 0.0038375809 0 0.0076923316
|
||||
1200 34675.07 0 0.0041824195 0.0042017298 0 0.0083841493
|
||||
1300 33080.294 0 0.0045258945 0.0045816356 0 0.0091075301
|
||||
1400 34927.288 0 0.0048252992 0.0049215701 0 0.0097468693
|
||||
1500 34338.558 0 0.0051959155 0.0053020102 0 0.010497926
|
||||
1600 34686.248 0 0.0055111463 0.0056220225 0 0.011133169
|
||||
1700 34336.158 0 0.0059240394 0.0059060319 0 0.011830071
|
||||
1800 34315.859 0 0.0063027944 0.0063004467 0 0.012603241
|
||||
1900 35096.721 0 0.0066098525 0.00672222 0 0.013332073
|
||||
2000 33544.18 0 0.0069401261 0.007074124 0 0.01401425
|
||||
2100 33863.219 0 0.0072726502 0.0074175954 0 0.014690246
|
||||
2200 34705.892 0 0.0075586722 0.0077552683 0 0.015313941
|
||||
2300 34025.357 0 0.0079046728 0.0081760519 0 0.016080725
|
||||
2400 34741.849 0 0.008252969 0.0085203087 0 0.016773278
|
||||
2500 34406.959 0 0.0085370091 0.0088556377 0 0.017392647
|
||||
2600 34062.63 0 0.0088134153 0.0092536326 0 0.018067048
|
||||
2700 34677.666 0 0.0090592854 0.0096225881 0 0.018681874
|
||||
2800 33464.216 0 0.0093984162 0.0099647695 0 0.019363186
|
||||
2900 32920.721 0 0.0098222985 0.010366517 0 0.020188816
|
||||
3000 34539.66 0 0.010133317 0.01068102 0 0.020814337
|
||||
Loop time of 1.12143 on 4 procs for 3000 steps with 3600 atoms
|
||||
|
||||
Performance: 2311.341 tau/day, 2675.163 timesteps/s
|
||||
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.036017 | 0.042828 | 0.051558 | 2.7 | 3.82
|
||||
Output | 0.0012608 | 0.0025993 | 0.0063775 | 4.3 | 0.23
|
||||
Modify | 0.9002 | 0.93095 | 0.99546 | 3.9 | 83.01
|
||||
Other | | 0.1451 | | | 12.93
|
||||
|
||||
Nlocal: 900.000 ave 900 max 900 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 61.0000 ave 61 max 61 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_r_1 string 2.0
|
||||
variable gamma_r_2 string 0.25
|
||||
variable gamma_r_3 string 0.1
|
||||
variable gamma_t_1 string 5.0
|
||||
variable gamma_t_2 string 7.0
|
||||
variable gamma_t_3 string 9.0
|
||||
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole ellipsoid
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.005 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for dipole/random
|
||||
set type * shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for shape
|
||||
set type * quat/random ${seed}
|
||||
set type * quat/random 198098
|
||||
Setting atom values ...
|
||||
4096 settings made for quat/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.219 | 5.219 | 5.219 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 1.4996338 0 0 0 0 0
|
||||
100 45690.838 0 0.00029994317 0.00029953902 0.00030002809 0.00089951027
|
||||
200 45571.166 0 0.00061376797 0.00060955238 0.00061153551 0.0018348559
|
||||
300 44693.418 0 0.00093058034 0.00089383536 0.00091554588 0.0027399616
|
||||
400 44831.846 0 0.001250227 0.0012230128 0.0012120517 0.0036852914
|
||||
500 45028.015 0 0.0015448869 0.0015339549 0.0014978843 0.0045767262
|
||||
600 45895.442 0 0.0018621952 0.0018169905 0.0018352784 0.0055144641
|
||||
700 45858.744 0 0.0021617097 0.0021137714 0.0021360394 0.0064115206
|
||||
800 45155.215 0 0.002428445 0.0024288837 0.0024516737 0.0073090023
|
||||
900 45427.427 0 0.0027265978 0.0027662531 0.0027329878 0.0082258387
|
||||
1000 45398.166 0 0.0030685345 0.0030805014 0.0029765916 0.0091256275
|
||||
1100 44622.428 0 0.0033766954 0.0033976168 0.0032745406 0.010048853
|
||||
1200 45500.277 0 0.0036410565 0.0036840528 0.0035831659 0.010908275
|
||||
1300 45265.8 0 0.0039143146 0.0039419334 0.0038761633 0.011732411
|
||||
1400 45482.435 0 0.0042006542 0.0043373651 0.004164002 0.012702021
|
||||
1500 45126.629 0 0.0044647379 0.0046021855 0.004487041 0.013553965
|
||||
1600 45178.172 0 0.0047726618 0.0049110287 0.0048012671 0.014484958
|
||||
1700 44918.685 0 0.005104787 0.0052522662 0.0050844375 0.015441491
|
||||
1800 44776.678 0 0.0054395368 0.0056092038 0.0054623875 0.016511128
|
||||
1900 46035.987 0 0.0057735872 0.0059357043 0.0057296009 0.017438892
|
||||
2000 45436.517 0 0.0060837459 0.0063485717 0.0059769119 0.018409229
|
||||
2100 45871.502 0 0.0063736337 0.0066551978 0.0063077439 0.019336575
|
||||
2200 45511.847 0 0.0066419141 0.0069700452 0.0065553318 0.020167291
|
||||
2300 45597.047 0 0.0069251517 0.0073015716 0.0068945654 0.021121289
|
||||
2400 44832.007 0 0.0071894253 0.0076238221 0.0071638554 0.021977103
|
||||
2500 45668.42 0 0.0074351304 0.0079594991 0.0075390719 0.022933701
|
||||
2600 45248.483 0 0.007781496 0.008293944 0.0077956068 0.023871047
|
||||
2700 45308.515 0 0.0080302993 0.0086329679 0.0081457335 0.024809001
|
||||
2800 45637.72 0 0.0083889026 0.0089173198 0.0086032427 0.025909465
|
||||
2900 45909.343 0 0.0087169392 0.009181179 0.0088778569 0.026775975
|
||||
3000 45213.613 0 0.0090508891 0.0094253485 0.0092660321 0.02774227
|
||||
Loop time of 4.13937 on 1 procs for 3000 steps with 4096 atoms
|
||||
|
||||
Performance: 626.183 tau/day, 724.749 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.24709 | 0.24709 | 0.24709 | 0.0 | 5.97
|
||||
Output | 0.004636 | 0.004636 | 0.004636 | 0.0 | 0.11
|
||||
Modify | 3.7604 | 3.7604 | 3.7604 | 0.0 | 90.85
|
||||
Other | | 0.1272 | | | 3.07
|
||||
|
||||
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 817.000 ave 817 max 817 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_r_1 string 2.0
|
||||
variable gamma_r_2 string 0.25
|
||||
variable gamma_r_3 string 0.1
|
||||
variable gamma_t_1 string 5.0
|
||||
variable gamma_t_2 string 7.0
|
||||
variable gamma_t_3 string 9.0
|
||||
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
|
||||
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole ellipsoid
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for dipole/random
|
||||
set type * shape 3.0 1.0 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for shape
|
||||
set type * quat/random ${seed}
|
||||
set type * quat/random 198098
|
||||
Setting atom values ...
|
||||
4096 settings made for quat/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.152 | 5.152 | 5.152 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 1.4996338 0 0 0 0 0
|
||||
100 45236.508 0 0.00030817418 0.00030717742 0.0003019227 0.0009172743
|
||||
200 45564.566 0 0.00062027526 0.00062110132 0.0006080391 0.0018494157
|
||||
300 46232.801 0 0.00091155216 0.00094473459 0.00093009391 0.0027863807
|
||||
400 45250.414 0 0.0011980791 0.0012538262 0.0012201461 0.0036720513
|
||||
500 45217.133 0 0.0015186813 0.0015752994 0.001509437 0.0046034177
|
||||
600 45531.276 0 0.0018194588 0.0019243758 0.0018209246 0.0055647592
|
||||
700 44834.624 0 0.0021277747 0.0022417115 0.0021352036 0.0065046898
|
||||
800 45413.998 0 0.0024558838 0.0025741787 0.0024088704 0.0074389329
|
||||
900 45668.624 0 0.0027366171 0.002858242 0.0027580782 0.0083529374
|
||||
1000 45809.223 0 0.0030331425 0.003186293 0.0030414906 0.0092609261
|
||||
1100 45193.019 0 0.0033199824 0.0034668659 0.003298885 0.010085733
|
||||
1200 44522.927 0 0.0036503132 0.0037490684 0.0036089852 0.011008367
|
||||
1300 45214.567 0 0.0039958617 0.0040881934 0.0038709079 0.011954963
|
||||
1400 45217.997 0 0.004276499 0.0044624985 0.0041104891 0.012849487
|
||||
1500 45497.171 0 0.0045943272 0.0047116875 0.0044113504 0.013717365
|
||||
1600 45905.187 0 0.0049004996 0.0049982014 0.0047394999 0.014638201
|
||||
1700 45551.346 0 0.0051540939 0.0053187249 0.0050861052 0.015558924
|
||||
1800 45347.782 0 0.0054101891 0.0056306 0.0053515873 0.016392376
|
||||
1900 45107.895 0 0.005743705 0.0059584896 0.0056220384 0.017324233
|
||||
2000 45043.389 0 0.0059803588 0.006230449 0.005911555 0.018122363
|
||||
2100 45433.293 0 0.0062610364 0.0066140744 0.0062152977 0.019090408
|
||||
2200 45804.217 0 0.0064995183 0.0068831274 0.0064971789 0.019879825
|
||||
2300 45697.516 0 0.0067910846 0.0071845673 0.0068046192 0.020780271
|
||||
2400 45447.422 0 0.0071022706 0.0074743709 0.0070983185 0.02167496
|
||||
2500 45395.18 0 0.0073817023 0.0077467991 0.0074263196 0.022554821
|
||||
2600 45943.044 0 0.0075953233 0.007997707 0.0076508583 0.023243889
|
||||
2700 45859.978 0 0.0079082128 0.0082090043 0.0078853376 0.024002555
|
||||
2800 45822.007 0 0.0082607534 0.0084510061 0.0081985549 0.024910314
|
||||
2900 45438.456 0 0.0085958203 0.0088807705 0.0084755353 0.025952126
|
||||
3000 45060.957 0 0.0089017992 0.0090966159 0.0086718875 0.026670303
|
||||
Loop time of 1.23282 on 4 procs for 3000 steps with 4096 atoms
|
||||
|
||||
Performance: 2102.502 tau/day, 2433.452 timesteps/s
|
||||
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 8.5831e-06 | 8.5831e-06 | 8.5831e-06 | 0.0 | 0.00
|
||||
Comm | 0.10931 | 0.11473 | 0.11748 | 0.9 | 9.31
|
||||
Output | 0.001375 | 0.0018924 | 0.0034099 | 2.0 | 0.15
|
||||
Modify | 0.97744 | 0.99158 | 1.0089 | 1.3 | 80.43
|
||||
Other | | 0.1246 | | | 10.11
|
||||
|
||||
Nlocal: 1024.00 ave 1035 max 1016 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
43
examples/USER/brownian/point/in2d.point
Normal file
43
examples/USER/brownian/point/in2d.point
Normal file
@ -0,0 +1,43 @@
|
||||
##### dynamics of non-interacting point particles in 2D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 5.0
|
||||
variable gamma_t string 1.0
|
||||
variable params string ${rng}_${temp}_${gamma_t}
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||
# x y z xu yu zu fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
44
examples/USER/brownian/point/in3d.point
Normal file
44
examples/USER/brownian/point/in3d.point
Normal file
@ -0,0 +1,44 @@
|
||||
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 5.0
|
||||
variable gamma_t string 1.0
|
||||
variable params string ${rng}_${temp}_${gamma_t}
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||
# x y z xu yu zu fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
|
||||
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.1
Normal file
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.1
Normal file
@ -0,0 +1,119 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### dynamics of non-interacting point particles in 2D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 5.0
|
||||
variable gamma_t string 1.0
|
||||
variable params string ${rng}_${temp}_${gamma_t}
|
||||
variable params string gaussian_${temp}_${gamma_t}
|
||||
variable params string gaussian_5.0_${gamma_t}
|
||||
variable params string gaussian_5.0_1.0
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.003 seconds
|
||||
mass * 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 0.99972222 0 0 0 0 0
|
||||
100 1022861.2 0 0.010252464 0.0095481044 0 0.019800568
|
||||
200 986781.19 0 0.020552091 0.019485252 0 0.040037343
|
||||
300 1030219 0 0.030642552 0.028377678 0 0.05902023
|
||||
400 1003322.5 0 0.040610693 0.038179284 0 0.078789978
|
||||
500 989343.12 0 0.049978908 0.047445856 0 0.097424764
|
||||
600 1029781.3 0 0.059551719 0.057941149 0 0.11749287
|
||||
700 999447.72 0 0.06979546 0.067552325 0 0.13734778
|
||||
800 995373.97 0 0.080049251 0.078006344 0 0.1580556
|
||||
900 1011991.4 0 0.089753134 0.087065214 0 0.17681835
|
||||
1000 1006017.1 0 0.10041092 0.097934217 0 0.19834514
|
||||
1100 997762.63 0 0.11229742 0.10841547 0 0.22071289
|
||||
1200 1011707.8 0 0.12006388 0.1190115 0 0.23907538
|
||||
1300 1012099.1 0 0.13097486 0.12996632 0 0.26094117
|
||||
1400 997602.43 0 0.14345778 0.13830585 0 0.28176362
|
||||
1500 1005358.1 0 0.15441686 0.14927539 0 0.30369225
|
||||
1600 1007081.8 0 0.16496828 0.15936363 0 0.3243319
|
||||
1700 990284.9 0 0.1747286 0.16818246 0 0.34291106
|
||||
1800 969006.97 0 0.18228778 0.17972813 0 0.3620159
|
||||
1900 998066.69 0 0.19338277 0.19226121 0 0.38564397
|
||||
2000 972300.66 0 0.20352485 0.20145928 0 0.40498413
|
||||
2100 985025.88 0 0.21283854 0.21090075 0 0.42373929
|
||||
2200 1010964.6 0 0.22279055 0.22110734 0 0.44389789
|
||||
2300 975819.44 0 0.23128131 0.23226488 0 0.46354619
|
||||
2400 977043.53 0 0.24284105 0.24301689 0 0.48585794
|
||||
2500 969708.21 0 0.25415238 0.25354284 0 0.50769522
|
||||
2600 981969.5 0 0.26457173 0.26318018 0 0.52775192
|
||||
2700 987261.1 0 0.27497004 0.27761213 0 0.55258218
|
||||
2800 1005751.1 0 0.28530448 0.28715428 0 0.57245876
|
||||
2900 975930.11 0 0.29394811 0.29896948 0 0.59291759
|
||||
3000 997388.08 0 0.30674701 0.31193573 0 0.61868274
|
||||
Loop time of 1.501 on 1 procs for 3000 steps with 3600 atoms
|
||||
|
||||
Performance: 1726.852 tau/day, 1998.672 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.00059271 | 0.00059271 | 0.00059271 | 0.0 | 0.04
|
||||
Comm | 0.0055437 | 0.0055437 | 0.0055437 | 0.0 | 0.37
|
||||
Output | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 0.27
|
||||
Modify | 1.3852 | 1.3852 | 1.3852 | 0.0 | 92.28
|
||||
Other | | 0.1057 | | | 7.04
|
||||
|
||||
Nlocal: 3600.00 ave 3600 max 3600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 21
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.4
Normal file
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.4
Normal file
@ -0,0 +1,119 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### dynamics of non-interacting point particles in 2D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 5.0
|
||||
variable gamma_t string 1.0
|
||||
variable params string ${rng}_${temp}_${gamma_t}
|
||||
variable params string gaussian_${temp}_${gamma_t}
|
||||
variable params string gaussian_5.0_${gamma_t}
|
||||
variable params string gaussian_5.0_1.0
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass * 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 0.99972222 0 0 0 0 0
|
||||
100 1017972.1 0 0.010094052 0.0097502899 0 0.019844342
|
||||
200 1004552.1 0 0.020125116 0.01957629 0 0.039701406
|
||||
300 1017712.9 0 0.030271373 0.029411656 0 0.059683029
|
||||
400 1016693.8 0 0.040610061 0.038605869 0 0.07921593
|
||||
500 999527.84 0 0.049451389 0.049042225 0 0.098493614
|
||||
600 961157.92 0 0.059691948 0.059033176 0 0.11872512
|
||||
700 1006804.9 0 0.071205977 0.069972106 0 0.14117808
|
||||
800 1007321.8 0 0.081136977 0.079825976 0 0.16096295
|
||||
900 1002801.7 0 0.091236148 0.090833816 0 0.18206996
|
||||
1000 1010134.7 0 0.10091362 0.10023906 0 0.20115269
|
||||
1100 990246.55 0 0.1118367 0.11141049 0 0.22324719
|
||||
1200 1010555.5 0 0.12091736 0.12355456 0 0.24447192
|
||||
1300 997117.19 0 0.13099592 0.13292775 0 0.26392367
|
||||
1400 1020817.1 0 0.14167961 0.14172898 0 0.28340859
|
||||
1500 1015048.1 0 0.15225884 0.15162948 0 0.30388833
|
||||
1600 990291.98 0 0.16460973 0.16251919 0 0.32712891
|
||||
1700 980848.58 0 0.17380313 0.17351201 0 0.34731513
|
||||
1800 1000673.8 0 0.18383991 0.18175453 0 0.36559445
|
||||
1900 1009388.9 0 0.19411523 0.19367453 0 0.38778976
|
||||
2000 1005935.9 0 0.2015342 0.20585359 0 0.40738779
|
||||
2100 985500.56 0 0.21161056 0.21238463 0 0.42399519
|
||||
2200 997241.34 0 0.21841986 0.22117922 0 0.43959908
|
||||
2300 1011672.3 0 0.22688099 0.23155741 0 0.4584384
|
||||
2400 989837.68 0 0.23849839 0.24219 0 0.48068839
|
||||
2500 1035706.8 0 0.24541408 0.24947563 0 0.49488971
|
||||
2600 992370.08 0 0.25537803 0.25758332 0 0.51296135
|
||||
2700 990586.56 0 0.26542605 0.26762286 0 0.53304892
|
||||
2800 1002767.3 0 0.27570392 0.27874972 0 0.55445363
|
||||
2900 995307.27 0 0.28580946 0.29115624 0 0.5769657
|
||||
3000 1024317.7 0 0.29493208 0.30208924 0 0.59702132
|
||||
Loop time of 0.413047 on 4 procs for 3000 steps with 3600 atoms
|
||||
|
||||
Performance: 6275.312 tau/day, 7263.093 timesteps/s
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.00016236 | 0.00016338 | 0.00016403 | 0.0 | 0.04
|
||||
Comm | 0.0026367 | 0.0030084 | 0.0031497 | 0.4 | 0.73
|
||||
Output | 0.0011849 | 0.0013574 | 0.0018065 | 0.7 | 0.33
|
||||
Modify | 0.34447 | 0.35223 | 0.36357 | 1.2 | 85.28
|
||||
Other | | 0.05629 | | | 13.63
|
||||
|
||||
Nlocal: 900.000 ave 906 max 891 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.1
Normal file
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.1
Normal file
@ -0,0 +1,119 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 5.0
|
||||
variable gamma_t string 1.0
|
||||
variable params string ${rng}_${temp}_${gamma_t}
|
||||
variable params string gaussian_${temp}_${gamma_t}
|
||||
variable params string gaussian_5.0_${gamma_t}
|
||||
variable params string gaussian_5.0_1.0
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass * 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.694 | 2.694 | 2.694 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 1.4996338 0 0 0 0 0
|
||||
100 1500286.3 0 0.0098123603 0.010352169 0.010242435 0.030406964
|
||||
200 1488308 0 0.019934427 0.019968198 0.020471735 0.06037436
|
||||
300 1484472.4 0 0.029397156 0.030749312 0.030121294 0.090267762
|
||||
400 1517938.7 0 0.039217504 0.041440617 0.040512943 0.12117106
|
||||
500 1492769.5 0 0.04890343 0.051561801 0.050614941 0.15108017
|
||||
600 1510159.6 0 0.059770181 0.061650364 0.061298117 0.18271866
|
||||
700 1485424.1 0 0.070537955 0.071144877 0.071141546 0.21282438
|
||||
800 1496377.2 0 0.081291995 0.082546059 0.080653381 0.24449144
|
||||
900 1484409.1 0 0.090940427 0.093298981 0.091328056 0.27556746
|
||||
1000 1503322.4 0 0.10176921 0.10246052 0.10151773 0.30574747
|
||||
1100 1503322.4 0 0.11295993 0.11052632 0.11053406 0.33402031
|
||||
1200 1489236.2 0 0.12509723 0.11961982 0.12146498 0.36618203
|
||||
1300 1476050.3 0 0.13449034 0.12941323 0.1309765 0.39488007
|
||||
1400 1520818.7 0 0.14613571 0.13788044 0.14083944 0.42485558
|
||||
1500 1498936.4 0 0.15752286 0.15057712 0.15063399 0.45873397
|
||||
1600 1507524.1 0 0.16793678 0.16095681 0.16063531 0.4895289
|
||||
1700 1480581.2 0 0.17748019 0.172614 0.16922383 0.51931802
|
||||
1800 1505353.6 0 0.18850931 0.18304171 0.18063119 0.55218221
|
||||
1900 1491234.7 0 0.19836402 0.19306339 0.1929707 0.58439811
|
||||
2000 1519868.8 0 0.20698191 0.20211344 0.20328302 0.61237838
|
||||
2100 1493919.5 0 0.21453524 0.21186097 0.21423293 0.64062914
|
||||
2200 1517098.6 0 0.2257338 0.22381647 0.22474081 0.67429108
|
||||
2300 1481270.7 0 0.23499747 0.23348379 0.23498244 0.70346369
|
||||
2400 1495445.1 0 0.24535894 0.24290239 0.24229161 0.73055293
|
||||
2500 1522839.3 0 0.25695938 0.25109669 0.25214541 0.76020148
|
||||
2600 1518697.4 0 0.26680819 0.26120216 0.2604112 0.78842155
|
||||
2700 1529283.1 0 0.27524422 0.26942681 0.27148042 0.81615146
|
||||
2800 1500557.5 0 0.28436226 0.27957592 0.27935619 0.84329437
|
||||
2900 1509711.1 0 0.2948528 0.28562401 0.29055956 0.87103637
|
||||
3000 1522712.8 0 0.30347033 0.2975063 0.30121685 0.90219348
|
||||
Loop time of 2.35056 on 1 procs for 3000 steps with 4096 atoms
|
||||
|
||||
Performance: 1102.718 tau/day, 1276.293 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.00077772 | 0.00077772 | 0.00077772 | 0.0 | 0.03
|
||||
Comm | 0.010985 | 0.010985 | 0.010985 | 0.0 | 0.47
|
||||
Output | 0.0045807 | 0.0045807 | 0.0045807 | 0.0 | 0.19
|
||||
Modify | 2.2116 | 2.2116 | 2.2116 | 0.0 | 94.09
|
||||
Other | | 0.1226 | | | 5.22
|
||||
|
||||
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 24
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:02
|
||||
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.4
Normal file
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.4
Normal file
@ -0,0 +1,119 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||
|
||||
variable rng string gaussian
|
||||
variable seed string 198098
|
||||
variable temp string 5.0
|
||||
variable gamma_t string 1.0
|
||||
variable params string ${rng}_${temp}_${gamma_t}
|
||||
variable params string gaussian_${temp}_${gamma_t}
|
||||
variable params string gaussian_5.0_${gamma_t}
|
||||
variable params string gaussian_5.0_1.0
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass * 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.672 | 2.672 | 2.672 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 1.4996338 0 0 0 0 0
|
||||
100 1515328.2 0 0.010465453 0.010044629 0.0097242319 0.030234314
|
||||
200 1510820.8 0 0.020658886 0.019954762 0.020008864 0.060622512
|
||||
300 1482006.5 0 0.030402195 0.029802874 0.030047586 0.090252655
|
||||
400 1492228.5 0 0.039622543 0.038899144 0.040381854 0.11890354
|
||||
500 1494985.5 0 0.050523465 0.050022913 0.050186478 0.15073286
|
||||
600 1516047.4 0 0.061111845 0.061433818 0.059195364 0.18174103
|
||||
700 1510021.8 0 0.071636778 0.072829755 0.06946406 0.21393059
|
||||
800 1505964.7 0 0.08240965 0.08433785 0.078799851 0.24554735
|
||||
900 1491035.9 0 0.093659937 0.094517749 0.08812559 0.27630328
|
||||
1000 1516599.6 0 0.10436496 0.10431759 0.097480868 0.30616342
|
||||
1100 1495170.3 0 0.11468757 0.111397 0.1069763 0.33306087
|
||||
1200 1500630.6 0 0.12360977 0.12264534 0.11583999 0.3620951
|
||||
1300 1474889.5 0 0.13432447 0.13471694 0.12702491 0.39606632
|
||||
1400 1487145.8 0 0.14573239 0.14431493 0.13669403 0.42674135
|
||||
1500 1519496.7 0 0.15610742 0.15505416 0.14600182 0.4571634
|
||||
1600 1525674.1 0 0.16728653 0.1649354 0.15562133 0.48784325
|
||||
1700 1540725.4 0 0.17846447 0.17666562 0.16531781 0.52044791
|
||||
1800 1512334.8 0 0.18872753 0.18538847 0.17450009 0.54861609
|
||||
1900 1498371.4 0 0.19688928 0.19333299 0.18581712 0.5760394
|
||||
2000 1546459.4 0 0.20955053 0.20243854 0.19613897 0.60812803
|
||||
2100 1509712.9 0 0.21922567 0.20940597 0.20567239 0.63430404
|
||||
2200 1509630.4 0 0.23067999 0.21856734 0.21619911 0.66544645
|
||||
2300 1483929.1 0 0.24160803 0.231048 0.22617193 0.69882797
|
||||
2400 1488492.1 0 0.25399491 0.24082678 0.23972356 0.73454526
|
||||
2500 1508107.9 0 0.26608734 0.25316913 0.2486814 0.76793787
|
||||
2600 1511952.1 0 0.27523956 0.2623673 0.25706539 0.79467225
|
||||
2700 1488888.8 0 0.28518299 0.27425585 0.26728622 0.82672506
|
||||
2800 1515428.4 0 0.29595429 0.28589969 0.27781327 0.85966725
|
||||
2900 1504312.1 0 0.30393798 0.29533034 0.28725362 0.88652194
|
||||
3000 1521521.3 0 0.31445132 0.30117607 0.29959324 0.91522062
|
||||
Loop time of 0.708196 on 4 procs for 3000 steps with 4096 atoms
|
||||
|
||||
Performance: 3660.004 tau/day, 4236.115 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.00020647 | 0.00021023 | 0.0002141 | 0.0 | 0.03
|
||||
Comm | 0.0045607 | 0.0050649 | 0.0053098 | 0.4 | 0.72
|
||||
Output | 0.0013759 | 0.002265 | 0.0037355 | 1.9 | 0.32
|
||||
Modify | 0.57353 | 0.58931 | 0.6109 | 1.8 | 83.21
|
||||
Other | | 0.1113 | | | 15.72
|
||||
|
||||
Nlocal: 1024.00 ave 1043 max 1001 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
45
examples/USER/brownian/sphere/in2d.sphere
Normal file
45
examples/USER/brownian/sphere/in2d.sphere
Normal file
@ -0,0 +1,45 @@
|
||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_t string 5.0
|
||||
variable gamma_r string 0.7
|
||||
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||
# x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
45
examples/USER/brownian/sphere/in3d.sphere
Normal file
45
examples/USER/brownian/sphere/in3d.sphere
Normal file
@ -0,0 +1,45 @@
|
||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_t string 5.0
|
||||
variable gamma_r string 0.7
|
||||
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||
# x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1
Normal file
@ -0,0 +1,126 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_t string 5.0
|
||||
variable gamma_r string 0.7
|
||||
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_5.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.005 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
3600 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 0.99972222 0 0 0 0 0
|
||||
100 20867.136 0 0.00040006704 0.00039570887 0 0.00079577592
|
||||
200 20835.491 0 0.00077560901 0.00080455484 0 0.0015801638
|
||||
300 20813.122 0 0.0011737739 0.0012172689 0 0.0023910428
|
||||
400 21137.397 0 0.0015587675 0.0016096093 0 0.0031683768
|
||||
500 21167.188 0 0.0019294105 0.0020251322 0 0.0039545428
|
||||
600 21345.908 0 0.0023105313 0.0024111742 0 0.0047217054
|
||||
700 21086.272 0 0.0027236116 0.0027846006 0 0.0055082122
|
||||
800 20840.906 0 0.0031505299 0.0031810732 0 0.0063316031
|
||||
900 20916.456 0 0.0035525852 0.0035981301 0 0.0071507153
|
||||
1000 20752.249 0 0.0039147929 0.0039791172 0 0.0078939101
|
||||
1100 20643.612 0 0.0042977921 0.0043701484 0 0.0086679405
|
||||
1200 21085.63 0 0.0045584242 0.0047475091 0 0.0093059332
|
||||
1300 20900.794 0 0.0049718803 0.0051481706 0 0.010120051
|
||||
1400 20980.731 0 0.0054234603 0.0054230724 0 0.010846533
|
||||
1500 20916.308 0 0.0058502946 0.0058114313 0 0.011661726
|
||||
1600 20949.786 0 0.0062258463 0.006208129 0 0.012433975
|
||||
1700 20531.205 0 0.0066276219 0.006595921 0 0.013223543
|
||||
1800 21418.472 0 0.0070077409 0.007030461 0 0.014038202
|
||||
1900 21291.928 0 0.0074052208 0.0074333041 0 0.014838525
|
||||
2000 20893.895 0 0.0077407477 0.007901402 0 0.01564215
|
||||
2100 21218.001 0 0.0080384756 0.0082611258 0 0.016299601
|
||||
2200 21116.189 0 0.0084325164 0.008617977 0 0.017050493
|
||||
2300 20718.83 0 0.0089455345 0.0091768161 0 0.018122351
|
||||
2400 20719.164 0 0.0093666455 0.0095272546 0 0.0188939
|
||||
2500 20991.382 0 0.009706795 0.0098256506 0 0.019532446
|
||||
2600 20515.74 0 0.0099247069 0.010329841 0 0.020254548
|
||||
2700 21001.55 0 0.010448354 0.010693502 0 0.021141855
|
||||
2800 21363.824 0 0.010990971 0.011142092 0 0.022133063
|
||||
2900 20497.025 0 0.011399704 0.011504868 0 0.022904573
|
||||
3000 20726.572 0 0.011785354 0.01187482 0 0.023660175
|
||||
Loop time of 1.76023 on 1 procs for 3000 steps with 3600 atoms
|
||||
|
||||
Performance: 1472.538 tau/day, 1704.326 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.026518 | 0.026518 | 0.026518 | 0.0 | 1.51
|
||||
Output | 0.0040107 | 0.0040107 | 0.0040107 | 0.0 | 0.23
|
||||
Modify | 1.6194 | 1.6194 | 1.6194 | 0.0 | 92.00
|
||||
Other | | 0.1103 | | | 6.27
|
||||
|
||||
Nlocal: 3600.00 ave 3600 max 3600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 121.000 ave 121 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4
Normal file
@ -0,0 +1,126 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_t string 5.0
|
||||
variable gamma_r string 0.7
|
||||
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_5.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -30 30 -30 30 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
3600 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 0.99972222 0 0 0 0 0
|
||||
100 21085.797 0 0.00042014118 0.00040399828 0 0.00082413946
|
||||
200 20598.717 0 0.00081715618 0.00082613236 0 0.0016432885
|
||||
300 21040.226 0 0.0012412527 0.0012520475 0 0.0024933002
|
||||
400 21289.734 0 0.0016129899 0.001634482 0 0.003247472
|
||||
500 20951.595 0 0.0020104279 0.0020197694 0 0.0040301973
|
||||
600 20984.974 0 0.0023965593 0.0024277086 0 0.0048242679
|
||||
700 21252.602 0 0.0028349303 0.0028407812 0 0.0056757114
|
||||
800 20951.95 0 0.0032674595 0.0032573476 0 0.0065248071
|
||||
900 20828.611 0 0.003647953 0.0036650963 0 0.0073130493
|
||||
1000 21073.256 0 0.0040238604 0.0040103537 0 0.0080342142
|
||||
1100 21104.396 0 0.0043694059 0.0044146515 0 0.0087840574
|
||||
1200 20580.591 0 0.0047638237 0.0047646659 0 0.0095284896
|
||||
1300 20667.623 0 0.0051512568 0.0051134445 0 0.010264701
|
||||
1400 20466.72 0 0.0055921578 0.005517863 0 0.011110021
|
||||
1500 20842.366 0 0.0059747304 0.0059374031 0 0.011912134
|
||||
1600 20867.02 0 0.0065493697 0.0064163066 0 0.012965676
|
||||
1700 21021.077 0 0.0070208005 0.0068164842 0 0.013837285
|
||||
1800 21191.183 0 0.0073708939 0.0073226521 0 0.014693546
|
||||
1900 20792.8 0 0.0076984189 0.0077400043 0 0.015438423
|
||||
2000 21296.326 0 0.0081882545 0.0081503672 0 0.016338622
|
||||
2100 21085.097 0 0.008596146 0.0086041272 0 0.017200273
|
||||
2200 20506.523 0 0.0089905439 0.0091045462 0 0.01809509
|
||||
2300 21068.555 0 0.0094163509 0.0094703314 0 0.018886682
|
||||
2400 21128.867 0 0.0097349212 0.0098535832 0 0.019588504
|
||||
2500 21009.514 0 0.010218059 0.010244621 0 0.020462679
|
||||
2600 21177.52 0 0.01060437 0.010642719 0 0.021247089
|
||||
2700 20832.56 0 0.011052623 0.011078899 0 0.022131522
|
||||
2800 21298.053 0 0.011439708 0.011587702 0 0.023027411
|
||||
2900 21002.28 0 0.011863624 0.01199682 0 0.023860443
|
||||
3000 20737.939 0 0.012229608 0.012324579 0 0.024554186
|
||||
Loop time of 0.492798 on 4 procs for 3000 steps with 3600 atoms
|
||||
|
||||
Performance: 5259.763 tau/day, 6087.689 timesteps/s
|
||||
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.018005 | 0.021524 | 0.025207 | 2.2 | 4.37
|
||||
Output | 0.0013187 | 0.0018334 | 0.0032332 | 1.9 | 0.37
|
||||
Modify | 0.37545 | 0.38775 | 0.40664 | 1.9 | 78.68
|
||||
Other | | 0.08169 | | | 16.58
|
||||
|
||||
Nlocal: 900.000 ave 900 max 900 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 61.0000 ave 61 max 61 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1
Normal file
@ -0,0 +1,126 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_t string 5.0
|
||||
variable gamma_r string 0.7
|
||||
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_5.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.005 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 1.4996338 0 0 0 0 0
|
||||
100 32032.279 0 0.00040227568 0.00039159837 0.00040147813 0.0011953522
|
||||
200 31673.093 0 0.00077657885 0.00077292327 0.00079963705 0.0023491392
|
||||
300 31476.164 0 0.0011712083 0.0011606723 0.0012089537 0.0035408343
|
||||
400 31911.374 0 0.0015803424 0.001562091 0.0016042321 0.0047466655
|
||||
500 31182.011 0 0.0019677217 0.0019269105 0.0020015977 0.0058962298
|
||||
600 31206.05 0 0.0023360975 0.0023134398 0.0024213372 0.0070708745
|
||||
700 31278.057 0 0.0026966955 0.0027129858 0.0028721373 0.0082818187
|
||||
800 31677.724 0 0.0031197964 0.003134834 0.0032726303 0.0095272607
|
||||
900 31312.741 0 0.0035636612 0.0035573653 0.0037328373 0.010853864
|
||||
1000 31426.075 0 0.0039774626 0.003952159 0.0041879386 0.01211756
|
||||
1100 31361.699 0 0.0044256852 0.004320566 0.004638132 0.013384383
|
||||
1200 31559.778 0 0.0048338539 0.0047210601 0.0050296056 0.01458452
|
||||
1300 31716.797 0 0.0052239651 0.0050796723 0.0054794684 0.015783106
|
||||
1400 31231.077 0 0.0055890568 0.005472377 0.0059264123 0.016987846
|
||||
1500 31605.513 0 0.0059876582 0.0058974054 0.0063452478 0.018230311
|
||||
1600 31551.402 0 0.006413094 0.0062665632 0.0067442106 0.019423868
|
||||
1700 31725.868 0 0.0068244611 0.0067189707 0.0071424779 0.02068591
|
||||
1800 31385.794 0 0.0071570297 0.0070502303 0.0075240296 0.02173129
|
||||
1900 31754.094 0 0.0075638662 0.0074243015 0.0079935325 0.0229817
|
||||
2000 31668.959 0 0.0080059944 0.0079019753 0.0084000614 0.024308031
|
||||
2100 31781.994 0 0.0084108141 0.0082719077 0.0088004977 0.02548322
|
||||
2200 31455.021 0 0.0088844434 0.0086931769 0.0091916929 0.026769313
|
||||
2300 31273.079 0 0.0093155639 0.0091027782 0.0095364621 0.027954804
|
||||
2400 31283.781 0 0.0098441686 0.0094496218 0.0099279073 0.029221698
|
||||
2500 31758.315 0 0.010372129 0.0097843406 0.010334653 0.030491123
|
||||
2600 31780.442 0 0.010770862 0.010313119 0.010637545 0.031721525
|
||||
2700 31552.277 0 0.011268703 0.010693437 0.01110762 0.033069759
|
||||
2800 31124.693 0 0.011661333 0.011100115 0.011480624 0.034242072
|
||||
2900 31438.795 0 0.012068847 0.011346633 0.011842006 0.035257486
|
||||
3000 31574.258 0 0.012482632 0.011691477 0.012210207 0.036384317
|
||||
Loop time of 2.8531 on 1 procs for 3000 steps with 4096 atoms
|
||||
|
||||
Performance: 908.486 tau/day, 1051.488 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.2425e-05 | 3.2425e-05 | 3.2425e-05 | 0.0 | 0.00
|
||||
Comm | 0.13219 | 0.13219 | 0.13219 | 0.0 | 4.63
|
||||
Output | 0.0045686 | 0.0045686 | 0.0045686 | 0.0 | 0.16
|
||||
Modify | 2.5857 | 2.5857 | 2.5857 | 0.0 | 90.63
|
||||
Other | | 0.1307 | | | 4.58
|
||||
|
||||
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4
Normal file
@ -0,0 +1,126 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||
|
||||
variable rng string uniform
|
||||
variable seed string 198098
|
||||
variable temp string 1.0
|
||||
variable gamma_t string 5.0
|
||||
variable gamma_r string 0.7
|
||||
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_${gamma_t}
|
||||
variable params string uniform_1.0_0.7_5.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.006 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 198098 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
pair_style none
|
||||
|
||||
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||
|
||||
#initialisation for the main run
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*]
|
||||
|
||||
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
timestep 0.00001
|
||||
thermo 100
|
||||
|
||||
# main run
|
||||
run 3000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||
0 1.4996338 0 0 0 0 0
|
||||
100 30882.707 0 0.00040787161 0.00039391576 0.00040796913 0.0012097565
|
||||
200 31370.751 0 0.00081742036 0.00078240455 0.0008195167 0.0024193416
|
||||
300 31469.51 0 0.0012118299 0.0011819412 0.0012477119 0.003641483
|
||||
400 31696.58 0 0.0015540547 0.0015849689 0.0015836091 0.0047226327
|
||||
500 31488.269 0 0.0019638041 0.0019659637 0.0020547832 0.005984551
|
||||
600 30942.589 0 0.0023273784 0.0023572171 0.0024715245 0.00715612
|
||||
700 31228.473 0 0.0027821732 0.002735338 0.0028734675 0.0083909787
|
||||
800 31426.92 0 0.0031663838 0.0031092782 0.0033231014 0.0095987634
|
||||
900 31447.595 0 0.003539588 0.003564381 0.003753036 0.010857005
|
||||
1000 31363.911 0 0.0039854308 0.003937555 0.0041203919 0.012043378
|
||||
1100 31522.958 0 0.0043009285 0.0043676491 0.0044799414 0.013148519
|
||||
1200 31403.033 0 0.0046361199 0.0047513598 0.0049014974 0.014288977
|
||||
1300 31752.182 0 0.0049824718 0.0051327113 0.0053130614 0.015428244
|
||||
1400 31336.955 0 0.0054251445 0.0055442325 0.0057472998 0.016716677
|
||||
1500 31224.306 0 0.0059295596 0.0059920697 0.0061375228 0.018059152
|
||||
1600 31744.535 0 0.0063845142 0.0063600989 0.0064833215 0.019227935
|
||||
1700 31472.081 0 0.0068360092 0.0067985824 0.0069464303 0.020581022
|
||||
1800 31577.334 0 0.0073001079 0.0071355564 0.0073400543 0.021775719
|
||||
1900 31521.234 0 0.0077178677 0.0074371106 0.007708008 0.022862986
|
||||
2000 31045.148 0 0.0080515968 0.0078583776 0.0081000219 0.024009996
|
||||
2100 31289.809 0 0.0084280175 0.0082322226 0.0084475904 0.02510783
|
||||
2200 31505.455 0 0.008802925 0.0085708943 0.0087648194 0.026138639
|
||||
2300 31882.722 0 0.0092223105 0.0089242925 0.0092643028 0.027410906
|
||||
2400 31028.15 0 0.0095737559 0.0093585981 0.0096771837 0.028609538
|
||||
2500 31581.041 0 0.0099316284 0.009785264 0.010100235 0.029817127
|
||||
2600 31272.119 0 0.010332986 0.01007291 0.010474606 0.030880502
|
||||
2700 31537.8 0 0.010751592 0.010565273 0.01093107 0.032247935
|
||||
2800 31060.697 0 0.011156729 0.011010751 0.011260025 0.033427506
|
||||
2900 31541.612 0 0.011542003 0.011499419 0.011642873 0.034684295
|
||||
3000 31305.382 0 0.011876832 0.011866445 0.012052577 0.035795854
|
||||
Loop time of 1.00142 on 4 procs for 3000 steps with 4096 atoms
|
||||
|
||||
Performance: 2588.329 tau/day, 2995.751 timesteps/s
|
||||
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.084416 | 0.10685 | 0.12695 | 5.7 | 10.67
|
||||
Output | 0.001471 | 0.0019466 | 0.0033245 | 1.8 | 0.19
|
||||
Modify | 0.66585 | 0.70645 | 0.78995 | 6.0 | 70.54
|
||||
Other | | 0.1862 | | | 18.59
|
||||
|
||||
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 353.000 ave 353 max 353 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
60
examples/USER/brownian/spherical_ABP/in2d.abp
Normal file
60
examples/USER/brownian/spherical_ABP/in2d.abp
Normal file
@ -0,0 +1,60 @@
|
||||
# 2D overdamped active brownian particle dynamics (ABP)
|
||||
# with WCA potential
|
||||
|
||||
variable gamma_t string 1.0
|
||||
variable gamma_r string 1.0
|
||||
variable temp string 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp string 4.0
|
||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
region box block -16 16 -16 16 -0.2 0.2
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
# more careful with neighbors since higher diffusion in abps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
# WCA potential (purely repulsive)
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.1224
|
||||
pair_modify shift yes
|
||||
|
||||
# overdamped brownian dynamics time-step
|
||||
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
# self-propulsion force along the dipole direction
|
||||
fix activity all propel/self dipole ${fp}
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step pe ke c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 100
|
||||
run 5000
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step temp epair c_msd[*] c_press
|
||||
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 20000
|
||||
67
examples/USER/brownian/spherical_ABP/in3d.ideal_abp
Normal file
67
examples/USER/brownian/spherical_ABP/in3d.ideal_abp
Normal file
@ -0,0 +1,67 @@
|
||||
# 3D overdamped active brownian dynamics with no interactions
|
||||
|
||||
variable gamma_t string 3.0
|
||||
variable gamma_r string 1.0
|
||||
variable temp string 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp string 4.0
|
||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
pair_style none
|
||||
|
||||
# overdamped brownian dynamics time-step
|
||||
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
# self-propulsion force along the dipole direction
|
||||
fix activity all propel/self dipole ${fp}
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step ke pe c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 100
|
||||
run 5000
|
||||
reset_timestep 0
|
||||
|
||||
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||
# brownian motion, which is
|
||||
#
|
||||
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
|
||||
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
|
||||
#
|
||||
# with d being simulation dimension
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*] c_press
|
||||
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 12000
|
||||
|
||||
# if you want to check that rotational diffusion is behaving as expected,
|
||||
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||
# which should decay exponentially with timescale (d-1)*D_r (with d
|
||||
# being simulation dimension)
|
||||
|
||||
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type &
|
||||
# x y xu yu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
#run 120000
|
||||
@ -0,0 +1,221 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2D overdamped active brownian particle dynamics (ABP)
|
||||
# with WCA potential
|
||||
|
||||
variable gamma_t string 1.0
|
||||
variable gamma_r string 1.0
|
||||
variable temp string 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp string 4.0
|
||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_1.0_${gamma_r}_${fp}
|
||||
variable params string 1.0_1.0_1.0_${fp}
|
||||
variable params string 1.0_1.0_1.0_4.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -16 16 -16 16 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 1024 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 1974019 1.0
|
||||
Setting atom values ...
|
||||
1024 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
# more careful with neighbors since higher diffusion in abps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
# WCA potential (purely repulsive)
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.1224
|
||||
pair_modify shift yes
|
||||
|
||||
# overdamped brownian dynamics time-step
|
||||
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
|
||||
# self-propulsion force along the dipole direction
|
||||
fix activity all propel/self dipole ${fp}
|
||||
fix activity all propel/self dipole 4.0
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step pe ke c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 100
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.1224
|
||||
ghost atom cutoff = 2.1224
|
||||
binsize = 1.0612, bins = 48 48 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/2d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes
|
||||
Step PotEng KinEng c_press
|
||||
0 0 0.99902344 -0.53979198
|
||||
100 0 1.026585e+10 -0.5398101
|
||||
200 0 1.0630628e+10 -0.53977393
|
||||
300 0 1.03483e+10 -0.53977041
|
||||
400 0 1.049279e+10 -0.53974314
|
||||
500 0 1.0832067e+10 -0.53979451
|
||||
600 0 1.0403632e+10 -0.53976233
|
||||
700 0 1.0334726e+10 -0.53976174
|
||||
800 0 1.0119596e+10 -0.53969338
|
||||
900 0 1.0786136e+10 -0.53970415
|
||||
1000 0 1.0539036e+10 -0.53974577
|
||||
1100 0 1.0643695e+10 -0.53982431
|
||||
1200 0 1.0234642e+10 -0.53976823
|
||||
1300 0 1.036268e+10 -0.53981454
|
||||
1400 0 1.0605702e+10 -0.53988117
|
||||
1500 0 1.0517916e+10 -0.53989207
|
||||
1600 0 1.0564482e+10 -0.53993016
|
||||
1700 0 1.0460152e+10 -0.53984454
|
||||
1800 0 1.0468566e+10 -0.53985574
|
||||
1900 0 1.0474075e+10 -0.53985439
|
||||
2000 0 1.0683568e+10 -0.53987349
|
||||
2100 0 1.0269077e+10 -0.53990709
|
||||
2200 0 1.0386943e+10 -0.53990068
|
||||
2300 0 1.0406078e+10 -0.53978402
|
||||
2400 0 1.0482072e+10 -0.53980757
|
||||
2500 0 1.0442975e+10 -0.53982657
|
||||
2600 0 1.0292103e+10 -0.53985533
|
||||
2700 0 1.1106453e+10 -0.53991861
|
||||
2800 0 1.0395289e+10 -0.53990138
|
||||
2900 0 1.034021e+10 -0.53992375
|
||||
3000 0 1.0434718e+10 -0.53995566
|
||||
3100 0 1.0194094e+10 -0.53993997
|
||||
3200 0 1.0411552e+10 -0.54000097
|
||||
3300 0 1.0214175e+10 -0.53999884
|
||||
3400 0 1.0434719e+10 -0.54000005
|
||||
3500 0 1.0529638e+10 -0.53998281
|
||||
3600 0 1.0406541e+10 -0.54000141
|
||||
3700 0 1.0577151e+10 -0.54002354
|
||||
3800 0 1.0488249e+10 -0.53996003
|
||||
3900 0 1.0316153e+10 -0.54002024
|
||||
4000 0 1.0491289e+10 -0.5400259
|
||||
4100 0 1.0587981e+10 -0.5399811
|
||||
4200 0 1.0332035e+10 -0.53997951
|
||||
4300 0 1.0776469e+10 -0.53994151
|
||||
4400 0 1.0982142e+10 -0.53983842
|
||||
4500 0 1.0796919e+10 -0.5398414
|
||||
4600 0 1.0324249e+10 -0.53979712
|
||||
4700 0 1.0420899e+10 -0.53981967
|
||||
4800 0 1.0274188e+10 -0.53976759
|
||||
4900 0 1.0411535e+10 -0.5397757
|
||||
5000 0 1.0399215e+10 -0.53980199
|
||||
Loop time of 1.34285 on 1 procs for 5000 steps with 1024 atoms
|
||||
|
||||
Performance: 0.032 tau/day, 3723.422 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.25309 | 0.25309 | 0.25309 | 0.0 | 18.85
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.068734 | 0.068734 | 0.068734 | 0.0 | 5.12
|
||||
Output | 0.0012887 | 0.0012887 | 0.0012887 | 0.0 | 0.10
|
||||
Modify | 0.96552 | 0.96552 | 0.96552 | 0.0 | 71.90
|
||||
Other | | 0.05422 | | | 4.04
|
||||
|
||||
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 201.000 ave 201 max 201 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2112.00 ave 2112 max 2112 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2112
|
||||
Ave neighs/atom = 2.0625000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step temp epair c_msd[*] c_press
|
||||
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 20000
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes
|
||||
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||
0 1.0409381e+10 0 0 0 0 0 -0.53980199
|
||||
1000 107022.73 0.0080050427 0.020451432 0.021388798 0 0.04184023 -0.54900967
|
||||
2000 107475.82 0.017262846 0.040669645 0.044251149 0 0.084920794 -0.42740968
|
||||
3000 105388.35 0.042257875 0.062828995 0.05845782 0 0.12128682 -0.31792184
|
||||
4000 106238.38 0.052733384 0.079036841 0.079396453 0 0.15843329 -0.24243699
|
||||
5000 102904.54 0.088524456 0.095977642 0.099533961 0 0.1955116 -0.093468615
|
||||
6000 105274.15 0.065334999 0.11591691 0.11675531 0 0.23267222 -0.21904478
|
||||
7000 108903.41 0.06724271 0.13694218 0.13914947 0 0.27609164 -0.15913012
|
||||
8000 101451.44 0.097201152 0.15704893 0.16178845 0 0.31883738 -0.055786965
|
||||
9000 106808.72 0.084301668 0.18029391 0.175753 0 0.3560469 0.014898739
|
||||
10000 107381.19 0.088583354 0.2000753 0.19569789 0 0.39577319 0.19417596
|
||||
11000 102105.78 0.081066654 0.22042599 0.21914042 0 0.43956641 0.060574143
|
||||
12000 105384.94 0.098716908 0.24382064 0.24673594 0 0.49055657 0.17067875
|
||||
13000 107479.53 0.099989043 0.26942088 0.27207566 0 0.54149654 0.25514896
|
||||
14000 102938.12 0.093252916 0.28529564 0.28698837 0 0.57228401 0.19976355
|
||||
15000 104408.02 0.11900926 0.31291315 0.31195058 0 0.62486373 0.36956014
|
||||
16000 103447.68 0.09627777 0.34145225 0.33159885 0 0.6730511 0.29857404
|
||||
17000 108400.05 0.11433561 0.36561966 0.36068301 0 0.72630267 0.41922801
|
||||
18000 103363.68 0.11040153 0.38709746 0.39228677 0 0.77938423 0.38111686
|
||||
19000 103310.43 0.10660536 0.41406235 0.40975085 0 0.8238132 0.36022184
|
||||
20000 102692.1 0.13517651 0.43870812 0.44138776 0 0.88009588 0.51144366
|
||||
Loop time of 5.66207 on 1 procs for 20000 steps with 1024 atoms
|
||||
|
||||
Performance: 3051.889 tau/day, 3532.279 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.3123 | 1.3123 | 1.3123 | 0.0 | 23.18
|
||||
Neigh | 0.011856 | 0.011856 | 0.011856 | 0.0 | 0.21
|
||||
Comm | 0.2747 | 0.2747 | 0.2747 | 0.0 | 4.85
|
||||
Output | 0.0011516 | 0.0011516 | 0.0011516 | 0.0 | 0.02
|
||||
Modify | 3.8451 | 3.8451 | 3.8451 | 0.0 | 67.91
|
||||
Other | | 0.2169 | | | 3.83
|
||||
|
||||
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 184.000 ave 184 max 184 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2558.00 ave 2558 max 2558 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2558
|
||||
Ave neighs/atom = 2.4980469
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -0,0 +1,221 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2D overdamped active brownian particle dynamics (ABP)
|
||||
# with WCA potential
|
||||
|
||||
variable gamma_t string 1.0
|
||||
variable gamma_r string 1.0
|
||||
variable temp string 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp string 4.0
|
||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_1.0_${gamma_r}_${fp}
|
||||
variable params string 1.0_1.0_1.0_${fp}
|
||||
variable params string 1.0_1.0_1.0_4.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 2
|
||||
newton off
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||
region box block -16 16 -16 16 -0.2 0.2
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 1024 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 1974019 1.0
|
||||
Setting atom values ...
|
||||
1024 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
# more careful with neighbors since higher diffusion in abps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
# WCA potential (purely repulsive)
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.1224
|
||||
pair_modify shift yes
|
||||
|
||||
# overdamped brownian dynamics time-step
|
||||
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
|
||||
# self-propulsion force along the dipole direction
|
||||
fix activity all propel/self dipole ${fp}
|
||||
fix activity all propel/self dipole 4.0
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step pe ke c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 100
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.1224
|
||||
ghost atom cutoff = 2.1224
|
||||
binsize = 1.0612, bins = 48 48 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/2d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes
|
||||
Step PotEng KinEng c_press
|
||||
0 0 0.99902344 -0.53979198
|
||||
100 0 1.0503521e+10 -0.53983092
|
||||
200 0 1.0390343e+10 -0.5398287
|
||||
300 0 1.0493441e+10 -0.53979247
|
||||
400 0 1.0545991e+10 -0.53978678
|
||||
500 0 1.0266398e+10 -0.53986297
|
||||
600 0 1.0484775e+10 -0.53978746
|
||||
700 0 1.0583596e+10 -0.53969114
|
||||
800 0 1.0521919e+10 -0.53968754
|
||||
900 0 1.0492019e+10 -0.53958643
|
||||
1000 0 1.0298052e+10 -0.53949872
|
||||
1100 0 1.0531424e+10 -0.53955431
|
||||
1200 0 1.0635635e+10 -0.53960048
|
||||
1300 0 1.0633405e+10 -0.53966331
|
||||
1400 0 1.0195401e+10 -0.53968849
|
||||
1500 0 1.0593758e+10 -0.53969763
|
||||
1600 0 1.0425238e+10 -0.53971936
|
||||
1700 0 1.0470017e+10 -0.53981957
|
||||
1800 0 1.0545953e+10 -0.53987747
|
||||
1900 0 1.0425015e+10 -0.53990412
|
||||
2000 0 1.0655092e+10 -0.5399511
|
||||
2100 0 1.0197224e+10 -0.53988687
|
||||
2200 0 1.0448012e+10 -0.53986066
|
||||
2300 0 1.0355268e+10 -0.53980415
|
||||
2400 0 1.0246979e+10 -0.53979737
|
||||
2500 0 1.0021539e+10 -0.5397919
|
||||
2600 0 1.0200824e+10 -0.5397575
|
||||
2700 0 1.0721591e+10 -0.53973512
|
||||
2800 0 1.0354562e+10 -0.5397127
|
||||
2900 0 1.0306795e+10 -0.5396946
|
||||
3000 0 1.0301339e+10 -0.53968642
|
||||
3100 0 1.0435826e+10 -0.53970945
|
||||
3200 0 1.019524e+10 -0.53969746
|
||||
3300 0 1.0550481e+10 -0.53967977
|
||||
3400 0 1.0283446e+10 -0.53971102
|
||||
3500 0 1.0956695e+10 -0.53976173
|
||||
3600 0 1.0271033e+10 -0.53983632
|
||||
3700 0 1.0389461e+10 -0.53977293
|
||||
3800 0 1.0680515e+10 -0.53977425
|
||||
3900 0 1.0072183e+10 -0.53982922
|
||||
4000 0 1.0458036e+10 -0.53980042
|
||||
4100 0 1.0588689e+10 -0.53971405
|
||||
4200 0 1.0068308e+10 -0.5398033
|
||||
4300 0 1.0502064e+10 -0.53981291
|
||||
4400 0 1.0590544e+10 -0.5398346
|
||||
4500 0 1.0411612e+10 -0.5397916
|
||||
4600 0 1.0518596e+10 -0.53984868
|
||||
4700 0 1.0386105e+10 -0.53977803
|
||||
4800 0 1.029525e+10 -0.53970882
|
||||
4900 0 1.0519112e+10 -0.53969616
|
||||
5000 0 1.0335841e+10 -0.53976477
|
||||
Loop time of 0.471663 on 4 procs for 5000 steps with 1024 atoms
|
||||
|
||||
Performance: 0.092 tau/day, 10600.781 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.067099 | 0.07105 | 0.077898 | 1.6 | 15.06
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0581 | 0.066084 | 0.072322 | 2.0 | 14.01
|
||||
Output | 0.0014644 | 0.002618 | 0.0037239 | 1.6 | 0.56
|
||||
Modify | 0.24817 | 0.25719 | 0.26697 | 1.3 | 54.53
|
||||
Other | | 0.07472 | | | 15.84
|
||||
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 105.000 ave 105 max 105 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 544.000 ave 544 max 544 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2176
|
||||
Ave neighs/atom = 2.1250000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
# MSD
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step temp epair c_msd[*] c_press
|
||||
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 20000
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes
|
||||
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||
0 1.0345945e+10 0 0 0 0 0 -0.53976477
|
||||
1000 100114.28 0.0029703577 0.020320684 0.020950989 0 0.041271673 -0.43948247
|
||||
2000 106825.83 0.020969054 0.039616412 0.039459167 0 0.079075578 -0.22765541
|
||||
3000 105287.4 0.037343571 0.056828177 0.058639835 0 0.11546801 -0.11728136
|
||||
4000 104522.23 0.052237136 0.080264931 0.080863543 0 0.16112847 0.033230576
|
||||
5000 103277.94 0.053791862 0.099188864 0.10141444 0 0.20060331 0.073591503
|
||||
6000 104252.87 0.073304776 0.11964238 0.1215576 0 0.24119999 0.22062305
|
||||
7000 105184.19 0.089054043 0.13691291 0.14216478 0 0.27907769 0.29015692
|
||||
8000 104211.82 0.072577918 0.15820522 0.15658491 0 0.31479013 0.25908291
|
||||
9000 99242.172 0.071616004 0.17658708 0.17479704 0 0.35138412 0.26305532
|
||||
10000 105070.83 0.077009979 0.20175025 0.19871513 0 0.40046538 0.34120567
|
||||
11000 106421.07 0.098623061 0.22472634 0.22671582 0 0.45144216 0.44021335
|
||||
12000 103209.85 0.12032847 0.25004966 0.25368441 0 0.50373406 0.57344873
|
||||
13000 107156.89 0.1058386 0.27283231 0.2744873 0 0.54731961 0.47957408
|
||||
14000 108119.3 0.1204768 0.29333677 0.30054535 0 0.59388213 0.51832639
|
||||
15000 105477.62 0.12510026 0.32217621 0.32806599 0 0.6502422 0.50174158
|
||||
16000 106676.27 0.10893618 0.34980866 0.36031184 0 0.7101205 0.44769198
|
||||
17000 103048.41 0.10625673 0.3781797 0.37970499 0 0.75788468 0.42803898
|
||||
18000 109454.8 0.10555778 0.40997694 0.41396777 0 0.82394471 0.41380982
|
||||
19000 107459.73 0.11267582 0.43757738 0.43577856 0 0.87335594 0.4917748
|
||||
20000 101991.9 0.084279008 0.45363612 0.46278076 0 0.91641688 0.41707912
|
||||
Loop time of 1.80877 on 4 procs for 20000 steps with 1024 atoms
|
||||
|
||||
Performance: 9553.439 tau/day, 11057.221 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.34461 | 0.36424 | 0.40948 | 4.4 | 20.14
|
||||
Neigh | 0.0031493 | 0.003215 | 0.0032432 | 0.1 | 0.18
|
||||
Comm | 0.19538 | 0.20419 | 0.2104 | 1.2 | 11.29
|
||||
Output | 0.00054121 | 0.00087297 | 0.0018425 | 0.0 | 0.05
|
||||
Modify | 0.98335 | 1.0156 | 1.0791 | 3.8 | 56.15
|
||||
Other | | 0.2207 | | | 12.20
|
||||
|
||||
Nlocal: 256.000 ave 261 max 252 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 93.0000 ave 100 max 83 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 662.250 ave 693 max 635 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2649
|
||||
Ave neighs/atom = 2.5869141
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -0,0 +1,210 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3D overdamped active brownian dynamics with no interactions
|
||||
|
||||
variable gamma_t string 3.0
|
||||
variable gamma_r string 1.0
|
||||
variable temp string 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp string 4.0
|
||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_3.0_${gamma_r}_${fp}
|
||||
variable params string 1.0_3.0_1.0_${fp}
|
||||
variable params string 1.0_3.0_1.0_4.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.004 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 1974019 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
pair_style none
|
||||
|
||||
# overdamped brownian dynamics time-step
|
||||
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
|
||||
# self-propulsion force along the dipole direction
|
||||
fix activity all propel/self dipole ${fp}
|
||||
fix activity all propel/self dipole 4.0
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step ke pe c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 100
|
||||
run 5000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes
|
||||
Step KinEng PotEng c_press
|
||||
0 1.4996338 0 0.068021726
|
||||
100 5.184227e+09 0 0.06801544
|
||||
200 5.2165482e+09 0 0.068010729
|
||||
300 5.2782092e+09 0 0.068009058
|
||||
400 5.3244927e+09 0 0.068003481
|
||||
500 5.2376606e+09 0 0.067998237
|
||||
600 5.2735634e+09 0 0.067998037
|
||||
700 5.2692439e+09 0 0.068025402
|
||||
800 5.2667984e+09 0 0.068030143
|
||||
900 5.242057e+09 0 0.0680246
|
||||
1000 5.2557468e+09 0 0.068028348
|
||||
1100 5.2975687e+09 0 0.068029528
|
||||
1200 5.2081927e+09 0 0.068017542
|
||||
1300 5.2636873e+09 0 0.068012572
|
||||
1400 5.2187907e+09 0 0.06802049
|
||||
1500 5.2349541e+09 0 0.0680373
|
||||
1600 5.216092e+09 0 0.068056885
|
||||
1700 5.2598019e+09 0 0.068069504
|
||||
1800 5.2569065e+09 0 0.068065306
|
||||
1900 5.2072055e+09 0 0.068074863
|
||||
2000 5.2092961e+09 0 0.068061619
|
||||
2100 5.2918572e+09 0 0.068076418
|
||||
2200 5.2680626e+09 0 0.068072149
|
||||
2300 5.242958e+09 0 0.06806486
|
||||
2400 5.2494099e+09 0 0.06805038
|
||||
2500 5.2055798e+09 0 0.068072194
|
||||
2600 5.2264829e+09 0 0.068069312
|
||||
2700 5.3557342e+09 0 0.068064812
|
||||
2800 5.2186177e+09 0 0.068042942
|
||||
2900 5.2652497e+09 0 0.068044214
|
||||
3000 5.1894899e+09 0 0.068044801
|
||||
3100 5.241524e+09 0 0.068056675
|
||||
3200 5.1915006e+09 0 0.06805641
|
||||
3300 5.2367825e+09 0 0.068049946
|
||||
3400 5.2288011e+09 0 0.068060182
|
||||
3500 5.2704335e+09 0 0.068070881
|
||||
3600 5.2886558e+09 0 0.068050439
|
||||
3700 5.1976022e+09 0 0.068045927
|
||||
3800 5.1525512e+09 0 0.068054494
|
||||
3900 5.2212395e+09 0 0.068061432
|
||||
4000 5.2309575e+09 0 0.068070842
|
||||
4100 5.2260184e+09 0 0.068078378
|
||||
4200 5.2829349e+09 0 0.068071652
|
||||
4300 5.2204917e+09 0 0.068083072
|
||||
4400 5.255242e+09 0 0.068066175
|
||||
4500 5.2435681e+09 0 0.068050802
|
||||
4600 5.2483356e+09 0 0.06805658
|
||||
4700 5.2365098e+09 0 0.068041845
|
||||
4800 5.2254325e+09 0 0.068038583
|
||||
4900 5.1842852e+09 0 0.068028401
|
||||
5000 5.2240722e+09 0 0.068031544
|
||||
Loop time of 5.14275 on 1 procs for 5000 steps with 4096 atoms
|
||||
|
||||
Performance: 0.008 tau/day, 972.242 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.26842 | 0.26842 | 0.26842 | 0.0 | 5.22
|
||||
Output | 0.0035088 | 0.0035088 | 0.0035088 | 0.0 | 0.07
|
||||
Modify | 4.6588 | 4.6588 | 4.6588 | 0.0 | 90.59
|
||||
Other | | 0.212 | | | 4.12
|
||||
|
||||
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 817.000 ave 817 max 817 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||
# brownian motion, which is
|
||||
#
|
||||
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
|
||||
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
|
||||
#
|
||||
# with d being simulation dimension
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*] c_press
|
||||
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 12000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||
0 5.2240722e+09 0 0 0 0 0 0.068031544
|
||||
1000 52651.581 0 0.0066842466 0.0067977045 0.0066831353 0.020165086 0.060774985
|
||||
2000 52835.806 0 0.013693443 0.014008773 0.013518945 0.041221161 0.094748037
|
||||
3000 52097.629 0 0.020666918 0.021696789 0.020665685 0.063029392 0.10673866
|
||||
4000 52579.452 0 0.028145318 0.028504548 0.02830967 0.084959536 0.13358122
|
||||
5000 51255.456 0 0.035019271 0.034644123 0.03638843 0.10605182 0.13507609
|
||||
6000 52730.035 0 0.041412307 0.042689213 0.043339117 0.12744064 0.16497663
|
||||
7000 52247.642 0 0.048119396 0.050556395 0.050706527 0.14938232 0.16360301
|
||||
8000 52169.849 0 0.055241196 0.058678631 0.059373122 0.17329295 0.1676169
|
||||
9000 52520.526 0 0.063519587 0.066592779 0.066988842 0.19710121 0.17142694
|
||||
10000 53519.297 0 0.07164814 0.074576535 0.075619236 0.22184391 0.15619444
|
||||
11000 52937.293 0 0.077992504 0.083184462 0.082988794 0.24416576 0.15257327
|
||||
12000 51762.283 0 0.085959749 0.090992292 0.08984213 0.26679417 0.15996211
|
||||
Loop time of 11.6748 on 1 procs for 12000 steps with 4096 atoms
|
||||
|
||||
Performance: 888.063 tau/day, 1027.851 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0024164 | 0.0024164 | 0.0024164 | 0.0 | 0.02
|
||||
Comm | 0.048127 | 0.048127 | 0.048127 | 0.0 | 0.41
|
||||
Output | 0.0019393 | 0.0019393 | 0.0019393 | 0.0 | 0.02
|
||||
Modify | 11.12 | 11.12 | 11.12 | 0.0 | 95.24
|
||||
Other | | 0.5027 | | | 4.31
|
||||
|
||||
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 75
|
||||
Dangerous builds = 0
|
||||
|
||||
# if you want to check that rotational diffusion is behaving as expected,
|
||||
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||
# which should decay exponentially with timescale (d-1)*D_r (with d
|
||||
# being simulation dimension)
|
||||
|
||||
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
#run 120000
|
||||
Total wall time: 0:00:16
|
||||
@ -0,0 +1,210 @@
|
||||
LAMMPS (8 Apr 2021)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3D overdamped active brownian dynamics with no interactions
|
||||
|
||||
variable gamma_t string 3.0
|
||||
variable gamma_r string 1.0
|
||||
variable temp string 1.0
|
||||
variable seed equal 1974019
|
||||
variable fp string 4.0
|
||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||
variable params string 1.0_3.0_${gamma_r}_${fp}
|
||||
variable params string 1.0_3.0_1.0_${fp}
|
||||
variable params string 1.0_3.0_1.0_4.0
|
||||
|
||||
units lj
|
||||
atom_style hybrid dipole sphere
|
||||
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||
dimension 3
|
||||
newton off
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||
region box block -8 8 -8 8 -8 8
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4096 atoms
|
||||
create_atoms CPU = 0.002 seconds
|
||||
mass * 1.0
|
||||
set type * dipole/random ${seed} 1.0
|
||||
set type * dipole/random 1974019 1.0
|
||||
Setting atom values ...
|
||||
4096 settings made for dipole/random
|
||||
velocity all create 1.0 1 loop geom
|
||||
|
||||
pair_style none
|
||||
|
||||
# overdamped brownian dynamics time-step
|
||||
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
|
||||
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
|
||||
# self-propulsion force along the dipole direction
|
||||
fix activity all propel/self dipole ${fp}
|
||||
fix activity all propel/self dipole 4.0
|
||||
|
||||
compute press all pressure NULL virial
|
||||
|
||||
thermo_style custom step ke pe c_press
|
||||
|
||||
#equilibration
|
||||
timestep 0.0000000001
|
||||
thermo 100
|
||||
run 5000
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes
|
||||
Step KinEng PotEng c_press
|
||||
0 1.4996338 0 0.068021726
|
||||
100 5.2484581e+09 0 0.068010768
|
||||
200 5.277936e+09 0 0.068024039
|
||||
300 5.2651427e+09 0 0.068014821
|
||||
400 5.2066432e+09 0 0.068027583
|
||||
500 5.2250276e+09 0 0.068030242
|
||||
600 5.239771e+09 0 0.068018406
|
||||
700 5.1953674e+09 0 0.068017081
|
||||
800 5.2097107e+09 0 0.068010167
|
||||
900 5.2559863e+09 0 0.068012923
|
||||
1000 5.2743197e+09 0 0.068017855
|
||||
1100 5.1999741e+09 0 0.068014189
|
||||
1200 5.3216344e+09 0 0.068005604
|
||||
1300 5.2839264e+09 0 0.067982558
|
||||
1400 5.2462761e+09 0 0.067977843
|
||||
1500 5.2208208e+09 0 0.067979594
|
||||
1600 5.2740284e+09 0 0.067972573
|
||||
1700 5.1919692e+09 0 0.067974452
|
||||
1800 5.2497614e+09 0 0.067966417
|
||||
1900 5.2910442e+09 0 0.067976096
|
||||
2000 5.27238e+09 0 0.067963979
|
||||
2100 5.3305398e+09 0 0.06795661
|
||||
2200 5.205471e+09 0 0.067970212
|
||||
2300 5.1803713e+09 0 0.067931775
|
||||
2400 5.2134311e+09 0 0.067941825
|
||||
2500 5.2367424e+09 0 0.067963456
|
||||
2600 5.2246738e+09 0 0.067957556
|
||||
2700 5.2514573e+09 0 0.067960724
|
||||
2800 5.2601577e+09 0 0.067965167
|
||||
2900 5.2422855e+09 0 0.067956561
|
||||
3000 5.1796674e+09 0 0.067946764
|
||||
3100 5.2308189e+09 0 0.067946585
|
||||
3200 5.1835395e+09 0 0.067951909
|
||||
3300 5.2762112e+09 0 0.067963199
|
||||
3400 5.3224133e+09 0 0.067944918
|
||||
3500 5.2314242e+09 0 0.06795318
|
||||
3600 5.2760337e+09 0 0.067958005
|
||||
3700 5.2549349e+09 0 0.06795228
|
||||
3800 5.3343065e+09 0 0.067944561
|
||||
3900 5.2440993e+09 0 0.067947433
|
||||
4000 5.2565026e+09 0 0.067962624
|
||||
4100 5.1766738e+09 0 0.067949542
|
||||
4200 5.2058437e+09 0 0.067959946
|
||||
4300 5.2777775e+09 0 0.067945883
|
||||
4400 5.2020331e+09 0 0.067953495
|
||||
4500 5.1417619e+09 0 0.067944161
|
||||
4600 5.2672994e+09 0 0.067936777
|
||||
4700 5.222847e+09 0 0.067943025
|
||||
4800 5.2467842e+09 0 0.06794191
|
||||
4900 5.2784378e+09 0 0.067939495
|
||||
5000 5.2563969e+09 0 0.067940246
|
||||
Loop time of 1.55848 on 4 procs for 5000 steps with 4096 atoms
|
||||
|
||||
Performance: 0.028 tau/day, 3208.260 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.15304 | 0.15677 | 0.16459 | 1.2 | 10.06
|
||||
Output | 0.0012078 | 0.0021182 | 0.0047011 | 3.2 | 0.14
|
||||
Modify | 1.1966 | 1.2236 | 1.2761 | 2.8 | 78.51
|
||||
Other | | 0.176 | | | 11.29
|
||||
|
||||
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 353.000 ave 353 max 353 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||
# brownian motion, which is
|
||||
#
|
||||
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
|
||||
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
|
||||
#
|
||||
# with d being simulation dimension
|
||||
compute msd all msd
|
||||
|
||||
thermo_style custom step ke pe c_msd[*] c_press
|
||||
|
||||
|
||||
timestep 0.00001
|
||||
thermo 1000
|
||||
|
||||
# main run
|
||||
run 12000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
|
||||
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||
0 5.2563969e+09 0 0 0 0 0 0.067940246
|
||||
1000 52568.549 0 0.0067249858 0.0066478843 0.0066014231 0.019974293 0.066777589
|
||||
2000 52836.937 0 0.013611101 0.013799663 0.013161144 0.040571907 0.066769693
|
||||
3000 52129.467 0 0.020360834 0.02089829 0.01995025 0.061209374 0.060026879
|
||||
4000 52075.177 0 0.027638751 0.028062314 0.026895904 0.082596969 0.078290387
|
||||
5000 52203.996 0 0.034087112 0.034933104 0.033832559 0.10285278 0.083657551
|
||||
6000 52986.764 0 0.041562413 0.042238976 0.040542538 0.12434393 0.11542014
|
||||
7000 51941.229 0 0.049216989 0.049250201 0.047598008 0.1460652 0.13739893
|
||||
8000 52618.713 0 0.057198947 0.057409217 0.05404895 0.16865711 0.13681938
|
||||
9000 52501.332 0 0.066447829 0.065262287 0.062271789 0.19398191 0.14306596
|
||||
10000 52545.628 0 0.073800792 0.072510553 0.070100713 0.21641206 0.14689578
|
||||
11000 52416.561 0 0.081881868 0.080638809 0.078969817 0.24149049 0.15608324
|
||||
12000 52271.578 0 0.090521937 0.088555992 0.08592156 0.26499949 0.1474981
|
||||
Loop time of 3.13506 on 4 procs for 12000 steps with 4096 atoms
|
||||
|
||||
Performance: 3307.113 tau/day, 3827.677 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.00060225 | 0.00060934 | 0.00061345 | 0.0 | 0.02
|
||||
Comm | 0.029197 | 0.029376 | 0.029582 | 0.1 | 0.94
|
||||
Output | 0.00060606 | 0.00087148 | 0.0016448 | 0.0 | 0.03
|
||||
Modify | 2.84 | 2.8773 | 2.8942 | 1.3 | 91.78
|
||||
Other | | 0.2269 | | | 7.24
|
||||
|
||||
Nlocal: 1024.00 ave 1037 max 999 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 73
|
||||
Dangerous builds = 0
|
||||
|
||||
# if you want to check that rotational diffusion is behaving as expected,
|
||||
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||
# which should decay exponentially with timescale (d-1)*D_r (with d
|
||||
# being simulation dimension)
|
||||
|
||||
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
|
||||
#dump_modify 1 first yes sort id
|
||||
|
||||
#run 120000
|
||||
Total wall time: 0:00:04
|
||||
24
examples/USER/mdi/README
Normal file
24
examples/USER/mdi/README
Normal file
@ -0,0 +1,24 @@
|
||||
This dir contains scripts that demonstrate how to use LAMMPS as an
|
||||
MDI engine. LAMMPS as an engine performs the MD timestepping.
|
||||
The driver is a simple Python script. Every timestep the driver
|
||||
sends one or more commands to LAMMPS.
|
||||
|
||||
--------------
|
||||
|
||||
The Script.sh file has comands to perform some very simple example
|
||||
runs.
|
||||
|
||||
--------------
|
||||
|
||||
More complex calculations using LAMMPS as an MDI engine will
|
||||
typically require the use of an MDI driver. Several MDI drivers
|
||||
support calculations with LAMMPS, and include:
|
||||
|
||||
Ab Initio Molecular Dynamics (AIMD) Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_AIMD_Driver
|
||||
|
||||
Nudged Elastic Band (NEB) Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_NEB_Driver
|
||||
|
||||
Metadynamics Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_Metadynamics
|
||||
16
examples/USER/mdi/Script.sh
Normal file
16
examples/USER/mdi/Script.sh
Normal file
@ -0,0 +1,16 @@
|
||||
#!/bin/bash
|
||||
# sample launch scripts
|
||||
|
||||
|
||||
# TCP, running LAMMPS on one proc
|
||||
|
||||
python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
|
||||
../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
|
||||
wait
|
||||
|
||||
|
||||
# TCP, running LAMMPS on two procs
|
||||
|
||||
python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
|
||||
mpiexec -n 2 ../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
|
||||
wait
|
||||
24
examples/USER/mdi/driver.py
Normal file
24
examples/USER/mdi/driver.py
Normal file
@ -0,0 +1,24 @@
|
||||
import sys
|
||||
import mdi
|
||||
|
||||
use_mpi4py = False
|
||||
try:
|
||||
from mpi4py import MPI
|
||||
use_mpi4py = True
|
||||
except:
|
||||
pass
|
||||
|
||||
# Initialize the MDI Library
|
||||
mdi.MDI_Init(sys.argv[2])
|
||||
|
||||
# Connect to the engine
|
||||
comm = mdi.MDI_Accept_communicator()
|
||||
|
||||
# Determine the name of the engine
|
||||
mdi.MDI_Send_Command("<NAME", comm)
|
||||
name = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH, mdi.MDI_CHAR, comm)
|
||||
|
||||
print("Engine name: " + str(name))
|
||||
|
||||
# Send the "EXIT" command to the engine
|
||||
mdi.MDI_Send_Command("EXIT", comm)
|
||||
92
examples/USER/mdi/lammps.data
Normal file
92
examples/USER/mdi/lammps.data
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS data file for water
|
||||
|
||||
24 atoms
|
||||
16 bonds
|
||||
8 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
0.0 4.9325 xlo xhi
|
||||
0.0 4.9325 ylo yhi
|
||||
0.0 4.9325 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.9994
|
||||
2 1.008
|
||||
|
||||
Pair Coeffs
|
||||
|
||||
1 0.102 3.188
|
||||
2 0.000 0.000
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 450 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 55.0 104.52
|
||||
|
||||
Atoms
|
||||
|
||||
1 0 1 -0.83400 2.17919 0.196156 4.15513
|
||||
2 0 2 0.41700 2.29785 4.8353 0.126003
|
||||
3 0 2 0.41700 1.82037 1.07996 4.23498
|
||||
4 0 1 -0.83400 4.65839 0.120414 0.305758
|
||||
5 0 2 0.41700 4.67446 -0.0220991 4.29186
|
||||
6 0 2 0.41700 4.28188 0.994196 0.410515
|
||||
7 0 1 -0.83400 3.65045 2.40907 0.344349
|
||||
8 0 2 0.41700 3.52052 2.1838 4.35565
|
||||
9 0 2 0.41700 4.26579 3.14208 0.327669
|
||||
10 0 1 -0.83400 1.21327 2.62177 4.15519
|
||||
11 0 2 0.41700 1.47452 3.53837 4.0667
|
||||
12 0 2 0.41700 1.20743 2.46396 0.16677
|
||||
13 0 1 -0.83400 4.45777 4.47325 2.74192
|
||||
14 0 2 0.41700 4.53396 4.49652 1.78804
|
||||
15 0 2 0.41700 4.21354 3.56943 2.94119
|
||||
16 0 1 -0.83400 2.04119 4.41585 1.64725
|
||||
17 0 2 0.41700 2.26934 4.77582 2.50434
|
||||
18 0 2 0.41700 1.69079 3.54574 1.83793
|
||||
19 0 1 -0.83400 3.73384 1.97964 2.81949
|
||||
20 0 2 0.41700 3.41083 2.22014 1.95113
|
||||
21 0 2 0.41700 3.91914 1.04272 2.75561
|
||||
22 0 1 -0.83400 1.20859 2.09853 1.68186
|
||||
23 0 2 0.41700 1.01865 2.25693 2.60655
|
||||
24 0 2 0.41700 1.16884 1.14674 1.58832
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
5 1 7 8
|
||||
6 1 7 9
|
||||
7 1 10 11
|
||||
8 1 10 12
|
||||
9 1 13 14
|
||||
10 1 13 15
|
||||
11 1 16 17
|
||||
12 1 16 18
|
||||
13 1 19 20
|
||||
14 1 19 21
|
||||
15 1 22 23
|
||||
16 1 22 24
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
3 1 8 7 9
|
||||
4 1 11 10 12
|
||||
5 1 14 13 15
|
||||
6 1 17 16 18
|
||||
7 1 20 19 21
|
||||
8 1 23 22 24
|
||||
28
examples/USER/mdi/lammps.in
Normal file
28
examples/USER/mdi/lammps.in
Normal file
@ -0,0 +1,28 @@
|
||||
units real
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
special_bonds amber
|
||||
|
||||
atom_modify sort 0 0
|
||||
|
||||
read_data lammps.data
|
||||
|
||||
timestep 1.0
|
||||
|
||||
dump 1 all custom 1 dump.lammpstrj id element xu yu zu
|
||||
dump 2 all custom 1 dump.force id element fx fy fz
|
||||
dump 3 all xyz 1 dump.xyz
|
||||
dump_modify 1 element O H
|
||||
dump_modify 2 element O H
|
||||
|
||||
thermo_style multi
|
||||
thermo 1
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 70.0
|
||||
|
||||
mdi/engine
|
||||
@ -1,54 +0,0 @@
|
||||
dimension 2
|
||||
boundary p p p
|
||||
|
||||
variable L equal 20
|
||||
region total block -$L $L -$L $L -0.5 0.5
|
||||
lattice hex 0.3
|
||||
create_box 2 total
|
||||
create_atoms 1 box
|
||||
|
||||
# Set random fraction to passive:
|
||||
set type 1 type/fraction 2 0.5 1337
|
||||
|
||||
# Purely repulsive particles:
|
||||
variable rc equal "2^(1.0/6.0)"
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
mass * 1.0
|
||||
|
||||
fix step all nve
|
||||
fix temp all langevin 1.0 1.0 1.0 13
|
||||
fix twod all enforce2d
|
||||
|
||||
neighbor 0.6 bin
|
||||
|
||||
dump traj all custom 250 2d_active.dump.bin id type x y z
|
||||
|
||||
thermo_style custom time step pe ke etotal temp
|
||||
thermo 1000
|
||||
run 5000
|
||||
|
||||
group one type 1
|
||||
group two type 2
|
||||
|
||||
compute ke1 one ke
|
||||
compute ke2 two ke
|
||||
|
||||
thermo_style custom step pe ke etotal temp c_ke1 c_ke2
|
||||
|
||||
fix active all propel/self velocity 1.0
|
||||
|
||||
# With active force there is more motion so increase bin size:
|
||||
neighbor 1.0 bin
|
||||
run 10000
|
||||
|
||||
# Only make type 1 active:
|
||||
fix active all propel/self velocity 1.0 types 1
|
||||
|
||||
# With active force there is more motion so increase bin size:
|
||||
neighbor 1.0 bin
|
||||
run 10000
|
||||
|
||||
|
||||
@ -1,37 +0,0 @@
|
||||
dimension 2
|
||||
boundary p p p
|
||||
|
||||
variable L equal 20
|
||||
region total block -$L $L -$L $L -0.5 0.5
|
||||
lattice hex 0.3
|
||||
create_box 2 total
|
||||
create_atoms 1 box
|
||||
|
||||
# Set random fraction to passive:
|
||||
set type 1 type/fraction 2 0.5 1337
|
||||
|
||||
# Purely repulsive particles:
|
||||
variable rc equal "2^(1.0/6.0)"
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
mass * 1.0
|
||||
|
||||
fix step all nve
|
||||
fix twod all enforce2d
|
||||
|
||||
neighbor 0.6 bin
|
||||
|
||||
dump traj all custom 250 2d_active.dump.bin id type x y z
|
||||
|
||||
thermo_style custom step pe ke etotal temp
|
||||
thermo 1000
|
||||
run 10000
|
||||
|
||||
fix active all propel/self velocity 1.0
|
||||
fix fric all viscous 1.0
|
||||
|
||||
# With active force there is more motion so increase bin size:
|
||||
neighbor 1.0 bin
|
||||
run 10000
|
||||
@ -1,40 +0,0 @@
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
atom_style ellipsoid
|
||||
variable L equal 20
|
||||
region total block -$L $L -$L $L -$L $L
|
||||
lattice sc 0.1
|
||||
create_box 2 total
|
||||
create_atoms 1 box
|
||||
|
||||
# Set random fraction to passive:
|
||||
set type 1 type/fraction 2 0.5 1337
|
||||
|
||||
# Purely repulsive particles:
|
||||
variable rc equal "2^(1.0/6.0)"
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
# mass * 1.0
|
||||
set type * shape 1.0 1.0 1.0
|
||||
set type * density 1.9098593171027443
|
||||
set type * quat 0 0 1 0
|
||||
|
||||
fix step all nve/asphere
|
||||
fix temp all langevin 1.0 1.0 1.0 13 angmom 3.333333333
|
||||
|
||||
neighbor 0.6 bin
|
||||
|
||||
dump traj all custom 100 3d_active.dump.bin id type x y z fx fy fz
|
||||
|
||||
thermo_style custom step pe ke etotal temp
|
||||
thermo 100
|
||||
run 500
|
||||
|
||||
fix active all propel/self quat 1.0
|
||||
|
||||
# With active force there is more motion so increase bin size:
|
||||
neighbor 1.0 bin
|
||||
run 500
|
||||
@ -86,7 +86,7 @@ pair_style gran/hertz/history &
|
||||
${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
|
||||
pair_coeff * *
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor ${skin} multi
|
||||
thermo ${logfreq}
|
||||
|
||||
comm_style brick
|
||||
|
||||
@ -49,7 +49,7 @@ pair_style gran/hertz/history &
|
||||
${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
|
||||
pair_coeff * *
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor ${skin} multi
|
||||
thermo ${logfreq}
|
||||
|
||||
comm_style brick
|
||||
|
||||
20015
examples/multi/data.powerlaw
Normal file
20015
examples/multi/data.powerlaw
Normal file
File diff suppressed because it is too large
Load Diff
67
examples/multi/in.colloid
Normal file
67
examples/multi/in.colloid
Normal file
@ -0,0 +1,67 @@
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.1
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 5 box
|
||||
create_atoms 1 box
|
||||
|
||||
#Roughly equally partition atoms between types 1-4
|
||||
set group all type/fraction 2 0.500 23984
|
||||
set group all type/fraction 3 0.333 43684
|
||||
set group all type/fraction 4 0.250 87811
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||
delete_atoms region sphere1
|
||||
delete_atoms region sphere2
|
||||
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||
|
||||
set type 1 mass 400
|
||||
set type 2 mass 1
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi #multi/old
|
||||
neigh_modify delay 0 collection/type 2 1*4 5
|
||||
comm_modify mode multi reduce/multi #multi/old
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style colloid 20.0
|
||||
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||
|
||||
|
||||
|
||||
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 &
|
||||
mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 1000 dump.colloid
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type &
|
||||
# zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type &
|
||||
# zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 2000
|
||||
50
examples/multi/in.granular
Normal file
50
examples/multi/in.granular
Normal file
@ -0,0 +1,50 @@
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.5
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
change_box all triclinic
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||
delete_atoms region sphere1
|
||||
delete_atoms region sphere2
|
||||
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||
|
||||
set type 2 mass 400
|
||||
set type 1 mass 1
|
||||
set type 2 diameter 20
|
||||
set type 1 diameter 1
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi #multi/old
|
||||
neigh_modify delay 0 collection/interval 2 1 20
|
||||
comm_modify mode multi vel yes reduce/multi #multi/old
|
||||
|
||||
# granular potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-3
|
||||
|
||||
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 2000
|
||||
33
examples/multi/in.powerlaw
Normal file
33
examples/multi/in.powerlaw
Normal file
@ -0,0 +1,33 @@
|
||||
# Shear power-law distributed granular particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
read_data data.powerlaw
|
||||
change_box all triclinic
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi
|
||||
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
|
||||
comm_modify mode multi vel yes reduce/multi
|
||||
|
||||
# granular potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-4
|
||||
|
||||
# dump 1 all custom 20000 dump.granular id x y z radius
|
||||
|
||||
thermo_style custom step temp epair etotal press vol pxy
|
||||
thermo 100
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 1000
|
||||
183
examples/multi/log.30Nov20.colloid.intel.1
Normal file
183
examples/multi/log.30Nov20.colloid.intel.1
Normal file
@ -0,0 +1,183 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 5 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
#Roughly equally partition atoms between types 1-4
|
||||
set group all type/fraction 2 0.500 23984
|
||||
Setting atom values ...
|
||||
1768 settings made for type/fraction
|
||||
set group all type/fraction 3 0.333 43684
|
||||
Setting atom values ...
|
||||
1255 settings made for type/fraction
|
||||
set group all type/fraction 4 0.250 87811
|
||||
Setting atom values ...
|
||||
927 settings made for type/fraction
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 289 atoms, new total = 3311
|
||||
delete_atoms region sphere2
|
||||
Deleted 287 atoms, new total = 3024
|
||||
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 1 mass 400
|
||||
Setting atom values ...
|
||||
753 settings made for mass
|
||||
set type 2 mass 1
|
||||
Setting atom values ...
|
||||
722 settings made for mass
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi #multi/old
|
||||
neigh_modify delay 0 collection/type 2 1*4 5
|
||||
comm_modify mode multi reduce/multi #multi/old
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style colloid 20.0
|
||||
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||
|
||||
|
||||
|
||||
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 1000 dump.colloid
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 2, bins = 95 95 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair colloid, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395241 0.121 36000
|
||||
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||
2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
|
||||
3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
|
||||
4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
|
||||
5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
|
||||
6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702
|
||||
7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386
|
||||
8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372
|
||||
9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764
|
||||
10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941
|
||||
11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993
|
||||
12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363
|
||||
13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226
|
||||
14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372
|
||||
15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715
|
||||
16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607
|
||||
17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6
|
||||
18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856
|
||||
19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867
|
||||
20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666
|
||||
21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277
|
||||
22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593
|
||||
23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968
|
||||
24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941
|
||||
25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154
|
||||
26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774
|
||||
27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521
|
||||
28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093
|
||||
29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945
|
||||
30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305
|
||||
31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392
|
||||
32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609
|
||||
33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572
|
||||
34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49
|
||||
35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819
|
||||
36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608
|
||||
37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772
|
||||
38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511
|
||||
39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647
|
||||
40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198
|
||||
41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649
|
||||
42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804
|
||||
43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893
|
||||
44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262
|
||||
45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842
|
||||
46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151
|
||||
47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334
|
||||
48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246
|
||||
49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093
|
||||
50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715
|
||||
Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms
|
||||
|
||||
Performance: 1093493.133 tau/day, 2531.234 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.789 | 10.789 | 10.789 | 0.0 | 54.62
|
||||
Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59
|
||||
Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70
|
||||
Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01
|
||||
Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11
|
||||
Other | | 0.7856 | | | 3.98
|
||||
|
||||
Nlocal: 3026.00 ave 3026 max 3026 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 584.000 ave 584 max 584 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 25892.0 ave 25892 max 25892 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 25892
|
||||
Ave neighs/atom = 8.5565102
|
||||
Neighbor list builds = 4330
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:19
|
||||
183
examples/multi/log.30Nov20.colloid.intel.4
Normal file
183
examples/multi/log.30Nov20.colloid.intel.4
Normal file
@ -0,0 +1,183 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 5 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
#Roughly equally partition atoms between types 1-4
|
||||
set group all type/fraction 2 0.500 23984
|
||||
Setting atom values ...
|
||||
1768 settings made for type/fraction
|
||||
set group all type/fraction 3 0.333 43684
|
||||
Setting atom values ...
|
||||
1255 settings made for type/fraction
|
||||
set group all type/fraction 4 0.250 87811
|
||||
Setting atom values ...
|
||||
927 settings made for type/fraction
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 289 atoms, new total = 3311
|
||||
delete_atoms region sphere2
|
||||
Deleted 287 atoms, new total = 3024
|
||||
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 1 mass 400
|
||||
Setting atom values ...
|
||||
753 settings made for mass
|
||||
set type 2 mass 1
|
||||
Setting atom values ...
|
||||
722 settings made for mass
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi #multi/old
|
||||
neigh_modify delay 0 collection/type 2 1*4 5
|
||||
comm_modify mode multi reduce/multi #multi/old
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style colloid 20.0
|
||||
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||
|
||||
|
||||
|
||||
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 1000 dump.colloid
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 2, bins = 95 95 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair colloid, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/newton
|
||||
stencil: half/multi/2d
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.327 | 4.329 | 4.330 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395241 0.121 36000
|
||||
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
|
||||
3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289
|
||||
4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708
|
||||
5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295
|
||||
6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648
|
||||
7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448
|
||||
8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484
|
||||
9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609
|
||||
10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542
|
||||
11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927
|
||||
12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009
|
||||
13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654
|
||||
14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89
|
||||
15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786
|
||||
16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792
|
||||
17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809
|
||||
18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172
|
||||
19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244
|
||||
20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884
|
||||
21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487
|
||||
22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812
|
||||
23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427
|
||||
24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79
|
||||
25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756
|
||||
26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645
|
||||
27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657
|
||||
28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079
|
||||
29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99
|
||||
30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355
|
||||
31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196
|
||||
32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934
|
||||
33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442
|
||||
34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628
|
||||
35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725
|
||||
36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049
|
||||
37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825
|
||||
38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497
|
||||
39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469
|
||||
40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846
|
||||
41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515
|
||||
42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657
|
||||
43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024
|
||||
44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224
|
||||
45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959
|
||||
46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822
|
||||
47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892
|
||||
48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453
|
||||
49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918
|
||||
50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268
|
||||
Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms
|
||||
|
||||
Performance: 3091831.080 tau/day, 7157.016 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01
|
||||
Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04
|
||||
Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39
|
||||
Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01
|
||||
Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41
|
||||
Other | | 0.4281 | | | 6.13
|
||||
|
||||
Nlocal: 756.500 ave 839 max 673 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 292.500 ave 307 max 282 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 6435.25 ave 7367 max 5493 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 25741
|
||||
Ave neighs/atom = 8.5066094
|
||||
Neighbor list builds = 4335
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:07
|
||||
183
examples/multi/log.30Nov20.colloid.old.intel.1
Normal file
183
examples/multi/log.30Nov20.colloid.old.intel.1
Normal file
@ -0,0 +1,183 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 5 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
#Roughly equally partition atoms between types 1-4
|
||||
set group all type/fraction 2 0.500 23984
|
||||
Setting atom values ...
|
||||
1768 settings made for type/fraction
|
||||
set group all type/fraction 3 0.333 43684
|
||||
Setting atom values ...
|
||||
1255 settings made for type/fraction
|
||||
set group all type/fraction 4 0.250 87811
|
||||
Setting atom values ...
|
||||
927 settings made for type/fraction
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 289 atoms, new total = 3311
|
||||
delete_atoms region sphere2
|
||||
Deleted 287 atoms, new total = 3024
|
||||
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 1 mass 400
|
||||
Setting atom values ...
|
||||
753 settings made for mass
|
||||
set type 2 mass 1
|
||||
Setting atom values ...
|
||||
722 settings made for mass
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi/old #multi
|
||||
neigh_modify delay 0 #multi/custom 2 1*4 5
|
||||
comm_modify mode multi/old #multi multi/reduce
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style colloid 20.0
|
||||
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||
|
||||
|
||||
|
||||
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 1000 dump.colloid
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 2, bins = 95 95 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair colloid, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/old/newton
|
||||
stencil: half/multi/old/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395241 0.121 36000
|
||||
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||
2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
|
||||
3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
|
||||
4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
|
||||
5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
|
||||
6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702
|
||||
7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387
|
||||
8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802
|
||||
9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722
|
||||
10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135
|
||||
11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116
|
||||
12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208
|
||||
13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901
|
||||
14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344
|
||||
15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963
|
||||
16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043
|
||||
17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977
|
||||
18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99
|
||||
19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325
|
||||
20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745
|
||||
21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298
|
||||
22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199
|
||||
23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71
|
||||
24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334
|
||||
25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577
|
||||
26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041
|
||||
27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392
|
||||
28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419
|
||||
29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642
|
||||
30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15
|
||||
31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091
|
||||
32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726
|
||||
33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866
|
||||
34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869
|
||||
35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285
|
||||
36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264
|
||||
37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274
|
||||
38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252
|
||||
39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857
|
||||
40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905
|
||||
41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981
|
||||
42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931
|
||||
43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82
|
||||
44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18
|
||||
45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013
|
||||
46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611
|
||||
47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083
|
||||
48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933
|
||||
49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165
|
||||
50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069
|
||||
Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms
|
||||
|
||||
Performance: 756994.490 tau/day, 1752.302 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.918 | 10.918 | 10.918 | 0.0 | 38.26
|
||||
Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36
|
||||
Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51
|
||||
Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00
|
||||
Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57
|
||||
Other | | 0.9412 | | | 3.30
|
||||
|
||||
Nlocal: 3026.00 ave 3026 max 3026 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2292.00 ave 2292 max 2292 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 25767.0 ave 25767 max 25767 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 25767
|
||||
Ave neighs/atom = 8.5152016
|
||||
Neighbor list builds = 4332
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:28
|
||||
183
examples/multi/log.30Nov20.colloid.old.intel.4
Normal file
183
examples/multi/log.30Nov20.colloid.old.intel.4
Normal file
@ -0,0 +1,183 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 5 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
#Roughly equally partition atoms between types 1-4
|
||||
set group all type/fraction 2 0.500 23984
|
||||
Setting atom values ...
|
||||
1768 settings made for type/fraction
|
||||
set group all type/fraction 3 0.333 43684
|
||||
Setting atom values ...
|
||||
1255 settings made for type/fraction
|
||||
set group all type/fraction 4 0.250 87811
|
||||
Setting atom values ...
|
||||
927 settings made for type/fraction
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 289 atoms, new total = 3311
|
||||
delete_atoms region sphere2
|
||||
Deleted 287 atoms, new total = 3024
|
||||
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 1 mass 400
|
||||
Setting atom values ...
|
||||
753 settings made for mass
|
||||
set type 2 mass 1
|
||||
Setting atom values ...
|
||||
722 settings made for mass
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi/old #multi
|
||||
neigh_modify delay 0 #multi/custom 2 1*4 5
|
||||
comm_modify mode multi/old #multi multi/reduce
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style colloid 20.0
|
||||
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||
|
||||
|
||||
|
||||
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 1000 dump.colloid
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 2, bins = 95 95 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair colloid, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/multi/old/newton
|
||||
stencil: half/multi/old/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.406 | 4.410 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395241 0.121 36000
|
||||
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
|
||||
3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289
|
||||
4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521
|
||||
5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581
|
||||
6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994
|
||||
7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068
|
||||
8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899
|
||||
9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69
|
||||
10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271
|
||||
11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223
|
||||
12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869
|
||||
13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441
|
||||
14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432
|
||||
15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491
|
||||
16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633
|
||||
17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582
|
||||
18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933
|
||||
19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945
|
||||
20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271
|
||||
21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934
|
||||
22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03
|
||||
23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999
|
||||
24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323
|
||||
25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848
|
||||
26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597
|
||||
27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24
|
||||
28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441
|
||||
29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266
|
||||
30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051
|
||||
31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903
|
||||
32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077
|
||||
33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987
|
||||
34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964
|
||||
35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433
|
||||
36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246
|
||||
37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664
|
||||
38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421
|
||||
39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293
|
||||
40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176
|
||||
41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599
|
||||
42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922
|
||||
43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928
|
||||
44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954
|
||||
45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662
|
||||
46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162
|
||||
47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453
|
||||
48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543
|
||||
49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823
|
||||
50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277
|
||||
Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms
|
||||
|
||||
Performance: 2007847.166 tau/day, 4647.794 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98
|
||||
Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74
|
||||
Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79
|
||||
Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01
|
||||
Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19
|
||||
Other | | 0.5686 | | | 5.29
|
||||
|
||||
Nlocal: 756.500 ave 838 max 693 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1282.50 ave 1333 max 1216 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 6426.25 ave 7350 max 5786 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 25705
|
||||
Ave neighs/atom = 8.4947125
|
||||
Neighbor list builds = 4326
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:10
|
||||
175
examples/multi/log.30Nov20.granular.intel.1
Normal file
175
examples/multi/log.30Nov20.granular.intel.1
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.5
|
||||
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 154 atoms, new total = 3446
|
||||
delete_atoms region sphere2
|
||||
Deleted 158 atoms, new total = 3288
|
||||
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 2 mass 400
|
||||
Setting atom values ...
|
||||
2 settings made for mass
|
||||
set type 1 mass 1
|
||||
Setting atom values ...
|
||||
3288 settings made for mass
|
||||
set type 2 diameter 20
|
||||
Setting atom values ...
|
||||
2 settings made for diameter
|
||||
set type 1 diameter 1
|
||||
Setting atom values ...
|
||||
3288 settings made for diameter
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi #multi/old
|
||||
neigh_modify delay 0 collection/interval 2 1 20
|
||||
comm_modify mode multi vel yes reduce/multi #multi/old
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-3
|
||||
|
||||
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 21
|
||||
ghost atom cutoff = 21
|
||||
binsize = 1, bins = 85 85 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/multi/newton/tri
|
||||
stencil: half/multi/2d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395623 0.66837658 7200
|
||||
1000 0.32604952 0 0.32595042 0.17341597 7862.5013
|
||||
2000 0.12631038 0 0.12627198 0.069126477 8216.6956
|
||||
3000 0.069351715 0 0.069330635 0.040799593 8344.1931
|
||||
4000 0.045023755 0 0.04501007 0.029184795 8239.1832
|
||||
5000 0.032735149 0 0.0327252 0.025640841 7943.5691
|
||||
6000 0.026205227 0 0.026197262 0.021206924 7617.6672
|
||||
7000 0.02165475 0 0.021648168 0.018789365 7255.2897
|
||||
8000 0.018299317 0 0.018293755 0.019272158 6887.3386
|
||||
9000 0.016283763 0 0.016278813 0.020434892 6524.0274
|
||||
10000 0.015148918 0 0.015144313 0.021650465 6168.4941
|
||||
11000 0.014180465 0 0.014176155 0.022320009 5823.98
|
||||
12000 0.013505744 0 0.013501639 0.023978674 5492.4853
|
||||
13000 0.013009585 0 0.01300563 0.024391329 5175.7455
|
||||
14000 0.012494373 0 0.012490576 0.027331543 4874.3212
|
||||
15000 0.012057669 0 0.012054004 0.030561239 4589.518
|
||||
16000 0.011510988 0 0.01150749 0.034613772 4321.1694
|
||||
17000 0.011198594 0 0.01119519 0.042263536 4070.0115
|
||||
18000 0.010978603 0 0.010975266 0.053637275 3836.0304
|
||||
19000 0.010768789 0 0.010765516 0.069472547 3619.75
|
||||
20000 0.0102256 0 0.010222492 0.085332898 3420.2738
|
||||
21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821
|
||||
22000 0.006565581 0 0.0065635854 0.14807426 3071.3012
|
||||
23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162
|
||||
24000 0.0040345997 0 0.0040333734 0.237983 2792.2658
|
||||
25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475
|
||||
26000 0.0024157863 0 0.002415052 0.33851944 2578.4972
|
||||
27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264
|
||||
28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871
|
||||
29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208
|
||||
30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452
|
||||
31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456
|
||||
32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224
|
||||
33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345
|
||||
34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045
|
||||
35000 0.00075804791 0 0.0007578175 0.6359631 2072.525
|
||||
36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907
|
||||
37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831
|
||||
38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441
|
||||
39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127
|
||||
40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006
|
||||
41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939
|
||||
42000 0.00025394755 0 0.00025387036 0.80529272 1893.064
|
||||
43000 0.00021067821 0 0.00021061418 0.82962095 1872.365
|
||||
44000 0.00017927684 0 0.00017922235 0.85522899 1853.531
|
||||
45000 0.0001464225 0 0.000146378 0.87925998 1837.2423
|
||||
46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227
|
||||
47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605
|
||||
48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227
|
||||
49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811
|
||||
50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507
|
||||
Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms
|
||||
|
||||
Performance: 393345.914 tau/day, 910.523 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 44.691 | 44.691 | 44.691 | 0.0 | 81.38
|
||||
Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39
|
||||
Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37
|
||||
Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00
|
||||
Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43
|
||||
Other | | 0.7794 | | | 1.42
|
||||
|
||||
Nlocal: 3290.00 ave 3290 max 3290 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 525.000 ave 525 max 525 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 26732.0 ave 26732 max 26732 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 26732
|
||||
Ave neighs/atom = 8.1252280
|
||||
Neighbor list builds = 342
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:54
|
||||
175
examples/multi/log.30Nov20.granular.intel.4
Normal file
175
examples/multi/log.30Nov20.granular.intel.4
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.5
|
||||
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 154 atoms, new total = 3446
|
||||
delete_atoms region sphere2
|
||||
Deleted 158 atoms, new total = 3288
|
||||
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 2 mass 400
|
||||
Setting atom values ...
|
||||
2 settings made for mass
|
||||
set type 1 mass 1
|
||||
Setting atom values ...
|
||||
3288 settings made for mass
|
||||
set type 2 diameter 20
|
||||
Setting atom values ...
|
||||
2 settings made for diameter
|
||||
set type 1 diameter 1
|
||||
Setting atom values ...
|
||||
3288 settings made for diameter
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi #multi/old
|
||||
neigh_modify delay 0 collection/interval 2 1 20
|
||||
comm_modify mode multi vel yes reduce/multi #multi/old
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-3
|
||||
|
||||
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 21
|
||||
ghost atom cutoff = 21
|
||||
binsize = 1, bins = 85 85 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/multi/newton/tri
|
||||
stencil: half/multi/2d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395623 0.66837658 7200
|
||||
1000 0.32605303 0 0.32595393 0.17341558 7862.5037
|
||||
2000 0.12631567 0 0.12627728 0.069188881 8216.7174
|
||||
3000 0.069373812 0 0.069352726 0.040740832 8344.2982
|
||||
4000 0.045084633 0 0.045070929 0.029328609 8239.3656
|
||||
5000 0.032681746 0 0.032671813 0.025416741 7943.7831
|
||||
6000 0.026301239 0 0.026293245 0.021418793 7617.8426
|
||||
7000 0.021666723 0 0.021660138 0.018961011 7255.9338
|
||||
8000 0.018141337 0 0.018135823 0.019306113 6887.4963
|
||||
9000 0.015922309 0 0.015917469 0.020033398 6524.016
|
||||
10000 0.014744547 0 0.014740066 0.020959503 6168.1945
|
||||
11000 0.013872852 0 0.013868636 0.021708943 5823.3153
|
||||
12000 0.013321594 0 0.013317545 0.02332141 5491.4979
|
||||
13000 0.01269964 0 0.012695779 0.024796428 5174.6263
|
||||
14000 0.01227055 0 0.012266821 0.027785072 4873.4516
|
||||
15000 0.012120508 0 0.012116824 0.029656636 4588.8603
|
||||
16000 0.011612027 0 0.011608498 0.034695109 4320.4674
|
||||
17000 0.011216697 0 0.011213288 0.042746966 4069.4275
|
||||
18000 0.010950166 0 0.010946838 0.053528994 3835.5439
|
||||
19000 0.010887635 0 0.010884325 0.069684492 3619.562
|
||||
20000 0.010563449 0 0.010560238 0.08654561 3420.2636
|
||||
21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408
|
||||
22000 0.006929086 0 0.0069269799 0.15018917 3072.0438
|
||||
23000 0.0052239156 0 0.0052223277 0.19067193 2924.441
|
||||
24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426
|
||||
25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912
|
||||
26000 0.002549072 0 0.0025482972 0.33567824 2579.3738
|
||||
27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502
|
||||
28000 0.001772982 0 0.0017724431 0.41079958 2411.9111
|
||||
29000 0.001127719 0 0.0011273762 0.44752241 2341.1888
|
||||
30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611
|
||||
31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328
|
||||
32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674
|
||||
33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696
|
||||
34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504
|
||||
35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077
|
||||
36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251
|
||||
37000 0.0003540723 0 0.00035396468 0.68803919 2005.497
|
||||
38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345
|
||||
39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979
|
||||
40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695
|
||||
41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326
|
||||
42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474
|
||||
43000 0.00021545017 0 0.00021538468 0.82803644 1872.073
|
||||
44000 0.00017293257 0 0.00017288 0.85436769 1852.6548
|
||||
45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087
|
||||
46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977
|
||||
47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913
|
||||
48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082
|
||||
49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875
|
||||
50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247
|
||||
Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms
|
||||
|
||||
Performance: 1217551.996 tau/day, 2818.407 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21
|
||||
Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31
|
||||
Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10
|
||||
Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01
|
||||
Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32
|
||||
Other | | 0.5419 | | | 3.05
|
||||
|
||||
Nlocal: 822.500 ave 897 max 779 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 190.500 ave 211 max 179 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 6665.75 ave 7329 max 6104 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 26663
|
||||
Ave neighs/atom = 8.1042553
|
||||
Neighbor list builds = 342
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:17
|
||||
175
examples/multi/log.30Nov20.granular.old.intel.1
Normal file
175
examples/multi/log.30Nov20.granular.old.intel.1
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.5
|
||||
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 154 atoms, new total = 3446
|
||||
delete_atoms region sphere2
|
||||
Deleted 158 atoms, new total = 3288
|
||||
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 2 mass 400
|
||||
Setting atom values ...
|
||||
2 settings made for mass
|
||||
set type 1 mass 1
|
||||
Setting atom values ...
|
||||
3288 settings made for mass
|
||||
set type 2 diameter 20
|
||||
Setting atom values ...
|
||||
2 settings made for diameter
|
||||
set type 1 diameter 1
|
||||
Setting atom values ...
|
||||
3288 settings made for diameter
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi/old #multi
|
||||
neigh_modify delay 0 #collection/interval 2 1 20
|
||||
comm_modify mode multi/old vel yes #reduce/multi
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-3
|
||||
|
||||
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 21
|
||||
ghost atom cutoff = 21
|
||||
binsize = 1, bins = 85 85 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/multi/old/newton/tri
|
||||
stencil: half/multi/old/2d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395623 0.66837658 7200
|
||||
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
|
||||
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
|
||||
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
|
||||
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
|
||||
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
|
||||
6000 0.025856 0 0.025848141 0.021241317 7603.5534
|
||||
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
|
||||
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
|
||||
9000 0.016370159 0 0.016365184 0.020261904 6515.3445
|
||||
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
|
||||
11000 0.014156551 0 0.014152248 0.021324815 5815.4665
|
||||
12000 0.013725406 0 0.013721235 0.021159958 5483.6304
|
||||
13000 0.013215746 0 0.013211729 0.021685712 5165.4758
|
||||
14000 0.012398153 0 0.012394384 0.024155434 4862.8657
|
||||
15000 0.011842796 0 0.011839196 0.028503991 4577.9008
|
||||
16000 0.011433182 0 0.011429706 0.033564839 4309.8792
|
||||
17000 0.011166574 0 0.01116318 0.040592677 4058.9964
|
||||
18000 0.01100067 0 0.010997326 0.04899206 3825.155
|
||||
19000 0.010224474 0 0.010221366 0.063670337 3607.6577
|
||||
20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658
|
||||
21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002
|
||||
22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986
|
||||
23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014
|
||||
24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113
|
||||
25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604
|
||||
26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564
|
||||
27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379
|
||||
28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461
|
||||
29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308
|
||||
30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316
|
||||
31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683
|
||||
32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093
|
||||
33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574
|
||||
34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254
|
||||
35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217
|
||||
36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654
|
||||
37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901
|
||||
38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136
|
||||
39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531
|
||||
40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834
|
||||
41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027
|
||||
42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714
|
||||
43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408
|
||||
44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677
|
||||
45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144
|
||||
46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355
|
||||
47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285
|
||||
48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043
|
||||
49000 0.00018879338 0 0.000188736 0.95775166 1780.0323
|
||||
50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442
|
||||
Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms
|
||||
|
||||
Performance: 289297.713 tau/day, 669.671 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 56.696 | 56.696 | 56.696 | 0.0 | 75.93
|
||||
Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98
|
||||
Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29
|
||||
Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00
|
||||
Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29
|
||||
Other | | 1.125 | | | 1.51
|
||||
|
||||
Nlocal: 3290.00 ave 3290 max 3290 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6295.00 ave 6295 max 6295 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 53729.0 ave 53729 max 53729 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 53729
|
||||
Ave neighs/atom = 16.331003
|
||||
Neighbor list builds = 348
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:14
|
||||
175
examples/multi/log.30Nov20.granular.old.intel.4
Normal file
175
examples/multi/log.30Nov20.granular.old.intel.4
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Big colloid particles and small LJ particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.5
|
||||
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||
region box block 0 60 0 60 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 3600 atoms
|
||||
create_atoms CPU = 0.063 seconds
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
|
||||
# remove two spheres of small particles and add large particles in the voids
|
||||
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||
delete_atoms region sphere1
|
||||
Deleted 154 atoms, new total = 3446
|
||||
delete_atoms region sphere2
|
||||
Deleted 158 atoms, new total = 3288
|
||||
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
set type 2 mass 400
|
||||
Setting atom values ...
|
||||
2 settings made for mass
|
||||
set type 1 mass 1
|
||||
Setting atom values ...
|
||||
3288 settings made for mass
|
||||
set type 2 diameter 20
|
||||
Setting atom values ...
|
||||
2 settings made for diameter
|
||||
set type 1 diameter 1
|
||||
Setting atom values ...
|
||||
3288 settings made for diameter
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi/old #multi
|
||||
neigh_modify delay 0 #collection/interval 2 1 20
|
||||
comm_modify mode multi/old vel yes #reduce/multi
|
||||
|
||||
# colloid potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-3
|
||||
|
||||
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||
|
||||
thermo_style custom step temp epair etotal press vol
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 21
|
||||
ghost atom cutoff = 21
|
||||
binsize = 1, bins = 85 85 2
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/multi/old/newton/tri
|
||||
stencil: half/multi/old/2d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume
|
||||
0 1.44 0 1.4395623 0.66837658 7200
|
||||
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
|
||||
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
|
||||
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
|
||||
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
|
||||
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
|
||||
6000 0.025856 0 0.025848141 0.021241317 7603.5534
|
||||
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
|
||||
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
|
||||
9000 0.01637016 0 0.016365184 0.020261904 6515.3445
|
||||
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
|
||||
11000 0.014156553 0 0.01415225 0.021324818 5815.4665
|
||||
12000 0.013725412 0 0.01372124 0.021159958 5483.6304
|
||||
13000 0.013215733 0 0.013211716 0.021685624 5165.4758
|
||||
14000 0.012398179 0 0.012394411 0.024155572 4862.8657
|
||||
15000 0.01184269 0 0.01183909 0.028504106 4577.901
|
||||
16000 0.01143291 0 0.011429435 0.033564204 4309.88
|
||||
17000 0.011166204 0 0.01116281 0.040588854 4058.9972
|
||||
18000 0.011000875 0 0.010997532 0.048998904 3825.1569
|
||||
19000 0.010225905 0 0.010222797 0.063669588 3607.6622
|
||||
20000 0.0091390255 0 0.0091362477 0.088165402 3408.567
|
||||
21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936
|
||||
22000 0.00601731 0 0.0060154811 0.15261994 3064.3873
|
||||
23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782
|
||||
24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897
|
||||
25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164
|
||||
26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312
|
||||
27000 0.001700508 0 0.0016999912 0.37665013 2487.1626
|
||||
28000 0.0014434246 0 0.0014429859 0.41572163 2409.327
|
||||
29000 0.00089885063 0 0.00089857742 0.453431 2340.2313
|
||||
30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155
|
||||
31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349
|
||||
32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738
|
||||
33000 0.00044719326 0 0.00044705733 0.59696179 2142.571
|
||||
34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282
|
||||
35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008
|
||||
36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242
|
||||
37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235
|
||||
38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706
|
||||
39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838
|
||||
40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034
|
||||
41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108
|
||||
42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649
|
||||
43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672
|
||||
44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284
|
||||
45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755
|
||||
46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989
|
||||
47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606
|
||||
48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258
|
||||
49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032
|
||||
50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534
|
||||
Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms
|
||||
|
||||
Performance: 716540.413 tau/day, 1658.658 timesteps/s
|
||||
90.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14
|
||||
Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87
|
||||
Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09
|
||||
Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00
|
||||
Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27
|
||||
Other | | 0.7918 | | | 2.63
|
||||
|
||||
Nlocal: 822.500 ave 859 max 785 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 3049.75 ave 3089 max 2999 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 13440.5 ave 14459 max 11964 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 53762
|
||||
Ave neighs/atom = 16.341033
|
||||
Neighbor list builds = 348
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:30
|
||||
291
examples/multi/log.30Nov20.powerlaw.intel.1
Normal file
291
examples/multi/log.30Nov20.powerlaw.intel.1
Normal file
@ -0,0 +1,291 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Shear power-law distributed granular particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
read_data data.powerlaw
|
||||
Reading data file ...
|
||||
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10000 atoms
|
||||
reading velocities ...
|
||||
10000 velocities
|
||||
read_data CPU = 0.027 seconds
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi
|
||||
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
|
||||
comm_modify mode multi vel yes reduce/multi
|
||||
|
||||
# granular potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-4
|
||||
|
||||
# dump 1 all custom 20000 dump.granular id x y z radius
|
||||
|
||||
thermo_style custom step temp epair etotal press vol pxy
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 200000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 164.7888
|
||||
ghost atom cutoff = 164.7888
|
||||
binsize = 82.3944, bins = 4 4 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/multi/newton/tri
|
||||
stencil: half/multi/2d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.77 | 14.77 | 14.77 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume Pxy
|
||||
0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917
|
||||
1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806
|
||||
2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933
|
||||
3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442
|
||||
4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424
|
||||
5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634
|
||||
6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973
|
||||
7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709
|
||||
8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399
|
||||
9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514
|
||||
10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784
|
||||
11000 0.00018985439 0 0.00018983541 0.58006086 103595.49 -0.028574238
|
||||
12000 0.00018903569 0 0.00018901678 0.5794232 103595.49 -0.031151884
|
||||
13000 0.00019070382 0 0.00019068475 0.57890243 103595.49 -0.033469404
|
||||
14000 0.00019371625 0 0.00019369688 0.5787389 103595.49 -0.035646526
|
||||
15000 0.00019833475 0 0.00019831492 0.57883166 103595.49 -0.037709788
|
||||
16000 0.0002011729 0 0.00020115278 0.57875606 103595.49 -0.039452453
|
||||
17000 0.00020285197 0 0.00020283169 0.5786311 103595.49 -0.040960671
|
||||
18000 0.00020319174 0 0.00020317142 0.57842387 103595.49 -0.042257072
|
||||
19000 0.00020290253 0 0.00020288224 0.57795042 103595.49 -0.043364149
|
||||
20000 0.00020509848 0 0.00020507797 0.5771478 103595.49 -0.044392259
|
||||
21000 0.00021803258 0 0.00021801078 0.57569003 103595.49 -0.044749043
|
||||
22000 0.00020751217 0 0.00020749141 0.57477071 103595.49 -0.045719593
|
||||
23000 0.00022053275 0 0.0002205107 0.57409228 103595.49 -0.047332146
|
||||
24000 0.00022689646 0 0.00022687377 0.57325004 103595.49 -0.04871759
|
||||
25000 0.00025224804 0 0.00025222282 0.57283712 103595.49 -0.050254871
|
||||
26000 0.00025343198 0 0.00025340664 0.57238659 103595.49 -0.051604284
|
||||
27000 0.00026689801 0 0.00026687132 0.57221042 103595.49 -0.052915257
|
||||
28000 0.00027867954 0 0.00027865167 0.57197974 103595.49 -0.053832129
|
||||
29000 0.00028697929 0 0.00028695059 0.57177264 103595.49 -0.054693121
|
||||
30000 0.00028857612 0 0.00028854727 0.57145453 103595.49 -0.055559611
|
||||
31000 0.00029228405 0 0.00029225482 0.5711044 103595.49 -0.056492699
|
||||
32000 0.00029648627 0 0.00029645663 0.57060211 103595.49 -0.05729896
|
||||
33000 0.00030524162 0 0.00030521109 0.57002519 103595.49 -0.058201322
|
||||
34000 0.00031725644 0 0.00031722472 0.56920654 103595.49 -0.059128438
|
||||
35000 0.00032273791 0 0.00032270564 0.56844677 103595.49 -0.060009671
|
||||
36000 0.00033013013 0 0.00033009712 0.56795943 103595.49 -0.061074282
|
||||
37000 0.00033942153 0 0.00033938759 0.56749208 103595.49 -0.062058531
|
||||
38000 0.00035141528 0 0.00035138014 0.56682741 103595.49 -0.062953956
|
||||
39000 0.00036126777 0 0.00036123164 0.56655193 103595.49 -0.063757684
|
||||
40000 0.00037765934 0 0.00037762157 0.5661991 103595.49 -0.064535541
|
||||
41000 0.00040834365 0 0.00040830281 0.56554085 103595.49 -0.064688281
|
||||
42000 0.00042857233 0 0.00042852948 0.56474014 103595.49 -0.065262664
|
||||
43000 0.00042692021 0 0.00042687752 0.56362013 103595.49 -0.065276794
|
||||
44000 0.00040298912 0 0.00040294882 0.5631005 103595.49 -0.065626396
|
||||
45000 0.00040947381 0 0.00040943286 0.56291946 103595.49 -0.066167734
|
||||
46000 0.00040202686 0 0.00040198666 0.56273846 103595.49 -0.066543782
|
||||
47000 0.00038914356 0 0.00038910465 0.56265937 103595.49 -0.067359923
|
||||
48000 0.00038429737 0 0.00038425894 0.56274908 103595.49 -0.068231096
|
||||
49000 0.00036912968 0 0.00036909277 0.56261623 103595.49 -0.068791569
|
||||
50000 0.00035203094 0 0.00035199574 0.56257856 103595.49 -0.069298217
|
||||
51000 0.00034403223 0 0.00034399783 0.56236537 103595.49 -0.070273225
|
||||
52000 0.00034132431 0 0.00034129018 0.56220555 103595.49 -0.071740344
|
||||
53000 0.000335692 0 0.00033565843 0.56194913 103595.49 -0.072834415
|
||||
54000 0.00033048196 0 0.00033044891 0.56231491 103595.49 -0.073996938
|
||||
55000 0.00032751145 0 0.00032747869 0.56225025 103595.49 -0.07506664
|
||||
56000 0.00032696951 0 0.00032693682 0.56285506 103595.49 -0.076445354
|
||||
57000 0.00033158698 0 0.00033155382 0.56354729 103595.49 -0.077682996
|
||||
58000 0.00034300009 0 0.00034296579 0.56416964 103595.49 -0.078836604
|
||||
59000 0.00034340257 0 0.00034336823 0.56490867 103595.49 -0.079658197
|
||||
60000 0.00034736137 0 0.00034732663 0.56519398 103595.49 -0.080570223
|
||||
61000 0.00034984523 0 0.00034981025 0.5651693 103595.49 -0.081115325
|
||||
62000 0.00034995431 0 0.00034991932 0.56534549 103595.49 -0.081486038
|
||||
63000 0.00033854269 0 0.00033850883 0.56582558 103595.49 -0.081892374
|
||||
64000 0.00032621515 0 0.00032618253 0.5658388 103595.49 -0.082786608
|
||||
65000 0.00031773942 0 0.00031770764 0.56576287 103595.49 -0.083706189
|
||||
66000 0.00031772736 0 0.00031769558 0.56548117 103595.49 -0.084236463
|
||||
67000 0.0003148631 0 0.00031483161 0.56483795 103595.49 -0.084506082
|
||||
68000 0.00030359752 0 0.00030356716 0.56446443 103595.49 -0.084985509
|
||||
69000 0.00030395128 0 0.00030392088 0.56437593 103595.49 -0.085548157
|
||||
70000 0.00032811658 0 0.00032808376 0.56372411 103595.49 -0.085304154
|
||||
71000 0.00035494531 0 0.00035490981 0.56326137 103595.49 -0.085047806
|
||||
72000 0.0003253841 0 0.00032535156 0.56244462 103595.49 -0.085693663
|
||||
73000 0.00032328895 0 0.00032325662 0.5629287 103595.49 -0.086119464
|
||||
74000 0.00032650113 0 0.00032646848 0.56306166 103595.49 -0.087182721
|
||||
75000 0.00034303222 0 0.00034299792 0.56219559 103595.49 -0.086604025
|
||||
76000 0.00033786129 0 0.0003378275 0.56188071 103595.49 -0.086852177
|
||||
77000 0.00033559735 0 0.00033556379 0.5619155 103595.49 -0.08689764
|
||||
78000 0.00032579863 0 0.00032576605 0.56177059 103595.49 -0.087109469
|
||||
79000 0.00031610815 0 0.00031607654 0.56160391 103595.49 -0.087250861
|
||||
80000 0.00031246546 0 0.00031243422 0.56181676 103595.49 -0.087117648
|
||||
81000 0.00029392131 0 0.00029389192 0.56205441 103595.49 -0.087601617
|
||||
82000 0.00029624453 0 0.00029621491 0.56285229 103595.49 -0.08824145
|
||||
83000 0.00030538821 0 0.00030535767 0.5627754 103595.49 -0.088318188
|
||||
84000 0.00029587833 0 0.00029584874 0.56267246 103595.49 -0.08930338
|
||||
85000 0.00030551128 0 0.00030548073 0.56251282 103595.49 -0.0897211
|
||||
86000 0.00030000969 0 0.00029997969 0.56249642 103595.49 -0.089920789
|
||||
87000 0.00030211667 0 0.00030208646 0.56256648 103595.49 -0.090315024
|
||||
88000 0.00030524995 0 0.00030521943 0.5623007 103595.49 -0.090706456
|
||||
89000 0.00031961257 0 0.00031958061 0.56210244 103595.49 -0.090852204
|
||||
90000 0.0003195337 0 0.00031950175 0.56207472 103595.49 -0.090879606
|
||||
91000 0.00033860446 0 0.0003385706 0.56197196 103595.49 -0.090891252
|
||||
92000 0.0003327551 0 0.00033272183 0.56172473 103595.49 -0.090725694
|
||||
93000 0.00032983619 0 0.00032980321 0.5619443 103595.49 -0.090626404
|
||||
94000 0.00034024354 0 0.00034020952 0.56150371 103595.49 -0.090769983
|
||||
95000 0.00033201405 0 0.00033198084 0.56145998 103595.49 -0.09102312
|
||||
96000 0.00032851608 0 0.00032848323 0.56201045 103595.49 -0.09152522
|
||||
97000 0.0003353172 0 0.00033528367 0.56256203 103595.49 -0.092443634
|
||||
98000 0.00033453146 0 0.00033449801 0.5632537 103595.49 -0.093069693
|
||||
99000 0.00034432742 0 0.00034429299 0.56355465 103595.49 -0.093332298
|
||||
100000 0.00035299312 0 0.00035295782 0.56420115 103595.49 -0.093871701
|
||||
101000 0.00042149444 0 0.00042145229 0.56424332 103595.49 -0.094001873
|
||||
102000 0.0004580706 0 0.0004580248 0.56378535 103595.49 -0.093786943
|
||||
103000 0.00046113464 0 0.00046108853 0.56428549 103595.49 -0.093463429
|
||||
104000 0.00047583409 0 0.00047578651 0.5645355 103595.49 -0.093225615
|
||||
105000 0.00048367276 0 0.00048362439 0.56469488 103595.49 -0.092935582
|
||||
106000 0.00046931008 0 0.00046926315 0.56464923 103595.49 -0.09282958
|
||||
107000 0.00046460766 0 0.00046456119 0.56502528 103595.49 -0.093077749
|
||||
108000 0.00046398187 0 0.00046393547 0.56532911 103595.49 -0.09321949
|
||||
109000 0.00047530523 0 0.0004752577 0.56561281 103595.49 -0.093217991
|
||||
110000 0.00048531886 0 0.00048527033 0.56549262 103595.49 -0.092956034
|
||||
111000 0.00049659003 0 0.00049654038 0.56507505 103595.49 -0.092554122
|
||||
112000 0.00050113619 0 0.00050108607 0.56528891 103595.49 -0.092227508
|
||||
113000 0.0005138896 0 0.00051383821 0.56550655 103595.49 -0.092096556
|
||||
114000 0.00052560295 0 0.00052555039 0.56567551 103595.49 -0.09181586
|
||||
115000 0.00054349317 0 0.00054343882 0.56530917 103595.49 -0.090961623
|
||||
116000 0.00056022902 0 0.00056017299 0.56482302 103595.49 -0.090810658
|
||||
117000 0.00055876064 0 0.00055870476 0.56488791 103595.49 -0.090329656
|
||||
118000 0.00056191427 0 0.00056185808 0.56461166 103595.49 -0.090161067
|
||||
119000 0.0005488829 0 0.00054882801 0.56437975 103595.49 -0.090328459
|
||||
120000 0.00054084712 0 0.00054079303 0.564481 103595.49 -0.090602791
|
||||
121000 0.00053717105 0 0.00053711733 0.56481743 103595.49 -0.090309102
|
||||
122000 0.00053834163 0 0.00053828779 0.56385259 103595.49 -0.090433254
|
||||
123000 0.00053319394 0 0.00053314062 0.56335613 103595.49 -0.090723928
|
||||
124000 0.00053127439 0 0.00053122127 0.5631684 103595.49 -0.091178253
|
||||
125000 0.00053624623 0 0.00053619261 0.56387166 103595.49 -0.091701174
|
||||
126000 0.0005253773 0 0.00052532476 0.5639006 103595.49 -0.092033098
|
||||
127000 0.00052459276 0 0.0005245403 0.56361298 103595.49 -0.092219098
|
||||
128000 0.00054030806 0 0.00054025403 0.56307203 103595.49 -0.092196938
|
||||
129000 0.00055474894 0 0.00055469346 0.5622815 103595.49 -0.09178309
|
||||
130000 0.00057391115 0 0.00057385376 0.56244981 103595.49 -0.09170211
|
||||
131000 0.00058650769 0 0.00058644904 0.56195859 103595.49 -0.090649841
|
||||
132000 0.00058529163 0 0.0005852331 0.56162943 103595.49 -0.090167101
|
||||
133000 0.00062544817 0 0.00062538563 0.5594761 103595.49 -0.088989624
|
||||
134000 0.00063457749 0 0.00063451403 0.55917757 103595.49 -0.089702278
|
||||
135000 0.00065371789 0 0.00065365252 0.55885043 103595.49 -0.090030252
|
||||
136000 0.00070050714 0 0.00070043709 0.55854751 103595.49 -0.08960124
|
||||
137000 0.0006750775 0 0.00067501 0.55809563 103595.49 -0.090252473
|
||||
138000 0.00068827043 0 0.0006882016 0.55806674 103595.49 -0.090238994
|
||||
139000 0.00069748073 0 0.00069741098 0.55734587 103595.49 -0.090118549
|
||||
140000 0.00071065284 0 0.00071058177 0.55711669 103595.49 -0.090336074
|
||||
141000 0.00070994204 0 0.00070987104 0.55638115 103595.49 -0.089917062
|
||||
142000 0.00071514386 0 0.00071507235 0.55614391 103595.49 -0.090392071
|
||||
143000 0.00071334667 0 0.00071327533 0.55640687 103595.49 -0.091256718
|
||||
144000 0.00069553102 0 0.00069546147 0.55705702 103595.49 -0.091761396
|
||||
145000 0.00068849503 0 0.00068842618 0.55692035 103595.49 -0.091895738
|
||||
146000 0.00068407816 0 0.00068400975 0.55660026 103595.49 -0.092191588
|
||||
147000 0.00069521557 0 0.00069514605 0.55556456 103595.49 -0.092354739
|
||||
148000 0.00068349281 0 0.00068342446 0.55537498 103595.49 -0.092914636
|
||||
149000 0.00067959644 0 0.00067952848 0.55537695 103595.49 -0.093738463
|
||||
150000 0.00067100566 0 0.00067093856 0.55544851 103595.49 -0.094104003
|
||||
151000 0.00068044722 0 0.00068037917 0.5554655 103595.49 -0.094943239
|
||||
152000 0.00068109012 0 0.00068102201 0.55585405 103595.49 -0.095355111
|
||||
153000 0.00068666181 0 0.00068659314 0.55501583 103595.49 -0.095234652
|
||||
154000 0.00068283406 0 0.00068276578 0.55644996 103595.49 -0.095902623
|
||||
155000 0.00069836346 0 0.00069829363 0.55747472 103595.49 -0.096978444
|
||||
156000 0.00072807264 0 0.00072799984 0.55807332 103595.49 -0.097415305
|
||||
157000 0.00077300609 0 0.00077292879 0.55871196 103595.49 -0.098034508
|
||||
158000 0.00081631408 0 0.00081623245 0.558479 103595.49 -0.09825722
|
||||
159000 0.00079291984 0 0.00079284054 0.55784788 103595.49 -0.097758094
|
||||
160000 0.0008203256 0 0.00082024357 0.55700259 103595.49 -0.097519328
|
||||
161000 0.00081471235 0 0.00081463087 0.556622 103595.49 -0.097787992
|
||||
162000 0.00080692462 0 0.00080684393 0.5566795 103595.49 -0.097210216
|
||||
163000 0.00081149678 0 0.00081141564 0.55596697 103595.49 -0.097517476
|
||||
164000 0.00081577795 0 0.00081569637 0.55569684 103595.49 -0.096908869
|
||||
165000 0.00084604988 0 0.00084596528 0.55492052 103595.49 -0.095481627
|
||||
166000 0.00082198923 0 0.00082190703 0.5552628 103595.49 -0.09477531
|
||||
167000 0.00084903108 0 0.00084894618 0.55477991 103595.49 -0.094758799
|
||||
168000 0.00081613582 0 0.00081605421 0.55508416 103595.49 -0.094804088
|
||||
169000 0.00083341061 0 0.00083332727 0.55476794 103595.49 -0.094519882
|
||||
170000 0.00077835092 0 0.00077827308 0.55516626 103595.49 -0.094843673
|
||||
171000 0.00074843733 0 0.00074836249 0.55417469 103595.49 -0.094731356
|
||||
172000 0.0007425125 0 0.00074243825 0.55431854 103595.49 -0.095174333
|
||||
173000 0.00074144093 0 0.00074136678 0.55429464 103595.49 -0.094982598
|
||||
174000 0.00072375323 0 0.00072368086 0.55421045 103595.49 -0.09489531
|
||||
175000 0.0007270779 0 0.00072700519 0.55413607 103595.49 -0.094197685
|
||||
176000 0.00071114682 0 0.00071107571 0.55342226 103595.49 -0.093083865
|
||||
177000 0.00069325125 0 0.00069318193 0.55441386 103595.49 -0.093289572
|
||||
178000 0.00067686202 0 0.00067679434 0.55504892 103595.49 -0.093512587
|
||||
179000 0.00068326039 0 0.00068319206 0.55519365 103595.49 -0.093974329
|
||||
180000 0.00075070045 0 0.00075062538 0.55415541 103595.49 -0.09327459
|
||||
181000 0.00077670344 0 0.00077662577 0.55328725 103595.49 -0.092373689
|
||||
182000 0.00077422781 0 0.00077415038 0.553131 103595.49 -0.092353979
|
||||
183000 0.00080250542 0 0.00080242517 0.5519122 103595.49 -0.091897169
|
||||
184000 0.00081235214 0 0.00081227091 0.55172769 103595.49 -0.091906209
|
||||
185000 0.00078879443 0 0.00078871555 0.55145488 103595.49 -0.091198506
|
||||
186000 0.00078497746 0 0.00078489896 0.55202944 103595.49 -0.091674987
|
||||
187000 0.00079483049 0 0.000794751 0.55278073 103595.49 -0.092508295
|
||||
188000 0.00079056756 0 0.0007904885 0.55362903 103595.49 -0.092801369
|
||||
189000 0.00079162262 0 0.00079154346 0.55429061 103595.49 -0.092964781
|
||||
190000 0.00078121133 0 0.00078113321 0.55386716 103595.49 -0.092689851
|
||||
191000 0.00076574893 0 0.00076567235 0.5546533 103595.49 -0.093414672
|
||||
192000 0.00076215201 0 0.0007620758 0.55503049 103595.49 -0.093986391
|
||||
193000 0.00075652635 0 0.0007564507 0.55477696 103595.49 -0.094417347
|
||||
194000 0.00075725781 0 0.00075718208 0.55457687 103595.49 -0.094241721
|
||||
195000 0.0007434693 0 0.00074339496 0.55471575 103595.49 -0.094102015
|
||||
196000 0.00073792493 0 0.00073785114 0.55463671 103595.49 -0.094452279
|
||||
197000 0.00074673445 0 0.00074665978 0.55459327 103595.49 -0.09463863
|
||||
198000 0.00072734835 0 0.00072727561 0.55514628 103595.49 -0.094622434
|
||||
199000 0.00071846919 0 0.00071839734 0.55501969 103595.49 -0.094414887
|
||||
200000 0.00072384651 0 0.00072377412 0.55533335 103595.49 -0.094159469
|
||||
Loop time of 443.321 on 1 procs for 200000 steps with 10000 atoms
|
||||
|
||||
Performance: 194892.839 tau/day, 451.141 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 362.28 | 362.28 | 362.28 | 0.0 | 81.72
|
||||
Neigh | 1.737 | 1.737 | 1.737 | 0.0 | 0.39
|
||||
Comm | 5.0082 | 5.0082 | 5.0082 | 0.0 | 1.13
|
||||
Output | 0.01774 | 0.01774 | 0.01774 | 0.0 | 0.00
|
||||
Modify | 64.992 | 64.992 | 64.992 | 0.0 | 14.66
|
||||
Other | | 9.286 | | | 2.09
|
||||
|
||||
Nlocal: 10000.0 ave 10000 max 10000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 487.000 ave 487 max 487 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 34427.0 ave 34427 max 34427 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 34427
|
||||
Ave neighs/atom = 3.4427000
|
||||
Neighbor list builds = 244
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:07:23
|
||||
291
examples/multi/log.30Nov20.powerlaw.intel.4
Normal file
291
examples/multi/log.30Nov20.powerlaw.intel.4
Normal file
@ -0,0 +1,291 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Shear power-law distributed granular particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
dimension 2
|
||||
read_data data.powerlaw
|
||||
Reading data file ...
|
||||
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10000 atoms
|
||||
reading velocities ...
|
||||
10000 velocities
|
||||
read_data CPU = 0.114 seconds
|
||||
change_box all triclinic
|
||||
Changing box ...
|
||||
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||
|
||||
# multi neighbor and comm for efficiency
|
||||
|
||||
neighbor 1 multi
|
||||
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
|
||||
comm_modify mode multi vel yes reduce/multi
|
||||
|
||||
# granular potential
|
||||
|
||||
pair_style granular
|
||||
pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all enforce2d
|
||||
fix 3 all deform 1 xy erate 1e-4
|
||||
|
||||
# dump 1 all custom 20000 dump.granular id x y z radius
|
||||
|
||||
thermo_style custom step temp epair etotal press vol pxy
|
||||
thermo 1000
|
||||
|
||||
timestep 0.005
|
||||
|
||||
run 200000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 164.7888
|
||||
ghost atom cutoff = 164.7888
|
||||
binsize = 82.3944, bins = 4 4 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair granular, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/multi/newton/tri
|
||||
stencil: half/multi/2d/tri
|
||||
bin: multi
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes
|
||||
Step Temp E_pair TotEng Press Volume Pxy
|
||||
0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917
|
||||
1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806
|
||||
2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933
|
||||
3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442
|
||||
4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424
|
||||
5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634
|
||||
6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973
|
||||
7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709
|
||||
8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399
|
||||
9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514
|
||||
10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784
|
||||
11000 0.00018985439 0 0.00018983541 0.58006086 103595.49 -0.028574238
|
||||
12000 0.00018903569 0 0.00018901678 0.5794232 103595.49 -0.031151884
|
||||
13000 0.00019070382 0 0.00019068475 0.57890243 103595.49 -0.033469404
|
||||
14000 0.00019371625 0 0.00019369688 0.5787389 103595.49 -0.035646526
|
||||
15000 0.00019833475 0 0.00019831492 0.57883166 103595.49 -0.037709788
|
||||
16000 0.0002011729 0 0.00020115278 0.57875606 103595.49 -0.039452453
|
||||
17000 0.00020285197 0 0.00020283168 0.5786311 103595.49 -0.040960671
|
||||
18000 0.00020319173 0 0.00020317141 0.57842387 103595.49 -0.042257076
|
||||
19000 0.00020290253 0 0.00020288224 0.57795043 103595.49 -0.043364149
|
||||
20000 0.00020509847 0 0.00020507796 0.57714779 103595.49 -0.04439226
|
||||
21000 0.0002180326 0 0.0002180108 0.57569003 103595.49 -0.044749042
|
||||
22000 0.00020751218 0 0.00020749143 0.57477071 103595.49 -0.045719595
|
||||
23000 0.0002205328 0 0.00022051075 0.57409228 103595.49 -0.047332145
|
||||
24000 0.00022689643 0 0.00022687374 0.57325004 103595.49 -0.048717593
|
||||
25000 0.00025224797 0 0.00025222275 0.57283728 103595.49 -0.050255013
|
||||
26000 0.00025343192 0 0.00025340657 0.5723866 103595.49 -0.051604294
|
||||
27000 0.0002668981 0 0.00026687141 0.57221051 103595.49 -0.052915314
|
||||
28000 0.00027867942 0 0.00027865155 0.57197889 103595.49 -0.053831415
|
||||
29000 0.00028697868 0 0.00028694998 0.57177287 103595.49 -0.054693262
|
||||
30000 0.00028857623 0 0.00028854737 0.5714545 103595.49 -0.055559583
|
||||
31000 0.00029228526 0 0.00029225603 0.57110328 103595.49 -0.056491646
|
||||
32000 0.00029648479 0 0.00029645514 0.57060242 103595.49 -0.057299367
|
||||
33000 0.00030524226 0 0.00030521174 0.57003089 103595.49 -0.058207205
|
||||
34000 0.00031725278 0 0.00031722106 0.56920179 103595.49 -0.059123522
|
||||
35000 0.00032273715 0 0.00032270488 0.56844806 103595.49 -0.06001074
|
||||
36000 0.00033013214 0 0.00033009912 0.56795631 103595.49 -0.06107304
|
||||
37000 0.00033942364 0 0.00033938969 0.56749308 103595.49 -0.062060209
|
||||
38000 0.00035140856 0 0.00035137342 0.56682754 103595.49 -0.062954063
|
||||
39000 0.00036125739 0 0.00036122126 0.56654839 103595.49 -0.063755554
|
||||
40000 0.00037765404 0 0.00037761628 0.56619876 103595.49 -0.064535888
|
||||
41000 0.00040833154 0 0.00040829071 0.56554179 103595.49 -0.064688901
|
||||
42000 0.0004285629 0 0.00042852004 0.56474124 103595.49 -0.06526276
|
||||
43000 0.00042691211 0 0.00042686942 0.56362219 103595.49 -0.065275494
|
||||
44000 0.00040296803 0 0.00040292773 0.56310053 103595.49 -0.065625772
|
||||
45000 0.00040933842 0 0.00040929749 0.56291338 103595.49 -0.066164396
|
||||
46000 0.00040202229 0 0.00040198209 0.56273845 103595.49 -0.066541045
|
||||
47000 0.00038914157 0 0.00038910266 0.562658 103595.49 -0.067357923
|
||||
48000 0.00038428678 0 0.00038424835 0.5627468 103595.49 -0.068230972
|
||||
49000 0.00036912501 0 0.0003690881 0.56261857 103595.49 -0.068794933
|
||||
50000 0.00035203987 0 0.00035200467 0.56258099 103595.49 -0.069290362
|
||||
51000 0.00034400774 0 0.00034397334 0.56237066 103595.49 -0.070274303
|
||||
52000 0.00034126666 0 0.00034123253 0.56221436 103595.49 -0.071744779
|
||||
53000 0.00033563205 0 0.00033559849 0.56195218 103595.49 -0.072836324
|
||||
54000 0.0003304406 0 0.00033040756 0.5623187 103595.49 -0.073999087
|
||||
55000 0.00032742828 0 0.00032739553 0.56225383 103595.49 -0.075066978
|
||||
56000 0.00032696921 0 0.00032693651 0.56285643 103595.49 -0.076445225
|
||||
57000 0.0003316388 0 0.00033160564 0.56354513 103595.49 -0.077683955
|
||||
58000 0.00034325202 0 0.0003432177 0.56416895 103595.49 -0.078839054
|
||||
59000 0.0003433584 0 0.00034332406 0.56490343 103595.49 -0.079658776
|
||||
60000 0.00034732721 0 0.00034729247 0.5651932 103595.49 -0.080573609
|
||||
61000 0.00034978913 0 0.00034975415 0.56517379 103595.49 -0.081109788
|
||||
62000 0.00034995232 0 0.00034991733 0.56534537 103595.49 -0.081491908
|
||||
63000 0.00033854315 0 0.00033850929 0.56582246 103595.49 -0.081894953
|
||||
64000 0.0003260452 0 0.00032601259 0.56583259 103595.49 -0.082790811
|
||||
65000 0.00031763096 0 0.0003175992 0.56576947 103595.49 -0.083707224
|
||||
66000 0.00031761371 0 0.00031758194 0.56548785 103595.49 -0.084243042
|
||||
67000 0.00031503681 0 0.0003150053 0.56483862 103595.49 -0.08451056
|
||||
68000 0.0003036386 0 0.00030360824 0.56444755 103595.49 -0.084967521
|
||||
69000 0.00030398979 0 0.00030395939 0.56436362 103595.49 -0.085541879
|
||||
70000 0.0003281569 0 0.00032812409 0.56372598 103595.49 -0.085287975
|
||||
71000 0.00035614631 0 0.0003561107 0.56322133 103595.49 -0.084970215
|
||||
72000 0.00032709207 0 0.00032705936 0.56231837 103595.49 -0.085540239
|
||||
73000 0.00032545048 0 0.00032541793 0.56278947 103595.49 -0.085940822
|
||||
74000 0.00033285331 0 0.00033282002 0.56288405 103595.49 -0.08695227
|
||||
75000 0.00034622589 0 0.00034619127 0.56198219 103595.49 -0.086349357
|
||||
76000 0.00033654825 0 0.0003365146 0.56183659 103595.49 -0.086892729
|
||||
77000 0.00033550364 0 0.00033547009 0.56197292 103595.49 -0.087018641
|
||||
78000 0.00032680247 0 0.00032676979 0.56183307 103595.49 -0.087097072
|
||||
79000 0.00031624495 0 0.00031621333 0.56161689 103595.49 -0.087358849
|
||||
80000 0.0003124879 0 0.00031245665 0.5618608 103595.49 -0.087165611
|
||||
81000 0.00029451552 0 0.00029448606 0.56211081 103595.49 -0.087652479
|
||||
82000 0.00029588468 0 0.00029585509 0.5628096 103595.49 -0.08832193
|
||||
83000 0.00030483225 0 0.00030480177 0.56261673 103595.49 -0.088586937
|
||||
84000 0.00029556003 0 0.00029553047 0.56272654 103595.49 -0.089434209
|
||||
85000 0.00030506369 0 0.00030503319 0.5627918 103595.49 -0.089830152
|
||||
86000 0.00030015302 0 0.00030012301 0.56240656 103595.49 -0.090100219
|
||||
87000 0.00030322942 0 0.0003031991 0.56243997 103595.49 -0.090327187
|
||||
88000 0.00030569181 0 0.00030566124 0.56236256 103595.49 -0.090734148
|
||||
89000 0.00031220625 0 0.00031217503 0.5621542 103595.49 -0.090898044
|
||||
90000 0.00032214966 0 0.00032211744 0.56209534 103595.49 -0.090909986
|
||||
91000 0.00033884101 0 0.00033880712 0.56191673 103595.49 -0.090818046
|
||||
92000 0.00033260559 0 0.00033257233 0.56172194 103595.49 -0.090647169
|
||||
93000 0.00032732547 0 0.00032729274 0.5619652 103595.49 -0.090575176
|
||||
94000 0.00033817734 0 0.00033814352 0.56155436 103595.49 -0.090700379
|
||||
95000 0.00033009649 0 0.00033006348 0.56147407 103595.49 -0.090940641
|
||||
96000 0.00032882782 0 0.00032879494 0.56191577 103595.49 -0.091469188
|
||||
97000 0.00032856078 0 0.00032852793 0.56271585 103595.49 -0.092256803
|
||||
98000 0.00033030749 0 0.00033027446 0.56340097 103595.49 -0.093188128
|
||||
99000 0.00033611507 0 0.00033608146 0.56375754 103595.49 -0.093539699
|
||||
100000 0.00034990568 0 0.00034987069 0.56450225 103595.49 -0.093951624
|
||||
101000 0.00044441478 0 0.00044437034 0.56437908 103595.49 -0.094161976
|
||||
102000 0.00045403284 0 0.00045398743 0.56433013 103595.49 -0.093900071
|
||||
103000 0.00045412317 0 0.00045407776 0.56468095 103595.49 -0.093670567
|
||||
104000 0.00046494637 0 0.00046489988 0.56478442 103595.49 -0.093397211
|
||||
105000 0.00047962271 0 0.00047957475 0.56482329 103595.49 -0.093141318
|
||||
106000 0.00046840864 0 0.0004683618 0.56494359 103595.49 -0.092994704
|
||||
107000 0.00046432422 0 0.00046427779 0.56543377 103595.49 -0.093135897
|
||||
108000 0.0004655443 0 0.00046549774 0.5656898 103595.49 -0.093383926
|
||||
109000 0.0004863785 0 0.00048632986 0.5657434 103595.49 -0.093328929
|
||||
110000 0.00048804324 0 0.00048799443 0.5656147 103595.49 -0.09302382
|
||||
111000 0.00050352097 0 0.00050347062 0.56529279 103595.49 -0.092461373
|
||||
112000 0.00050474509 0 0.00050469461 0.56537494 103595.49 -0.092212501
|
||||
113000 0.0005125299 0 0.00051247865 0.56547326 103595.49 -0.092304578
|
||||
114000 0.00052700168 0 0.00052694898 0.56568076 103595.49 -0.092013613
|
||||
115000 0.00054217865 0 0.00054212444 0.56526328 103595.49 -0.091011537
|
||||
116000 0.00055122699 0 0.00055117186 0.56489606 103595.49 -0.090688925
|
||||
117000 0.00055802701 0 0.00055797121 0.56458767 103595.49 -0.090385903
|
||||
118000 0.00055416633 0 0.00055411091 0.56433528 103595.49 -0.090454192
|
||||
119000 0.00055519395 0 0.00055513843 0.56411926 103595.49 -0.090495063
|
||||
120000 0.0005535194 0 0.00055346405 0.56424847 103595.49 -0.090915789
|
||||
121000 0.00054781097 0 0.00054775619 0.56443756 103595.49 -0.090687173
|
||||
122000 0.00054528815 0 0.00054523362 0.56401103 103595.49 -0.090443168
|
||||
123000 0.0005456223 0 0.00054556773 0.56376875 103595.49 -0.090277114
|
||||
124000 0.00054080131 0 0.00054074723 0.563306 103595.49 -0.091297668
|
||||
125000 0.00054597 0 0.0005459154 0.56387718 103595.49 -0.091522394
|
||||
126000 0.000544669 0 0.00054461453 0.56318185 103595.49 -0.091100523
|
||||
127000 0.00054592361 0 0.00054586902 0.56328758 103595.49 -0.091299714
|
||||
128000 0.00056246325 0 0.000562407 0.56296852 103595.49 -0.091491356
|
||||
129000 0.00057655488 0 0.00057649723 0.56242057 103595.49 -0.091474584
|
||||
130000 0.00060363901 0 0.00060357864 0.56182729 103595.49 -0.091367782
|
||||
131000 0.00060590757 0 0.00060584698 0.56115572 103595.49 -0.090594163
|
||||
132000 0.00061689139 0 0.0006168297 0.56029248 103595.49 -0.089857939
|
||||
133000 0.00063288773 0 0.00063282444 0.55971427 103595.49 -0.08954619
|
||||
134000 0.00064153654 0 0.00064147238 0.55929877 103595.49 -0.089860563
|
||||
135000 0.00065473169 0 0.00065466622 0.5590797 103595.49 -0.089932375
|
||||
136000 0.0006814182 0 0.00068135006 0.55797116 103595.49 -0.08929097
|
||||
137000 0.00068344911 0 0.00068338077 0.55796657 103595.49 -0.089644888
|
||||
138000 0.00071510067 0 0.00071502916 0.55752379 103595.49 -0.089734088
|
||||
139000 0.00074772787 0 0.0007476531 0.55740054 103595.49 -0.089968295
|
||||
140000 0.00072706311 0 0.0007269904 0.55659113 103595.49 -0.090370844
|
||||
141000 0.0007179286 0 0.00071785681 0.55659012 103595.49 -0.089976688
|
||||
142000 0.00072587657 0 0.00072580399 0.55589037 103595.49 -0.090532153
|
||||
143000 0.00074470967 0 0.0007446352 0.55553128 103595.49 -0.091019969
|
||||
144000 0.00071737422 0 0.00071730248 0.55555994 103595.49 -0.090926005
|
||||
145000 0.00070363824 0 0.00070356787 0.55548936 103595.49 -0.0912353
|
||||
146000 0.00069604487 0 0.00069597527 0.55540516 103595.49 -0.091656715
|
||||
147000 0.00070047196 0 0.00070040191 0.55466746 103595.49 -0.092101291
|
||||
148000 0.00069764904 0 0.00069757927 0.55460283 103595.49 -0.092334573
|
||||
149000 0.00068884707 0 0.00068877819 0.55462796 103595.49 -0.0928736
|
||||
150000 0.00067704593 0 0.00067697823 0.55520015 103595.49 -0.093512131
|
||||
151000 0.00067702275 0 0.00067695505 0.55530068 103595.49 -0.094127311
|
||||
152000 0.000690717 0 0.00069064792 0.55432538 103595.49 -0.094248615
|
||||
153000 0.00067758953 0 0.00067752177 0.55460446 103595.49 -0.094839924
|
||||
154000 0.00067748542 0 0.00067741767 0.55532529 103595.49 -0.095832411
|
||||
155000 0.00068723442 0 0.0006871657 0.55637763 103595.49 -0.096838207
|
||||
156000 0.00071590663 0 0.00071583504 0.5569485 103595.49 -0.097686166
|
||||
157000 0.00078378647 0 0.0007837081 0.55755381 103595.49 -0.097968527
|
||||
158000 0.00080144334 0 0.00080136319 0.55741023 103595.49 -0.098119361
|
||||
159000 0.00079183165 0 0.00079175247 0.55756142 103595.49 -0.097925888
|
||||
160000 0.00081212358 0 0.00081204237 0.55669124 103595.49 -0.098171108
|
||||
161000 0.00082903843 0 0.00082895553 0.55608918 103595.49 -0.097827206
|
||||
162000 0.00084257416 0 0.0008424899 0.5560239 103595.49 -0.096775743
|
||||
163000 0.00086279615 0 0.00086270987 0.55550215 103595.49 -0.095981927
|
||||
164000 0.00092139657 0 0.00092130443 0.55395137 103595.49 -0.095215338
|
||||
165000 0.00095519936 0 0.00095510384 0.55376787 103595.49 -0.0945666
|
||||
166000 0.00092201276 0 0.00092192056 0.55373794 103595.49 -0.093531233
|
||||
167000 0.0008525194 0 0.00085243415 0.55375862 103595.49 -0.09389901
|
||||
168000 0.00081977785 0 0.00081969587 0.5536646 103595.49 -0.093829746
|
||||
169000 0.00079692467 0 0.00079684497 0.55416599 103595.49 -0.094433271
|
||||
170000 0.00077787798 0 0.0007778002 0.55416629 103595.49 -0.095043413
|
||||
171000 0.0007651362 0 0.00076505969 0.55418872 103595.49 -0.095212376
|
||||
172000 0.00074631438 0 0.00074623975 0.55403881 103595.49 -0.095463949
|
||||
173000 0.00074431288 0 0.00074423845 0.55415801 103595.49 -0.095319615
|
||||
174000 0.00073924649 0 0.00073917257 0.55373682 103595.49 -0.094724272
|
||||
175000 0.00070973165 0 0.00070966068 0.55393569 103595.49 -0.094201112
|
||||
176000 0.00069820766 0 0.00069813784 0.55341229 103595.49 -0.093530469
|
||||
177000 0.00070922657 0 0.00070915564 0.55282781 103595.49 -0.093282587
|
||||
178000 0.00073688566 0 0.00073681197 0.55223248 103595.49 -0.092190554
|
||||
179000 0.00072455886 0 0.0007244864 0.55244288 103595.49 -0.09182393
|
||||
180000 0.00071894558 0 0.00071887369 0.55281517 103595.49 -0.092177032
|
||||
181000 0.00071752475 0 0.000717453 0.55297293 103595.49 -0.09230934
|
||||
182000 0.00072247421 0 0.00072240196 0.55287294 103595.49 -0.092465908
|
||||
183000 0.00070596821 0 0.00070589761 0.5526242 103595.49 -0.092013313
|
||||
184000 0.00072460909 0 0.00072453663 0.55230817 103595.49 -0.092211243
|
||||
185000 0.00072499917 0 0.00072492667 0.55273387 103595.49 -0.092920761
|
||||
186000 0.00072852698 0 0.00072845413 0.55358929 103595.49 -0.093428623
|
||||
187000 0.00072515668 0 0.00072508417 0.55336733 103595.49 -0.093440126
|
||||
188000 0.00071355728 0 0.00071348593 0.55408468 103595.49 -0.094819333
|
||||
189000 0.00071703212 0 0.00071696042 0.55424355 103595.49 -0.096198144
|
||||
190000 0.00071808849 0 0.00071801668 0.55504118 103595.49 -0.097199842
|
||||
191000 0.00072458142 0 0.00072450896 0.55493515 103595.49 -0.097564772
|
||||
192000 0.00071472504 0 0.00071465357 0.55572657 103595.49 -0.097663072
|
||||
193000 0.00070803966 0 0.00070796886 0.55546116 103595.49 -0.097306162
|
||||
194000 0.00068236077 0 0.00068229254 0.55581155 103595.49 -0.097141594
|
||||
195000 0.00067304613 0 0.00067297882 0.55559507 103595.49 -0.096646489
|
||||
196000 0.00066680808 0 0.0006667414 0.55512029 103595.49 -0.096241456
|
||||
197000 0.00065829161 0 0.00065822578 0.55545375 103595.49 -0.095808778
|
||||
198000 0.0006617611 0 0.00066169492 0.55551074 103595.49 -0.095423531
|
||||
199000 0.00066805655 0 0.00066798975 0.55581298 103595.49 -0.095287337
|
||||
200000 0.00067263902 0 0.00067257175 0.55601669 103595.49 -0.095551006
|
||||
Loop time of 145.127 on 4 procs for 200000 steps with 10000 atoms
|
||||
|
||||
Performance: 595339.507 tau/day, 1378.101 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 57.89 | 91.946 | 113.82 | 229.7 | 63.36
|
||||
Neigh | 0.34276 | 0.48607 | 0.56708 | 13.1 | 0.33
|
||||
Comm | 6.569 | 28.916 | 63.505 | 417.0 | 19.92
|
||||
Output | 0.0087178 | 0.011935 | 0.01563 | 2.3 | 0.01
|
||||
Modify | 10.432 | 16.495 | 20.378 | 97.7 | 11.37
|
||||
Other | | 7.272 | | | 5.01
|
||||
|
||||
Nlocal: 2500.00 ave 2990 max 1652 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 228.000 ave 254 max 198 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 8611.25 ave 10364 max 5676 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 34445
|
||||
Ave neighs/atom = 3.4445000
|
||||
Neighbor list builds = 241
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:02:25
|
||||
@ -62,7 +62,7 @@ delete_atoms overlap 0.5 small big
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neighbor 0.3 multi
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify mode multi group big vel yes
|
||||
|
||||
Reference in New Issue
Block a user