diff --git a/examples/bd_sphere/README.txt b/examples/bd_sphere/README.txt new file mode 100644 index 0000000000..b044f11edc --- /dev/null +++ b/examples/bd_sphere/README.txt @@ -0,0 +1,22 @@ +The input file in2d.bd demonstrates how to run a 2d simulation +of particles undergoing overdamped brownian motion in both +translational and rotational degrees of freedom. + +The input file in3d_virial_on.bd demonstrates how to run a +similar simulation but in 3d. In this case, the virial +contribution of the brownian dynamics (the sum +sum_i /(3*volume) where W is +a random variable with mean 0 and variance dt) is +calculated via the fix_modify command. For long +enough times, this will be equal to rho*D_t*gamma_t +(the ideal gas term in equilibrium systems). + +To confirm rotational diffusion is working correctly, +run the above simulations with dump files on and +measure \sum_i, and one should +find that this decays as an exponential with +timescale 1/((d-1)*D_r). + +Note that both of the simulations above are not long +enough to get good statistics on e.g. ideal gas +pressure, rotational diffusion, or translational diffusion. diff --git a/examples/bd_sphere/in2d.bd b/examples/bd_sphere/in2d.bd new file mode 100644 index 0000000000..c11381ad5a --- /dev/null +++ b/examples/bd_sphere/in2d.bd @@ -0,0 +1,76 @@ +# 2d overdamped brownian dynamics + +variable rng string gaussian +variable gamma_t equal 4.0 +variable gamma_r equal 1.0 +variable D_t equal 7.0 +variable D_r equal 13.0 +variable seed equal 1974019 + + +variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} + + +log log_${params}_2d.lammps.log +units lj +atom_style hybrid dipole sphere +dimension 2 +newton off + + +lattice sq 0.4 +region box block -16 16 -16 16 -0.2 0.2 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment next three lines for dump output +#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 + + diff --git a/examples/bd_sphere/in3d_virial_on.bd b/examples/bd_sphere/in3d_virial_on.bd new file mode 100644 index 0000000000..1ef88930c1 --- /dev/null +++ b/examples/bd_sphere/in3d_virial_on.bd @@ -0,0 +1,77 @@ +# 3d overdamped brownian dynamics + + +variable rng string uniform +variable gamma_t equal 10.0 +variable gamma_r equal 1.0 +variable D_t equal 5.0 +variable D_r equal 15.0 +variable seed equal 553910 + + +variable params string ${rng}_${gamma_t}_${gamma_r}_${D_t}_${D_r} + + +log log_${params}_3d.lammps.log +units lj +atom_style hybrid dipole sphere +dimension 3 +newton off + + +lattice sc 0.4 +region box block -8 8 -8 8 -8 8 +create_box 1 box +create_atoms 1 box +mass * 1.0 +set type * dipole/random ${seed} 1.0 +velocity all create 1.0 1 loop geom + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix_modify 1 virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment the next three lines for dump file +#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type & +# x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +timestep 0.00001 +thermo 1000 + +# main run +run 120000 + + diff --git a/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log b/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log new file mode 100644 index 0000000000..72b90efe0e --- /dev/null +++ b/examples/bd_sphere/log_gaussian_4_1_7_13_2d.lammps.log @@ -0,0 +1,259 @@ +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 + + +neighbor 1.0 bin +neigh_modify every 1 delay 1 check yes + + + +pair_style none + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 7 ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 7 13 ${seed} rng ${rng} +fix 1 all bd/sphere 4 1 7 13 1974019 rng ${rng} +fix 1 all bd/sphere 4 1 7 13 1974019 rng gaussian +fix 2 all enforce2d + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes +Step Temp E_pair c_press + 0 1 0 0 + 50000 7.3671759e+10 0 0 +Loop time of 10.2295 on 1 procs for 50000 steps with 1024 atoms + +Performance: 0.042 tau/day, 4887.825 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.033217 | 0.033217 | 0.033217 | 0.0 | 0.32 +Output | 2.1435e-05 | 2.1435e-05 | 2.1435e-05 | 0.0 | 0.00 +Modify | 10.047 | 10.047 | 10.047 | 0.0 | 98.21 +Other | | 0.1497 | | | 1.46 + +Nlocal: 1024.00 ave 1024 max 1024 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 65.0000 ave 65 max 65 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment next three lines for dump output +#dump 1 all custom 2000 dump_${params}_2d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +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) = 4.664 | 4.664 | 4.664 Mbytes +Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press + 0 7.3671759e+10 0 0 0 0 0 0 + 1000 710744.42 0 0.1332856 0.13577642 0 0.26906203 0 + 2000 705025.5 0 0.27078701 0.27355073 0 0.54433774 0 + 3000 750845.29 0 0.41036556 0.39710766 0 0.80747321 0 + 4000 752542.47 0 0.53097803 0.53654063 0 1.0675187 0 + 5000 731812.26 0 0.66927129 0.65872533 0 1.3279966 0 + 6000 716119.24 0 0.79097615 0.76825364 0 1.5592298 0 + 7000 726294.28 0 0.93322099 0.91220222 0 1.8454232 0 + 8000 673771.54 0 1.0789689 1.031843 0 2.1108119 0 + 9000 757173.95 0 1.2328252 1.2024778 0 2.435303 0 + 10000 693711.95 0 1.3972184 1.3045575 0 2.7017759 0 + 11000 774897.65 0 1.584036 1.4168797 0 3.0009157 0 + 12000 764910.09 0 1.7344079 1.5751172 0 3.3095251 0 + 13000 752859.5 0 1.8538323 1.7336107 0 3.5874429 0 + 14000 746333.26 0 2.0392353 1.9027299 0 3.9419652 0 + 15000 735704.24 0 2.1714465 2.000952 0 4.1723985 0 + 16000 722768.01 0 2.258542 2.1084289 0 4.3669709 0 + 17000 741408.63 0 2.4194247 2.2469958 0 4.6664206 0 + 18000 713609.29 0 2.5366244 2.3325203 0 4.8691447 0 + 19000 770066.65 0 2.6662758 2.4726928 0 5.1389686 0 + 20000 739828.53 0 2.792873 2.6188232 0 5.4116962 0 + 21000 719478.96 0 2.9109491 2.7872008 0 5.6981499 0 + 22000 737448.77 0 3.0162218 2.9213733 0 5.9375951 0 + 23000 714695.3 0 3.1309486 3.0325142 0 6.1634628 0 + 24000 712386.78 0 3.31348 3.1323675 0 6.4458475 0 + 25000 747298.11 0 3.5148965 3.2978465 0 6.812743 0 + 26000 737240.19 0 3.7117818 3.4245004 0 7.1362822 0 + 27000 720878.36 0 3.8342853 3.5681829 0 7.4024682 0 + 28000 776824.55 0 3.9904931 3.6853691 0 7.6758622 0 + 29000 714696.4 0 4.0733919 3.8807741 0 7.954166 0 + 30000 725827.3 0 4.2213715 4.0552488 0 8.2766204 0 + 31000 737978.89 0 4.2918759 4.1795647 0 8.4714407 0 + 32000 766620.93 0 4.4620184 4.2765194 0 8.7385378 0 + 33000 714739.71 0 4.5942749 4.426881 0 9.0211559 0 + 34000 694821.06 0 4.686348 4.5057433 0 9.1920912 0 + 35000 721948.38 0 4.7526371 4.5689873 0 9.3216245 0 + 36000 713621.16 0 4.8645036 4.6355302 0 9.5000339 0 + 37000 704079.85 0 4.9652601 4.8235856 0 9.7888457 0 + 38000 706914.29 0 5.1045998 4.9585169 0 10.063117 0 + 39000 736940.33 0 5.2172626 5.1168713 0 10.334134 0 + 40000 738302.73 0 5.3720228 5.3207578 0 10.692781 0 + 41000 746518.85 0 5.5376524 5.5192708 0 11.056923 0 + 42000 719970.82 0 5.7610696 5.6335312 0 11.394601 0 + 43000 736875.87 0 5.8769052 5.7504356 0 11.627341 0 + 44000 765218.38 0 6.0308866 5.9650683 0 11.995955 0 + 45000 739382.69 0 6.1577029 6.0736304 0 12.231333 0 + 46000 730967.87 0 6.3846223 6.2090389 0 12.593661 0 + 47000 758881.95 0 6.5604053 6.3883315 0 12.948737 0 + 48000 751135.53 0 6.6160248 6.5199017 0 13.135926 0 + 49000 721058.97 0 6.6124519 6.6938253 0 13.306277 0 + 50000 686287.15 0 6.8527601 6.8518895 0 13.70465 0 + 51000 735175.7 0 6.9928329 6.8663476 0 13.85918 0 + 52000 760085.67 0 7.1009497 7.0345784 0 14.135528 0 + 53000 741211.89 0 7.2287282 7.2318431 0 14.460571 0 + 54000 723668.97 0 7.3732634 7.3847301 0 14.757994 0 + 55000 751846.88 0 7.5566634 7.4927365 0 15.0494 0 + 56000 762648.27 0 7.7651818 7.5379796 0 15.303161 0 + 57000 710175.2 0 7.9051989 7.6644542 0 15.569653 0 + 58000 740068.94 0 8.0296854 7.8307471 0 15.860433 0 + 59000 728119.43 0 8.1562433 8.039333 0 16.195576 0 + 60000 728768.48 0 8.316192 8.1643843 0 16.480576 0 + 61000 707538.83 0 8.3727565 8.3895027 0 16.762259 0 + 62000 713931.41 0 8.4657927 8.5517529 0 17.017546 0 + 63000 742604.95 0 8.6550684 8.7189851 0 17.374053 0 + 64000 738981.54 0 8.7331005 8.9208616 0 17.653962 0 + 65000 701685.87 0 8.898571 8.977933 0 17.876504 0 + 66000 716151.39 0 9.0229699 9.1292403 0 18.15221 0 + 67000 732641.29 0 9.151611 9.3249179 0 18.476529 0 + 68000 740870.85 0 9.233452 9.4667607 0 18.700213 0 + 69000 733159.17 0 9.1743719 9.5648134 0 18.739185 0 + 70000 693562.75 0 9.3414089 9.7425241 0 19.083933 0 + 71000 748694.53 0 9.5036102 9.8686571 0 19.372267 0 + 72000 721046.02 0 9.7116931 10.0195 0 19.731193 0 + 73000 736631.66 0 9.7095662 10.205306 0 19.914872 0 + 74000 751264.08 0 9.9413234 10.327844 0 20.269167 0 + 75000 729223.27 0 10.211903 10.412516 0 20.624419 0 + 76000 747811 0 10.332266 10.544251 0 20.876517 0 + 77000 717505.01 0 10.521195 10.737774 0 21.258969 0 + 78000 712288.89 0 10.712514 10.874932 0 21.587446 0 + 79000 728912.34 0 10.755227 10.968257 0 21.723484 0 + 80000 743505.67 0 11.026063 11.070234 0 22.096298 0 + 81000 732218.14 0 11.321417 11.31773 0 22.639147 0 + 82000 777186.61 0 11.480074 11.401465 0 22.881539 0 + 83000 734805.95 0 11.7524 11.62552 0 23.37792 0 + 84000 753703.38 0 11.863318 11.833925 0 23.697243 0 + 85000 755730.75 0 12.068564 11.937143 0 24.005707 0 + 86000 725021.19 0 12.258195 12.034586 0 24.292781 0 + 87000 731844.67 0 12.341844 12.331792 0 24.673636 0 + 88000 707368.15 0 12.431452 12.547314 0 24.978766 0 + 89000 784756.28 0 12.405699 12.686021 0 25.09172 0 + 90000 760278.97 0 12.542669 12.851925 0 25.394593 0 + 91000 753765.97 0 12.703534 13.08092 0 25.784454 0 + 92000 705869.22 0 12.971838 13.210092 0 26.18193 0 + 93000 741699.59 0 13.110745 13.383115 0 26.49386 0 + 94000 717372.41 0 13.252109 13.466388 0 26.718497 0 + 95000 721820.49 0 13.373146 13.660605 0 27.033751 0 + 96000 777409.97 0 13.596822 13.886961 0 27.483782 0 + 97000 741480.91 0 13.752545 14.204624 0 27.957169 0 + 98000 725755.72 0 13.918302 14.219292 0 28.137594 0 + 99000 729710.24 0 14.065417 14.213142 0 28.278559 0 + 100000 700366.74 0 14.278054 14.324135 0 28.602189 0 + 101000 722737.18 0 14.398464 14.46904 0 28.867505 0 + 102000 758930.85 0 14.408098 14.637964 0 29.046061 0 + 103000 725233.66 0 14.526482 14.719688 0 29.24617 0 + 104000 752416.52 0 14.641393 14.952087 0 29.59348 0 + 105000 769047.5 0 14.780788 15.182945 0 29.963733 0 + 106000 734849.98 0 14.840982 15.316112 0 30.157094 0 + 107000 720210.74 0 15.010029 15.372792 0 30.382821 0 + 108000 741216.55 0 15.113143 15.488575 0 30.601718 0 + 109000 714158.43 0 15.057499 15.592865 0 30.650364 0 + 110000 743262.25 0 15.381281 15.798368 0 31.179649 0 + 111000 728836.92 0 15.488226 16.034645 0 31.522871 0 + 112000 753490.67 0 15.679979 16.350819 0 32.030799 0 + 113000 730699.5 0 15.82813 16.680136 0 32.508266 0 + 114000 705526.22 0 16.099699 16.920095 0 33.019794 0 + 115000 752408.36 0 16.393466 17.053935 0 33.447401 0 + 116000 713697.16 0 16.634939 17.35349 0 33.98843 0 + 117000 690041.5 0 16.727379 17.457936 0 34.185315 0 + 118000 745594.37 0 16.838659 17.585392 0 34.424052 0 + 119000 714487.42 0 17.064214 17.743478 0 34.807692 0 + 120000 716557.14 0 17.105558 17.845925 0 34.951483 0 +Loop time of 25.2131 on 1 procs for 120000 steps with 1024 atoms + +Performance: 4112.144 tau/day, 4759.427 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 | 0.0016123 | 0.0016123 | 0.0016123 | 0.0 | 0.01 +Comm | 0.025898 | 0.025898 | 0.025898 | 0.0 | 0.10 +Output | 0.0037882 | 0.0037882 | 0.0037882 | 0.0 | 0.02 +Modify | 24.767 | 24.767 | 24.767 | 0.0 | 98.23 +Other | | 0.4146 | | | 1.64 + +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 = 1049 +Dangerous builds = 0 + + +Total wall time: 0:00:35 diff --git a/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log b/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log new file mode 100644 index 0000000000..fda48dc71a --- /dev/null +++ b/examples/bd_sphere/log_uniform_10_1_5_15_3d.lammps.log @@ -0,0 +1,259 @@ +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 553910 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 + + + +#compute d all property/atom mux muy muz + +fix 1 all bd/sphere ${gamma_t} ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 ${gamma_r} ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 ${D_t} ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 5 ${D_r} ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 5 15 ${seed} rng ${rng} +fix 1 all bd/sphere 10 1 5 15 553910 rng ${rng} +fix 1 all bd/sphere 10 1 5 15 553910 rng uniform +fix_modify 1 virial yes + +compute press all pressure NULL virial + +thermo_style custom step temp epair c_press + +#equilibration +timestep 0.0000000001 +thermo 50001 +run 50000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2118) +WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167) +Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes +Step Temp E_pair c_press + 0 1 0 -32553.271 + 50000 5.2351457e+10 0 -15026.42 +Loop time of 18.6303 on 1 procs for 50000 steps with 4096 atoms + +Performance: 0.023 tau/day, 2683.804 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.31439 | 0.31439 | 0.31439 | 0.0 | 1.69 +Output | 5.5046e-05 | 5.5046e-05 | 5.5046e-05 | 0.0 | 0.00 +Modify | 17.718 | 17.718 | 17.718 | 0.0 | 95.11 +Other | | 0.5974 | | | 3.21 + +Nlocal: 4096.00 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 817.000 ave 817 max 817 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0.0000000 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + + +#initialisation for the main run + +# MSD +compute msd all msd + + +thermo_style custom step temp epair c_msd[*] c_press + + +# write trajectory and thermo in a log-scale frequency +# uncomment the next three lines for dump file +#dump 1 all custom 10000 dump_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz +#dump_modify 1 first yes sort id + +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) = 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 5.2351457e+10 0 0 0 0 0 -233.83012 + 1000 522590.88 0 0.10259269 0.10487519 0.10391005 0.31137793 -13.730626 + 2000 521776.08 0 0.20662097 0.2118237 0.20371673 0.62216139 -141.90848 + 3000 529408.9 0 0.30711557 0.3105565 0.30293728 0.92060935 28.335187 + 4000 518069.42 0 0.39918073 0.40643835 0.40168024 1.2072993 -12.262269 + 5000 520487.75 0 0.50222348 0.50854461 0.50304351 1.5138116 303.56775 + 6000 527970.5 0 0.60443861 0.60363711 0.59884932 1.806925 218.55799 + 7000 519424.68 0 0.69529071 0.70025532 0.70347351 2.0990195 -363.51723 + 8000 521925.72 0 0.80545039 0.81520807 0.79930708 2.4199655 510.47732 + 9000 518397.28 0 0.91236827 0.9050426 0.89431985 2.7117307 537.74151 + 10000 525696.47 0 0.99494325 0.99433832 0.98574884 2.9750304 411.56896 + 11000 524505.88 0 1.0863677 1.1232636 1.0810609 3.2906921 32.652569 + 12000 525350.08 0 1.1816136 1.2412674 1.189996 3.612877 45.304061 + 13000 524598.12 0 1.2841566 1.3381915 1.2906249 3.912973 -376.50739 + 14000 525438.09 0 1.3964076 1.4420032 1.3915611 4.2299719 -31.273339 + 15000 523531.08 0 1.4829127 1.5436611 1.4892074 4.5157811 -357.26366 + 16000 532366.43 0 1.5871965 1.6432286 1.6020146 4.8324397 435.10667 + 17000 523629.21 0 1.6968632 1.7574539 1.6967316 5.1510487 280.59816 + 18000 521432.94 0 1.7973983 1.8462477 1.8087416 5.4523876 134.69384 + 19000 530778.78 0 1.888653 1.9328611 1.9268155 5.7483296 -64.346115 + 20000 525623.21 0 1.9718697 2.0048196 2.0068177 5.983507 73.884028 + 21000 524862.26 0 2.0414226 2.0967449 2.0878261 6.2259936 163.95173 + 22000 529123.04 0 2.143889 2.1850282 2.1972491 6.5261662 234.87793 + 23000 519629.76 0 2.2297952 2.2661611 2.2805197 6.776476 57.65702 + 24000 523746.18 0 2.3293654 2.3658544 2.3842082 7.079428 46.291089 + 25000 515851.07 0 2.4177426 2.4559274 2.5029961 7.3766661 -16.353546 + 26000 515592.59 0 2.5352044 2.5438918 2.5657776 7.6448738 -65.259248 + 27000 527764.96 0 2.6498176 2.6423592 2.6715377 7.9637146 324.48367 + 28000 527177.18 0 2.7405087 2.7431537 2.7702133 8.2538757 -47.906223 + 29000 521079.66 0 2.8294642 2.8410515 2.8546167 8.5251323 -135.36173 + 30000 526092.8 0 2.961898 2.9361476 2.9319586 8.8300042 206.28635 + 31000 529595.93 0 3.0638234 3.0128995 3.0434232 9.1201461 -35.946596 + 32000 521173.83 0 3.159344 3.1397814 3.1455147 9.4446401 328.73193 + 33000 522989.77 0 3.2567127 3.2348491 3.2444068 9.7359686 362.33435 + 34000 522930.45 0 3.3489514 3.3433962 3.3391822 10.03153 178.73773 + 35000 530664.64 0 3.4445399 3.4843743 3.4205275 10.349442 146.02898 + 36000 521443.26 0 3.520475 3.6171115 3.5179112 10.655498 244.07172 + 37000 529669.54 0 3.6076942 3.7233869 3.6169718 10.948053 79.46077 + 38000 527521.93 0 3.7093699 3.8275855 3.7451165 11.282072 -91.131074 + 39000 523237.65 0 3.8088585 3.9559041 3.8748751 11.639638 -70.265271 + 40000 522798.75 0 3.89319 4.0420406 3.9196106 11.854841 91.631855 + 41000 524228.77 0 3.9863379 4.1602581 4.0393136 12.18591 113.26515 + 42000 524546.08 0 4.0969366 4.2738786 4.1218115 12.492627 313.83957 + 43000 515948.22 0 4.2161418 4.3700009 4.2178962 12.804039 92.993253 + 44000 527319.42 0 4.3267431 4.4688062 4.3274029 13.122952 -118.91153 + 45000 526222.74 0 4.4289127 4.5531203 4.4604075 13.442441 -474.98113 + 46000 524617.54 0 4.5422968 4.6316235 4.5445894 13.71851 -303.23458 + 47000 524067.07 0 4.6284944 4.6989745 4.5884153 13.915884 -343.41107 + 48000 535659.25 0 4.7221068 4.7505302 4.7212887 14.193926 149.75872 + 49000 527425.65 0 4.8098179 4.8761354 4.8362998 14.522253 -272.18936 + 50000 516588.98 0 4.9077783 4.9950242 4.9826783 14.885481 -52.925733 + 51000 522291.86 0 5.0022325 5.0659091 5.0525647 15.120706 -52.985883 + 52000 530056.07 0 5.123751 5.1470734 5.1603805 15.431205 -231.29334 + 53000 525624.96 0 5.2412036 5.2543541 5.2717587 15.767316 294.19678 + 54000 524407.27 0 5.3530927 5.359043 5.342451 16.054587 -55.282671 + 55000 519989.37 0 5.4458173 5.4781678 5.413865 16.33785 -135.28414 + 56000 524987.68 0 5.5282178 5.5825979 5.5127172 16.623533 84.654044 + 57000 525610.66 0 5.6202713 5.6925409 5.5964466 16.909259 407.16526 + 58000 523097.93 0 5.7390671 5.7830376 5.6921201 17.214225 -271.05243 + 59000 525357.74 0 5.8037507 5.8654514 5.7920744 17.461276 -213.07815 + 60000 522185.96 0 5.9067925 5.9909357 5.903525 17.801253 330.09637 + 61000 527694.33 0 6.0576096 6.0907943 6.0202838 18.168688 310.22884 + 62000 522936.57 0 6.1422565 6.1888677 6.124212 18.455336 -24.591697 + 63000 526642.55 0 6.2261061 6.2832608 6.2023277 18.711695 -130.32823 + 64000 514826.49 0 6.3032614 6.3628539 6.3184362 18.984552 195.43036 + 65000 529338.23 0 6.4152502 6.4482512 6.4241507 19.287652 -77.817059 + 66000 527425.07 0 6.5122194 6.5052947 6.5518104 19.569324 8.0143425 + 67000 525258.85 0 6.6292334 6.6417881 6.6438938 19.914915 152.1905 + 68000 527067.89 0 6.7569918 6.6951219 6.7357134 20.187827 -337.54654 + 69000 522395.33 0 6.8401085 6.7836633 6.8243746 20.448146 34.755329 + 70000 522200.34 0 6.9549662 6.8773008 6.9537894 20.786056 352.30283 + 71000 527550.11 0 7.0441399 6.9837133 7.0860791 21.113932 171.42143 + 72000 529564.22 0 7.1744229 7.0581688 7.1507041 21.383296 269.04569 + 73000 524175.53 0 7.248828 7.1693905 7.2974868 21.715705 -84.993601 + 74000 528604.1 0 7.3358903 7.2983204 7.390523 22.024734 -6.8495991 + 75000 519136.15 0 7.445248 7.4224403 7.4690469 22.336735 250.23521 + 76000 518470.58 0 7.5747768 7.5354904 7.5612252 22.671492 274.53956 + 77000 518459.51 0 7.6660567 7.6557812 7.7020797 23.023918 430.07722 + 78000 516646.23 0 7.7596088 7.7130901 7.7896654 23.262364 536.21298 + 79000 517511.57 0 7.9021784 7.82098 7.8840028 23.607161 193.80468 + 80000 520654.84 0 7.991107 7.8932454 8.0049184 23.889271 -6.0066355 + 81000 522331.74 0 8.0616391 7.9990606 8.0954141 24.156114 47.271954 + 82000 521540.3 0 8.1268306 8.0763829 8.1861513 24.389365 36.265762 + 83000 529154.07 0 8.2537975 8.1854268 8.2745822 24.713807 113.94154 + 84000 525977.29 0 8.2999431 8.26591 8.2970498 24.862903 -72.444836 + 85000 520505.41 0 8.3872349 8.3551374 8.4251458 25.167518 -346.6703 + 86000 516334.67 0 8.4947842 8.4504822 8.5238751 25.469142 -3.8332672 + 87000 524745.34 0 8.5405071 8.5348571 8.6344387 25.709803 -149.22382 + 88000 521384.87 0 8.5798155 8.6260785 8.7133565 25.919251 22.009599 + 89000 519680.71 0 8.6657392 8.6857605 8.8319304 26.18343 -180.94487 + 90000 522482.4 0 8.7310324 8.7844751 8.9636862 26.479194 -102.50361 + 91000 527450.69 0 8.8250902 8.8445728 9.0456076 26.715271 325.68024 + 92000 519060.77 0 8.9054775 8.9412744 9.1259074 26.972659 130.73028 + 93000 518170.14 0 9.0378587 9.0315875 9.2346184 27.304065 -111.68498 + 94000 531639.53 0 9.1268874 9.0952299 9.3437063 27.565824 -26.423328 + 95000 519776.1 0 9.2332576 9.1903006 9.4516001 27.875158 -113.46356 + 96000 527082.72 0 9.2993234 9.2533436 9.534409 28.087076 -46.720611 + 97000 526965.16 0 9.3485677 9.3197496 9.6631942 28.331512 159.18386 + 98000 529790.04 0 9.4759113 9.5177629 9.783846 28.77752 343.32872 + 99000 520964.82 0 9.6488022 9.6573355 9.882432 29.18857 -257.85576 + 100000 520863.58 0 9.7452168 9.7659565 9.9878877 29.499061 -108.52324 + 101000 526760.86 0 9.8073751 9.8508213 10.127532 29.785728 120.22249 + 102000 519249.89 0 9.9315855 9.9767409 10.221605 30.129931 -176.50647 + 103000 525003.9 0 10.023982 10.062451 10.315002 30.401435 422.1401 + 104000 519112.73 0 10.086117 10.136879 10.415222 30.638218 -147.66505 + 105000 517898.24 0 10.180438 10.240942 10.525346 30.946725 158.63054 + 106000 528046.35 0 10.258163 10.41411 10.601663 31.273936 -128.04669 + 107000 527105.8 0 10.364015 10.485036 10.795177 31.644228 183.82165 + 108000 522024.28 0 10.450786 10.544065 10.902961 31.897812 -39.692553 + 109000 519497.83 0 10.556206 10.61633 11.046222 32.218758 173.75988 + 110000 521070.8 0 10.64856 10.745382 11.071387 32.465329 -128.45389 + 111000 525657.64 0 10.830485 10.852954 11.188295 32.871734 -214.60249 + 112000 519426.33 0 10.987769 10.97575 11.26012 33.223639 292.35901 + 113000 526472.45 0 11.029941 11.086376 11.418772 33.535089 189.69245 + 114000 520070.28 0 11.107229 11.183295 11.454757 33.745281 -40.433571 + 115000 525812.59 0 11.153992 11.305378 11.537521 33.99689 -106.38733 + 116000 524464.26 0 11.256779 11.413082 11.633295 34.303156 -159.59643 + 117000 519838.94 0 11.344413 11.480104 11.706366 34.530883 -2.0346135 + 118000 524075.83 0 11.441416 11.597533 11.783056 34.822005 -350.05313 + 119000 533816.71 0 11.52766 11.681986 11.917713 35.127359 -521.58975 + 120000 524509.31 0 11.63865 11.792667 12.080379 35.511696 273.09647 +Loop time of 46.6725 on 1 procs for 120000 steps with 4096 atoms + +Performance: 2221.438 tau/day, 2571.109 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 | 0.0063169 | 0.0063169 | 0.0063169 | 0.0 | 0.01 +Comm | 0.057082 | 0.057082 | 0.057082 | 0.0 | 0.12 +Output | 0.0068489 | 0.0068489 | 0.0068489 | 0.0 | 0.01 +Modify | 44.98 | 44.98 | 44.98 | 0.0 | 96.37 +Other | | 1.622 | | | 3.48 + +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 = 992 +Dangerous builds = 0 + + +Total wall time: 0:01:05