add/update USER-BROWNIAN example inputs and logs
This commit is contained in:
Axel Kohlmeyer
@ -1,19 +1,15 @@
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##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
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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 gamma_t equal 1.0
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variable temp 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 seed equal 1974019
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variable fp equal 4.0
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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 ${gamma_t}_${temp}_${fp}
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log log_${params}_2d.lammps.log
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units lj
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units lj
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dimension 2
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dimension 2
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newton off
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newton off
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lattice sq 0.4
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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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region box block -16 16 -16 16 -0.2 0.2
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create_box 1 box
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create_box 1 box
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@ -21,16 +17,13 @@ create_atoms 1 box
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mass * 1.0
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mass * 1.0
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velocity all create 1.0 1 loop geom
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velocity all create 1.0 1 loop geom
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neighbor 1.0 bin
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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neigh_modify every 1 delay 1 check yes
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pair_style none
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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 ${temp} ${seed} gamma_t ${gamma_t}
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fix vel all propel/self velocity ${fp}
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fix vel all propel/self velocity ${fp}
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fix 2 all enforce2d
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fix 2 all enforce2d
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fix_modify vel virial yes
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fix_modify vel virial yes
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@ -40,24 +33,21 @@ thermo_style custom step temp epair c_press
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#equilibration
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#equilibration
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timestep 0.0000000001
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timestep 0.0000000001
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thermo 50001
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thermo 500
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run 50000
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run 5000
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reset_timestep 0
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reset_timestep 0
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#initialisation for the main run
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#initialisation for the main run
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# MSD
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# MSD
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compute msd all 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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thermo_style custom step temp epair c_msd[*] c_press
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timestep 0.00001
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timestep 0.00001
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thermo 1000
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thermo 1000
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# main run
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# main run
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run 120000
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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
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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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 @@
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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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2 by 2 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 1.9862591e+10 0 -0.32013566
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1000 2.0093184e+10 0 -0.36609742
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1500 1.9562283e+10 0 -0.53349351
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2000 1.9903977e+10 0 0.63783249
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2500 2.0260128e+10 0 0.30046413
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3000 1.9948065e+10 0 -0.63093105
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3500 1.9507486e+10 0 0.48762848
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4000 2.0049087e+10 0 0.40289309
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4500 1.9975813e+10 0 0.57649363
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5000 2.0129291e+10 0 -0.41288352
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Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms
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Performance: 0.181 tau/day, 20924.952 timesteps/s
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92.6% CPU use with 4 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 | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34
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Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13
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Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27
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Other | | 0.06992 | | | 29.26
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 33.0000 ave 33 max 33 min
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Histogram: 4 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: 4 0 0 0 0 0 0 0 0 0
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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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|
||||||
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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 2.0109634e+10 0 0 0 0 0 -0.41288352
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1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126
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2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705
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3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601
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4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473
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5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791
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6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467
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7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646
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8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452
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9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228
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10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262
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||||||
|
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
|
||||||
@ -1,244 +0,0 @@
|
|||||||
units lj
|
|
||||||
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 = 0.001 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 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}
|
|
||||||
fix step all brownian 1 1974019 gamma_t 1
|
|
||||||
fix vel all propel/self velocity ${fp}
|
|
||||||
fix vel all propel/self velocity 4
|
|
||||||
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 50001
|
|
||||||
run 50000
|
|
||||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118)
|
|
||||||
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
|
|
||||||
50000 2.0329082e+10 0 -0.30450754
|
|
||||||
Loop time of 1.76045 on 1 procs for 50000 steps with 1024 atoms
|
|
||||||
|
|
||||||
Performance: 0.245 tau/day, 28401.873 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 | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.008736 | 0.008736 | 0.008736 | 0.0 | 0.50
|
|
||||||
Output | 2.3562e-05 | 2.3562e-05 | 2.3562e-05 | 0.0 | 0.00
|
|
||||||
Modify | 1.6284 | 1.6284 | 1.6284 | 0.0 | 92.50
|
|
||||||
Other | | 0.1233 | | | 7.00
|
|
||||||
|
|
||||||
Nlocal: 1024.00 ave 1024 max 1024 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 65.0000 ave 65 max 65 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
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
|
||||||
|
|
||||||
# MSD
|
|
||||||
compute msd all msd
|
|
||||||
|
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*] c_press
|
|
||||||
|
|
||||||
|
|
||||||
timestep 0.00001
|
|
||||||
thermo 1000
|
|
||||||
|
|
||||||
# main run
|
|
||||||
run 120000
|
|
||||||
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 Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
|
||||||
0 2.0329082e+10 0 0 0 0 0 -0.30450754
|
|
||||||
1000 194002.24 0 0.019541352 0.020412616 0 0.039953968 0.17960144
|
|
||||||
2000 201170.68 0 0.037773433 0.040755027 0 0.078528461 0.030184783
|
|
||||||
3000 200206.8 0 0.058949662 0.060726886 0 0.11967655 0.080592855
|
|
||||||
4000 205243 0 0.084357492 0.084713582 0 0.16907107 -0.9284229
|
|
||||||
5000 201741.41 0 0.1024163 0.10453135 0 0.20694765 0.31035655
|
|
||||||
6000 203143.61 0 0.12337925 0.12397645 0 0.2473557 -0.88772072
|
|
||||||
7000 202627.98 0 0.14537908 0.14173625 0 0.28711534 0.17510592
|
|
||||||
8000 200688.93 0 0.15993736 0.16450382 0 0.32444118 0.20926033
|
|
||||||
9000 200360.25 0 0.18277138 0.18597743 0 0.36874881 0.14728415
|
|
||||||
10000 203691.46 0 0.20588386 0.20467547 0 0.41055933 -0.041058877
|
|
||||||
11000 203028.99 0 0.2282616 0.21792715 0 0.44618875 0.14648625
|
|
||||||
12000 195738.49 0 0.24584925 0.22877733 0 0.47462658 0.11242329
|
|
||||||
13000 198977.93 0 0.26808832 0.25467835 0 0.52276667 -0.82500263
|
|
||||||
14000 193395.28 0 0.29074728 0.27404624 0 0.56479352 0.29664298
|
|
||||||
15000 200408 0 0.30241331 0.29063643 0 0.59304975 0.22506685
|
|
||||||
16000 194570.8 0 0.32914382 0.30896611 0 0.63810992 -0.011781021
|
|
||||||
17000 201699.18 0 0.34741469 0.33153019 0 0.67894488 -0.073195501
|
|
||||||
18000 198665.14 0 0.35708615 0.35032716 0 0.7074133 0.33684482
|
|
||||||
19000 201011.15 0 0.37328322 0.36518777 0 0.73847099 -0.20884796
|
|
||||||
20000 201387.99 0 0.39484415 0.3783921 0 0.77323625 -0.30200013
|
|
||||||
21000 202952.38 0 0.41838333 0.3958867 0 0.81427003 -0.98801165
|
|
||||||
22000 205150.98 0 0.44071908 0.42001514 0 0.86073422 -0.65548109
|
|
||||||
23000 200164.9 0 0.46156041 0.44411636 0 0.90567677 0.24186828
|
|
||||||
24000 196027.89 0 0.4834982 0.46586728 0 0.94936548 -0.43593925
|
|
||||||
25000 198438.08 0 0.50328321 0.4865808 0 0.98986402 -0.25516412
|
|
||||||
26000 200569.69 0 0.52535125 0.52102617 0 1.0463774 -0.41486705
|
|
||||||
27000 200598.31 0 0.52958053 0.53142647 0 1.061007 0.011109738
|
|
||||||
28000 205592.24 0 0.54694416 0.5464941 0 1.0934383 -0.18134038
|
|
||||||
29000 199085.55 0 0.57222754 0.57188852 0 1.1441161 -0.46788121
|
|
||||||
30000 201398.39 0 0.59813146 0.58520822 0 1.1833397 -0.15341079
|
|
||||||
31000 197674.44 0 0.61191002 0.60572867 0 1.2176387 0.25394145
|
|
||||||
32000 205188.42 0 0.63435682 0.63745001 0 1.2718068 0.26362999
|
|
||||||
33000 202316.72 0 0.66509392 0.65462302 0 1.3197169 -0.37062797
|
|
||||||
34000 200673.31 0 0.67923697 0.69170315 0 1.3709401 -0.36342828
|
|
||||||
35000 199626.58 0 0.71214435 0.71976006 0 1.4319044 0.14520308
|
|
||||||
36000 206317.51 0 0.73098443 0.75421862 0 1.4852031 -0.049274455
|
|
||||||
37000 200878.1 0 0.75404669 0.77976535 0 1.533812 -0.020890744
|
|
||||||
38000 204399.3 0 0.77905716 0.80048467 0 1.5795418 0.41855233
|
|
||||||
39000 194807.41 0 0.80901097 0.83413027 0 1.6431412 0.061887194
|
|
||||||
40000 197736.05 0 0.82530638 0.85259329 0 1.6778997 -0.21390647
|
|
||||||
41000 196234.62 0 0.84399769 0.87823172 0 1.7222294 -0.069449607
|
|
||||||
42000 202916.17 0 0.84692321 0.90553215 0 1.7524554 0.014080553
|
|
||||||
43000 199860.49 0 0.87526292 0.92743523 0 1.8026981 0.14037107
|
|
||||||
44000 195023.53 0 0.88991314 0.95932182 0 1.849235 -0.33208549
|
|
||||||
45000 195356.87 0 0.91402747 0.98447964 0 1.8985071 -0.54494657
|
|
||||||
46000 208076.31 0 0.92947502 1.0151107 0 1.9445857 -0.62483899
|
|
||||||
47000 196855.73 0 0.94724593 1.0592619 0 2.0065078 -0.20412571
|
|
||||||
48000 201398.95 0 0.98527482 1.0801565 0 2.0654313 -0.12234755
|
|
||||||
49000 196643.46 0 0.9999414 1.115902 0 2.1158434 -0.014252649
|
|
||||||
50000 195863.57 0 1.0150887 1.1141794 0 2.1292681 0.75335013
|
|
||||||
51000 206236.4 0 1.060301 1.1367091 0 2.1970101 -0.22091636
|
|
||||||
52000 202457.92 0 1.0661594 1.1431793 0 2.2093387 0.20119657
|
|
||||||
53000 200285.87 0 1.0911263 1.1652507 0 2.256377 0.64981185
|
|
||||||
54000 192647.27 0 1.1240369 1.1911613 0 2.3151982 -0.31991262
|
|
||||||
55000 203771.16 0 1.1340164 1.2059129 0 2.3399293 -0.69282837
|
|
||||||
56000 208567.7 0 1.1644643 1.2358751 0 2.4003394 -0.31413258
|
|
||||||
57000 197231.77 0 1.1817765 1.2580471 0 2.4398236 0.0033296714
|
|
||||||
58000 203466.84 0 1.2256115 1.297949 0 2.5235605 0.5978746
|
|
||||||
59000 204071.73 0 1.2635225 1.3217703 0 2.5852928 0.080439812
|
|
||||||
60000 204497.78 0 1.280816 1.3529427 0 2.6337587 -0.13596951
|
|
||||||
61000 201581.53 0 1.3062524 1.3840896 0 2.6903421 0.2402402
|
|
||||||
62000 201808.73 0 1.3158468 1.40441 0 2.7202568 -0.49735816
|
|
||||||
63000 195485.7 0 1.3246003 1.4115588 0 2.7361591 -0.034708225
|
|
||||||
64000 203289.43 0 1.3515942 1.4270935 0 2.7786877 -0.47288139
|
|
||||||
65000 198360.38 0 1.3655219 1.4410644 0 2.8065863 -0.60256944
|
|
||||||
66000 207037.46 0 1.4024293 1.447203 0 2.8496323 0.19886918
|
|
||||||
67000 197118.92 0 1.4400601 1.4746068 0 2.914667 0.53432407
|
|
||||||
68000 202323.37 0 1.4737023 1.4757925 0 2.9494948 -0.50123703
|
|
||||||
69000 202679.62 0 1.4996722 1.4982292 0 2.9979014 -0.36930796
|
|
||||||
70000 197067.46 0 1.5202881 1.5079024 0 3.0281905 0.20627183
|
|
||||||
71000 201481.55 0 1.5292493 1.5243374 0 3.0535868 0.1664502
|
|
||||||
72000 197565.37 0 1.5649605 1.5415579 0 3.1065184 0.1538837
|
|
||||||
73000 198996.68 0 1.5823587 1.5687541 0 3.1511128 0.33347453
|
|
||||||
74000 196056.36 0 1.5876207 1.5880262 0 3.1756469 0.51039007
|
|
||||||
75000 196383.82 0 1.6238368 1.6126393 0 3.2364761 0.58359751
|
|
||||||
76000 198050.9 0 1.6332373 1.6444992 0 3.2777365 -0.30732735
|
|
||||||
77000 198867.35 0 1.6713412 1.6649495 0 3.3362907 -0.77019295
|
|
||||||
78000 197809.01 0 1.7072475 1.6978103 0 3.4050578 0.062786188
|
|
||||||
79000 198410.74 0 1.7408508 1.7258001 0 3.4666509 0.13736398
|
|
||||||
80000 203417.5 0 1.757256 1.748869 0 3.506125 -0.020989175
|
|
||||||
81000 195062.76 0 1.7608203 1.7602204 0 3.5210407 0.013727312
|
|
||||||
82000 200632.52 0 1.7755665 1.7921425 0 3.567709 -0.052325244
|
|
||||||
83000 191576.45 0 1.7959579 1.8241176 0 3.6200755 -0.20352178
|
|
||||||
84000 200502.95 0 1.8249302 1.8426066 0 3.6675369 -0.38424345
|
|
||||||
85000 201308.33 0 1.8545228 1.8747626 0 3.7292854 0.68968471
|
|
||||||
86000 203836.21 0 1.8649352 1.9007982 0 3.7657335 -0.56168571
|
|
||||||
87000 208433.36 0 1.8740109 1.9350895 0 3.8091003 0.14026532
|
|
||||||
88000 198009.97 0 1.9059077 1.9537513 0 3.859659 0.017064255
|
|
||||||
89000 200694.98 0 1.9312351 1.9704954 0 3.9017306 -0.19090346
|
|
||||||
90000 200436.01 0 1.9567279 2.0115534 0 3.9682814 0.48791684
|
|
||||||
91000 201810.57 0 1.9784333 2.0255054 0 4.0039386 -0.21421409
|
|
||||||
92000 208365.35 0 2.0050623 2.049849 0 4.0549113 0.30465483
|
|
||||||
93000 197213.15 0 2.017481 2.0689265 0 4.0864075 0.22419309
|
|
||||||
94000 201428.76 0 2.0426301 2.0972527 0 4.1398828 -0.24230583
|
|
||||||
95000 198472.77 0 2.0677457 2.111042 0 4.1787877 0.13071029
|
|
||||||
96000 201070.22 0 2.1019013 2.1226741 0 4.2245754 0.15711614
|
|
||||||
97000 197899.22 0 2.1019041 2.1575764 0 4.2594805 -0.18586251
|
|
||||||
98000 196679.32 0 2.1162285 2.170629 0 4.2868575 -0.34056846
|
|
||||||
99000 197724.36 0 2.1326497 2.1886854 0 4.321335 0.58967646
|
|
||||||
100000 205354.32 0 2.1612412 2.2209085 0 4.3821498 0.044930992
|
|
||||||
101000 201516.54 0 2.1954542 2.2365787 0 4.4320329 0.065295032
|
|
||||||
102000 204976.1 0 2.2029662 2.2694803 0 4.4724465 0.11481479
|
|
||||||
103000 194476.8 0 2.2257884 2.2955314 0 4.5213197 -0.11610949
|
|
||||||
104000 203736.97 0 2.2268211 2.2907985 0 4.5176196 0.015187894
|
|
||||||
105000 196842.81 0 2.2620115 2.3381811 0 4.6001926 0.32154947
|
|
||||||
106000 202018.95 0 2.2836727 2.3560537 0 4.6397264 0.33256726
|
|
||||||
107000 198280.55 0 2.2802504 2.3840825 0 4.6643329 0.50865119
|
|
||||||
108000 198415.05 0 2.299079 2.402819 0 4.7018979 0.028090763
|
|
||||||
109000 214429.79 0 2.326329 2.4071902 0 4.7335192 0.33519083
|
|
||||||
110000 206059.4 0 2.3452258 2.431054 0 4.7762798 0.012116372
|
|
||||||
111000 198624.14 0 2.3484889 2.4352672 0 4.7837561 -0.35529818
|
|
||||||
112000 201890.76 0 2.3810208 2.4718016 0 4.8528225 -0.55980456
|
|
||||||
113000 199303.2 0 2.4011131 2.5070887 0 4.9082018 0.21744731
|
|
||||||
114000 207834.3 0 2.4341043 2.5221162 0 4.9562204 0.11696186
|
|
||||||
115000 202055.54 0 2.4714851 2.5576047 0 5.0290898 -0.42272945
|
|
||||||
116000 203298.5 0 2.5043401 2.5626771 0 5.0670173 0.17688701
|
|
||||||
117000 194028.49 0 2.5273873 2.5945816 0 5.1219689 -0.70088882
|
|
||||||
118000 201726.79 0 2.5475583 2.6532013 0 5.2007596 0.22458895
|
|
||||||
119000 200037.8 0 2.599892 2.6701733 0 5.2700653 0.036916228
|
|
||||||
120000 194969.52 0 2.623779 2.6921819 0 5.3159609 -0.6067451
|
|
||||||
Loop time of 4.32114 on 1 procs for 120000 steps with 1024 atoms
|
|
||||||
|
|
||||||
Performance: 23993.668 tau/day, 27770.449 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 | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Neigh | 0.00029646 | 0.00029646 | 0.00029646 | 0.0 | 0.01
|
|
||||||
Comm | 0.0079174 | 0.0079174 | 0.0079174 | 0.0 | 0.18
|
|
||||||
Output | 0.0044738 | 0.0044738 | 0.0044738 | 0.0 | 0.10
|
|
||||||
Modify | 3.9818 | 3.9818 | 3.9818 | 0.0 | 92.15
|
|
||||||
Other | | 0.3267 | | | 7.56
|
|
||||||
|
|
||||||
Nlocal: 1024.00 ave 1024 max 1024 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 = 153
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
|
|
||||||
Total wall time: 0:00:06
|
|
||||||
@ -1,72 +1,54 @@
|
|||||||
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
##### 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 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}
|
|
||||||
|
|
||||||
|
|
||||||
log log_${params}_2d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style hybrid dipole ellipsoid
|
atom_style hybrid dipole ellipsoid
|
||||||
dimension 2
|
dimension 2
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sq 0.4
|
lattice sq 0.4
|
||||||
region box block -30 30 -30 30 -0.2 0.2
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
mass * 1.0
|
mass * 1.0
|
||||||
set type * dipole/random ${seed} 1.0
|
set type * dipole/random ${seed} 1.0
|
||||||
set type * shape 3.0 1.0 1.0
|
set type * shape 3.0 1.0 1.0
|
||||||
set type * quat/random ${seed}
|
set type * quat/random ${seed}
|
||||||
velocity all create 1.0 1 loop geom
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pair_style none
|
pair_style none
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
||||||
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
||||||
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
||||||
dipole 1.0 0.0 0.0
|
dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
#initialisation for the main run
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*]
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
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
|
timestep 0.00001
|
||||||
thermo 50
|
thermo 100
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 30000
|
run 3000
|
||||||
|
|||||||
@ -1,73 +1,54 @@
|
|||||||
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
##### 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 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}
|
|
||||||
|
|
||||||
|
|
||||||
log log_${params}_3d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style hybrid dipole ellipsoid
|
atom_style hybrid dipole ellipsoid
|
||||||
dimension 3
|
dimension 3
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sc 0.4
|
lattice sc 0.4
|
||||||
region box block -8 8 -8 8 -8 8
|
region box block -8 8 -8 8 -8 8
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
mass * 1.0
|
mass * 1.0
|
||||||
set type * dipole/random ${seed} 1.0
|
set type * dipole/random ${seed} 1.0
|
||||||
set type * shape 3.0 1.0 1.0
|
set type * shape 3.0 1.0 1.0
|
||||||
set type * quat/random ${seed}
|
set type * quat/random ${seed}
|
||||||
velocity all create 1.0 1 loop geom
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pair_style none
|
pair_style none
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
||||||
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
||||||
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
||||||
dipole 1.0 0.0 0.0
|
dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
#initialisation for the main run
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*]
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
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
|
timestep 0.00001
|
||||||
thermo 50
|
thermo 100
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 30000
|
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
|
||||||
@ -1,25 +1,16 @@
|
|||||||
##### dynamics of non-interacting point particles in 2D #####
|
##### dynamics of non-interacting point particles in 2D #####
|
||||||
|
|
||||||
variable rng string gaussian
|
variable rng string gaussian
|
||||||
variable seed string 198098
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
|
||||||
|
|
||||||
variable temp string 5.0
|
|
||||||
|
|
||||||
variable gamma_t string 1.0
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
variable params string ${rng}_${temp}_${gamma_t}
|
|
||||||
|
|
||||||
|
|
||||||
log log_${params}_2d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style atomic
|
atom_style atomic
|
||||||
dimension 2
|
dimension 2
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sq 0.4
|
lattice sq 0.4
|
||||||
region box block -30 30 -30 30 -0.2 0.2
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
@ -27,36 +18,26 @@ create_atoms 1 box
|
|||||||
mass * 1.0
|
mass * 1.0
|
||||||
velocity all create 1.0 1 loop geom
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pair_style none
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
fix 1 all brownian ${temp} ${seed} rng ${rng} &
|
|
||||||
gamma_t ${gamma_t}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
#initialisation for the main run
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*]
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
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
|
timestep 0.00001
|
||||||
thermo 50
|
thermo 100
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 30000
|
run 3000
|
||||||
|
|
||||||
|
|||||||
@ -1,24 +1,16 @@
|
|||||||
##### overdamped dynamics of non-interacting point particles in 3D #####
|
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||||
|
|
||||||
variable rng string gaussian
|
variable rng string gaussian
|
||||||
variable seed string 198098
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
|
||||||
|
|
||||||
variable temp string 5.0
|
|
||||||
|
|
||||||
variable gamma_t string 1.0
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
variable params string ${rng}_${temp}_${gamma_t}
|
|
||||||
|
|
||||||
log log_${params}_3d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style atomic
|
atom_style atomic
|
||||||
dimension 3
|
dimension 3
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sc 0.4
|
lattice sc 0.4
|
||||||
region box block -8 8 -8 8 -8 8
|
region box block -8 8 -8 8 -8 8
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
@ -26,36 +18,27 @@ create_atoms 1 box
|
|||||||
mass * 1.0
|
mass * 1.0
|
||||||
velocity all create 1.0 1 loop geom
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pair_style none
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
fix 1 all brownian ${temp} ${seed} rng ${rng} &
|
|
||||||
gamma_t ${gamma_t}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
#initialisation for the main run
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*]
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
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
|
timestep 0.00001
|
||||||
thermo 50
|
thermo 100
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 30000
|
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
|
||||||
@ -1,27 +1,17 @@
|
|||||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||||
|
|
||||||
variable rng string uniform
|
variable rng string uniform
|
||||||
variable seed string 198098
|
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 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}
|
|
||||||
|
|
||||||
|
|
||||||
log log_${params}_2d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style hybrid dipole sphere
|
atom_style hybrid dipole sphere
|
||||||
dimension 2
|
dimension 2
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sq 0.4
|
lattice sq 0.4
|
||||||
region box block -30 30 -30 30 -0.2 0.2
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
@ -30,37 +20,26 @@ mass * 1.0
|
|||||||
set type * dipole/random ${seed} 1.0
|
set type * dipole/random ${seed} 1.0
|
||||||
velocity all create 1.0 1 loop geom
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pair_style none
|
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 ${temp} ${seed} rng ${rng} &
|
|
||||||
gamma_r ${gamma_r} gamma_t ${gamma_t}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
#initialisation for the main run
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*]
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
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
|
timestep 0.00001
|
||||||
thermo 50
|
thermo 100
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 30000
|
run 3000
|
||||||
|
|||||||
@ -1,27 +1,17 @@
|
|||||||
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||||
|
|
||||||
variable rng string uniform
|
variable rng string uniform
|
||||||
variable seed string 198098
|
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 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}
|
|
||||||
|
|
||||||
|
|
||||||
log log_${params}_3d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style hybrid dipole sphere
|
atom_style hybrid dipole sphere
|
||||||
dimension 3
|
dimension 3
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sc 0.4
|
lattice sc 0.4
|
||||||
region box block -8 8 -8 8 -8 8
|
region box block -8 8 -8 8 -8 8
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
@ -30,36 +20,26 @@ mass * 1.0
|
|||||||
set type * dipole/random ${seed} 1.0
|
set type * dipole/random ${seed} 1.0
|
||||||
velocity all create 1.0 1 loop geom
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pair_style none
|
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 ${temp} ${seed} rng ${rng} &
|
|
||||||
gamma_r ${gamma_r} gamma_t ${gamma_t}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#initialisation for the main run
|
#initialisation for the main run
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*]
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
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
|
timestep 0.00001
|
||||||
thermo 50
|
thermo 100
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 30000
|
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
|
||||||
@ -1,22 +1,18 @@
|
|||||||
# 2D overdamped active brownian particle dynamics (ABP)
|
# 2D overdamped active brownian particle dynamics (ABP)
|
||||||
# with WCA potential
|
# with WCA potential
|
||||||
|
|
||||||
variable gamma_t string 1.0
|
variable gamma_t string 1.0
|
||||||
variable gamma_r string 1.0
|
variable gamma_r string 1.0
|
||||||
variable temp string 1.0
|
variable temp string 1.0
|
||||||
variable seed equal 1974019
|
variable seed equal 1974019
|
||||||
variable fp string 4.0
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
|
||||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
|
||||||
|
|
||||||
|
|
||||||
log log_WCA_${params}_2d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style hybrid dipole sphere
|
atom_style hybrid dipole sphere
|
||||||
dimension 2
|
dimension 2
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sq 0.4
|
lattice sq 0.4
|
||||||
region box block -16 16 -16 16 -0.2 0.2
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
@ -29,41 +25,36 @@ velocity all create 1.0 1 loop geom
|
|||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 1 check yes
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
|
||||||
# WCA potential (purely repulsive)
|
# WCA potential (purely repulsive)
|
||||||
pair_style lj/cut 2.5
|
pair_style lj/cut 2.5
|
||||||
pair_coeff * * 1.0 1.0 1.1224
|
pair_coeff * * 1.0 1.0 1.1224
|
||||||
pair_modify shift yes
|
pair_modify shift yes
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# overdamped brownian dynamics time-step
|
# 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 ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
# self-propulsion force along the dipole direction
|
# self-propulsion force along the dipole direction
|
||||||
fix activity all propel/self dipole ${fp}
|
fix activity all propel/self dipole ${fp}
|
||||||
fix 2 all enforce2d
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
|
||||||
compute press all pressure NULL virial
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
thermo_style custom step temp epair c_press
|
thermo_style custom step pe ke c_press
|
||||||
|
|
||||||
#equilibration
|
#equilibration
|
||||||
timestep 0.0000000001
|
timestep 0.0000000001
|
||||||
thermo 50001
|
thermo 100
|
||||||
run 50000
|
run 5000
|
||||||
reset_timestep 0
|
reset_timestep 0
|
||||||
|
|
||||||
|
|
||||||
# MSD
|
# MSD
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*] c_press
|
thermo_style custom step temp epair c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
timestep 0.00001
|
timestep 0.00001
|
||||||
thermo 10000
|
thermo 1000
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 200000
|
run 20000
|
||||||
|
|||||||
@ -1,21 +1,17 @@
|
|||||||
# 3D overdamped active brownian dynamics with no interactions
|
# 3D overdamped active brownian dynamics with no interactions
|
||||||
|
|
||||||
variable gamma_t string 3.0
|
variable gamma_t string 3.0
|
||||||
variable gamma_r string 1.0
|
variable gamma_r string 1.0
|
||||||
variable temp string 1.0
|
variable temp string 1.0
|
||||||
variable seed equal 1974019
|
variable seed equal 1974019
|
||||||
variable fp string 4.0
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
|
||||||
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
|
||||||
|
|
||||||
|
|
||||||
log log_ideal_${params}_3d.lammps.log
|
|
||||||
units lj
|
units lj
|
||||||
atom_style hybrid dipole sphere
|
atom_style hybrid dipole sphere
|
||||||
dimension 3
|
dimension 3
|
||||||
newton off
|
newton off
|
||||||
|
|
||||||
|
|
||||||
lattice sc 0.4
|
lattice sc 0.4
|
||||||
region box block -8 8 -8 8 -8 8
|
region box block -8 8 -8 8 -8 8
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
@ -29,20 +25,18 @@ pair_style none
|
|||||||
# overdamped brownian dynamics time-step
|
# 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 ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
# self-propulsion force along the dipole direction
|
# self-propulsion force along the dipole direction
|
||||||
fix activity all propel/self dipole ${fp}
|
fix activity all propel/self dipole ${fp}
|
||||||
|
|
||||||
|
|
||||||
compute press all pressure NULL virial
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
thermo_style custom step temp epair c_press
|
thermo_style custom step ke pe c_press
|
||||||
|
|
||||||
#equilibration
|
#equilibration
|
||||||
timestep 0.0000000001
|
timestep 0.0000000001
|
||||||
thermo 50001
|
thermo 100
|
||||||
run 50000
|
run 5000
|
||||||
reset_timestep 0
|
reset_timestep 0
|
||||||
|
|
||||||
|
|
||||||
# MSD to demonstrate expected diffusive behaviour for ideal active
|
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||||
# brownian motion, which is
|
# brownian motion, which is
|
||||||
#
|
#
|
||||||
@ -52,15 +46,14 @@ reset_timestep 0
|
|||||||
# with d being simulation dimension
|
# with d being simulation dimension
|
||||||
compute msd all msd
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
thermo_style custom step temp epair c_msd[*] c_press
|
|
||||||
|
|
||||||
|
|
||||||
timestep 0.00001
|
timestep 0.00001
|
||||||
thermo 10000
|
thermo 1000
|
||||||
|
|
||||||
# main run
|
# main run
|
||||||
run 120000
|
run 12000
|
||||||
|
|
||||||
# if you want to check that rotational diffusion is behaving as expected,
|
# if you want to check that rotational diffusion is behaving as expected,
|
||||||
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||||
@ -68,7 +61,7 @@ run 120000
|
|||||||
# being simulation dimension)
|
# being simulation dimension)
|
||||||
|
|
||||||
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type &
|
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type &
|
||||||
# x y xu yu mux muy muz fx fy fz
|
# x y xu yu mux muy muz fx fy fz
|
||||||
#dump_modify 1 first yes sort id
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
#run 120000
|
#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
|
||||||
@ -1,163 +0,0 @@
|
|||||||
units lj
|
|
||||||
atom_style hybrid dipole sphere
|
|
||||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157)
|
|
||||||
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 ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 ${gamma_r} ${D_t} ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 ${D_t} ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 1 3 ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 1 3 1974019 dipole
|
|
||||||
# self-propulsion force along the dipole direction
|
|
||||||
fix activity all propel/self dipole ${fp}
|
|
||||||
fix activity all propel/self dipole 4
|
|
||||||
fix 2 all enforce2d
|
|
||||||
|
|
||||||
|
|
||||||
compute press all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair c_press
|
|
||||||
|
|
||||||
#equilibration
|
|
||||||
timestep 0.0000000001
|
|
||||||
thermo 50001
|
|
||||||
run 50000
|
|
||||||
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 Temp E_pair c_press
|
|
||||||
0 1 0 -0.53979198
|
|
||||||
50000 1.0902879e+10 0 -0.53710405
|
|
||||||
Loop time of 6.3887 on 1 procs for 50000 steps with 1024 atoms
|
|
||||||
|
|
||||||
Performance: 0.068 tau/day, 7826.319 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 | 0.34323 | 0.34323 | 0.34323 | 0.0 | 5.37
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.070232 | 0.070232 | 0.070232 | 0.0 | 1.10
|
|
||||||
Output | 2.5077e-05 | 2.5077e-05 | 2.5077e-05 | 0.0 | 0.00
|
|
||||||
Modify | 5.8232 | 5.8232 | 5.8232 | 0.0 | 91.15
|
|
||||||
Other | | 0.152 | | | 2.38
|
|
||||||
|
|
||||||
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 10000
|
|
||||||
|
|
||||||
# main run
|
|
||||||
run 200000
|
|
||||||
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 1.0902879e+10 0 0 0 0 0 -0.53710405
|
|
||||||
10000 103498.6 0.087662767 0.18719065 0.2007338 0 0.38792445 0.16080254
|
|
||||||
20000 104785.56 0.12719481 0.4197551 0.40722743 0 0.82698253 0.5007164
|
|
||||||
30000 103183.73 0.1126518 0.67800477 0.67921667 0 1.3572214 0.36634317
|
|
||||||
40000 102912.87 0.092584777 0.96234448 0.97188884 0 1.9342333 0.46170129
|
|
||||||
50000 103516.68 0.12761757 1.2381642 1.3203398 0 2.558504 0.85712805
|
|
||||||
60000 104999.77 0.14482924 1.5437166 1.6177103 0 3.1614269 1.1403162
|
|
||||||
70000 103925.7 0.11302021 1.886 1.9262949 0 3.8122949 1.1056086
|
|
||||||
80000 105000.14 0.14502228 2.205833 2.2668945 0 4.4727275 1.0757792
|
|
||||||
90000 105980.8 0.12089413 2.515801 2.647111 0 5.162912 1.1160525
|
|
||||||
100000 106557.86 0.10934038 2.7977098 2.8965145 0 5.6942242 0.56901933
|
|
||||||
110000 104241.46 0.12719985 3.1612652 3.2283956 0 6.3896608 0.95100999
|
|
||||||
120000 101910.56 0.12002691 3.5844099 3.5366227 0 7.1210326 1.2526653
|
|
||||||
130000 104435.28 0.10695039 3.8328815 3.8286503 0 7.6615318 1.6198184
|
|
||||||
140000 104864.99 0.11226471 4.1822059 4.285915 0 8.4681209 1.5190757
|
|
||||||
150000 103209.43 0.11229036 4.430069 4.5491143 0 8.9791833 1.1568204
|
|
||||||
160000 106692.61 0.11151476 4.7593714 5.0322819 0 9.7916533 1.2337266
|
|
||||||
170000 105232.19 0.12039818 5.0665907 5.3612901 0 10.427881 1.3881139
|
|
||||||
180000 107126.86 0.10793969 5.4129878 5.6391008 0 11.052089 1.6691607
|
|
||||||
190000 103814.36 0.096916503 5.7355093 5.9557837 0 11.691293 1.3863335
|
|
||||||
200000 103976.84 0.10928015 6.1871603 6.3393786 0 12.526539 1.1687077
|
|
||||||
Loop time of 27.4513 on 1 procs for 200000 steps with 1024 atoms
|
|
||||||
|
|
||||||
Performance: 6294.793 tau/day, 7285.640 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 | 3.2525 | 3.2525 | 3.2525 | 0.0 | 11.85
|
|
||||||
Neigh | 0.054678 | 0.054678 | 0.054678 | 0.0 | 0.20
|
|
||||||
Comm | 0.26582 | 0.26582 | 0.26582 | 0.0 | 0.97
|
|
||||||
Output | 0.0006103 | 0.0006103 | 0.0006103 | 0.0 | 0.00
|
|
||||||
Modify | 23.265 | 23.265 | 23.265 | 0.0 | 84.75
|
|
||||||
Other | | 0.6131 | | | 2.23
|
|
||||||
|
|
||||||
Nlocal: 1024.00 ave 1024 max 1024 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 166.000 ave 166 max 166 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 2634.00 ave 2634 max 2634 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 2634
|
|
||||||
Ave neighs/atom = 2.5722656
|
|
||||||
Neighbor list builds = 238
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:33
|
|
||||||
@ -1,150 +0,0 @@
|
|||||||
units lj
|
|
||||||
atom_style hybrid dipole sphere
|
|
||||||
WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (src/atom_vec_hybrid.cpp:157)
|
|
||||||
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 = 0.003 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 ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 ${gamma_r} ${D_t} ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 ${D_t} ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 1 ${D_r} ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 1 3 ${seed} dipole
|
|
||||||
fix step all brownian/sphere 1 1 1 3 1974019 dipole
|
|
||||||
# self-propulsion force along the dipole direction
|
|
||||||
fix activity all propel/self dipole ${fp}
|
|
||||||
fix activity all propel/self dipole 4
|
|
||||||
|
|
||||||
|
|
||||||
compute press all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair c_press
|
|
||||||
|
|
||||||
#equilibration
|
|
||||||
timestep 0.0000000001
|
|
||||||
thermo 50001
|
|
||||||
run 50000
|
|
||||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118)
|
|
||||||
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 Temp E_pair c_press
|
|
||||||
0 1 0 0.068021726
|
|
||||||
50000 1.0486812e+10 0 0.068203091
|
|
||||||
Loop time of 25.3706 on 1 procs for 50000 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 0.017 tau/day, 1970.786 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 | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.31005 | 0.31005 | 0.31005 | 0.0 | 1.22
|
|
||||||
Output | 3.2633e-05 | 3.2633e-05 | 3.2633e-05 | 0.0 | 0.00
|
|
||||||
Modify | 24.471 | 24.471 | 24.471 | 0.0 | 96.45
|
|
||||||
Other | | 0.5897 | | | 2.32
|
|
||||||
|
|
||||||
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*D_t + 2*fp**2/(gamma_t**2*(d-1)*D_r))*t
|
|
||||||
#
|
|
||||||
# with d being simulation dimension
|
|
||||||
compute msd all msd
|
|
||||||
|
|
||||||
|
|
||||||
thermo_style custom step temp epair c_msd[*] c_press
|
|
||||||
|
|
||||||
|
|
||||||
timestep 0.00001
|
|
||||||
thermo 10000
|
|
||||||
|
|
||||||
# main run
|
|
||||||
run 120000
|
|
||||||
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 Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
|
||||||
0 1.0486812e+10 0 0 0 0 0 0.068203091
|
|
||||||
10000 104209.87 0 0.25428952 0.2512451 0.23617807 0.74171269 0.1910208
|
|
||||||
20000 104433.46 0 0.55611319 0.57499464 0.54362634 1.6747342 0.27977792
|
|
||||||
30000 104615.53 0 0.88377871 0.8933002 0.88683731 2.6639162 0.31709969
|
|
||||||
40000 105930.5 0 1.2301515 1.262995 1.2479624 3.7411089 0.26149988
|
|
||||||
50000 105556.39 0 1.5798848 1.6402779 1.6392277 4.8593905 0.34401188
|
|
||||||
60000 104644.58 0 1.9782384 1.9902061 2.0327974 6.0012419 0.26709167
|
|
||||||
70000 104314.31 0 2.3681872 2.3695505 2.4241916 7.1619294 0.24191407
|
|
||||||
80000 105700 0 2.7109374 2.7434271 2.8309194 8.2852839 0.28355159
|
|
||||||
90000 103411.61 0 3.1023448 3.0881218 3.1599155 9.350382 0.3070844
|
|
||||||
100000 105432.12 0 3.4853878 3.4372177 3.5153198 10.437925 0.28141015
|
|
||||||
110000 105723.04 0 3.8405786 3.7967805 3.8738332 11.511192 0.33248553
|
|
||||||
120000 104734.31 0 4.2454301 4.1714561 4.2234474 12.640334 0.3603781
|
|
||||||
Loop time of 63.7803 on 1 procs for 120000 steps with 4096 atoms
|
|
||||||
|
|
||||||
Performance: 1625.581 tau/day, 1881.459 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 | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Neigh | 0.013032 | 0.013032 | 0.013032 | 0.0 | 0.02
|
|
||||||
Comm | 0.093045 | 0.093045 | 0.093045 | 0.0 | 0.15
|
|
||||||
Output | 0.00069845 | 0.00069845 | 0.00069845 | 0.0 | 0.00
|
|
||||||
Modify | 62.279 | 62.279 | 62.279 | 0.0 | 97.65
|
|
||||||
Other | | 1.394 | | | 2.19
|
|
||||||
|
|
||||||
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 = 2174
|
|
||||||
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: 0:01:29
|
|
||||||
Reference in New Issue
Block a user