add/update USER-BROWNIAN example inputs and logs
This commit is contained in:
Axel Kohlmeyer
@ -1,25 +1,16 @@
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##### dynamics of non-interacting point particles in 2D #####
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variable rng string gaussian
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variable seed string 198098
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variable rng string gaussian
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variable seed string 198098
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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log log_${params}_2d.lammps.log
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units lj
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atom_style atomic
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dimension 2
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newton off
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lattice sq 0.4
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region box block -30 30 -30 30 -0.2 0.2
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create_box 1 box
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@ -27,36 +18,26 @@ create_atoms 1 box
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mass * 1.0
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velocity all create 1.0 1 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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pair_style none
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fix 1 all brownian ${temp} ${seed} rng ${rng} &
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gamma_t ${gamma_t}
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fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
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#initialisation for the main run
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# MSD
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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thermo_style custom step temp epair c_msd[*]
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dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
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x y z xu yu zu fx fy fz
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dump_modify 1 first yes sort id
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#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
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# x y z xu yu zu fx fy fz
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#dump_modify 1 first yes sort id
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timestep 0.00001
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thermo 50
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thermo 100
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# main run
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run 30000
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run 3000
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@ -1,24 +1,16 @@
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##### overdamped dynamics of non-interacting point particles in 3D #####
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variable rng string gaussian
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variable seed string 198098
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variable rng string gaussian
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variable seed string 198098
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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log log_${params}_3d.lammps.log
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units lj
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atom_style atomic
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dimension 3
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newton off
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lattice sc 0.4
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region box block -8 8 -8 8 -8 8
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create_box 1 box
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@ -26,36 +18,27 @@ create_atoms 1 box
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mass * 1.0
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velocity all create 1.0 1 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 1 check yes
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pair_style none
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fix 1 all brownian ${temp} ${seed} rng ${rng} &
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gamma_t ${gamma_t}
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fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
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#initialisation for the main run
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# MSD
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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thermo_style custom step temp epair c_msd[*]
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dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
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x y z xu yu zu fx fy fz
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dump_modify 1 first yes sort id
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#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
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# x y z xu yu zu fx fy fz
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#dump_modify 1 first yes sort id
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timestep 0.00001
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thermo 50
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thermo 100
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# main run
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run 30000
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run 3000
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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 @@
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LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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##### dynamics of non-interacting point particles in 2D #####
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variable rng string gaussian
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variable seed string 198098
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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variable params string gaussian_${temp}_${gamma_t}
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variable params string gaussian_5.0_${gamma_t}
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variable params string gaussian_5.0_1.0
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units lj
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atom_style atomic
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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 -30 30 -30 30 -0.2 0.2
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create_box 1 box
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Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 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 3600 atoms
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create_atoms CPU = 0.003 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 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
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#dump_modify 1 first yes sort id
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timestep 0.00001
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thermo 100
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# main run
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run 3000
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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) = 2.664 | 2.664 | 2.664 Mbytes
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Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
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0 0.99972222 0 0 0 0 0
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100 1022861.2 0 0.010252464 0.0095481044 0 0.019800568
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200 986781.19 0 0.020552091 0.019485252 0 0.040037343
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300 1030219 0 0.030642552 0.028377678 0 0.05902023
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400 1003322.5 0 0.040610693 0.038179284 0 0.078789978
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500 989343.12 0 0.049978908 0.047445856 0 0.097424764
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600 1029781.3 0 0.059551719 0.057941149 0 0.11749287
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700 999447.72 0 0.06979546 0.067552325 0 0.13734778
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800 995373.97 0 0.080049251 0.078006344 0 0.1580556
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900 1011991.4 0 0.089753134 0.087065214 0 0.17681835
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1000 1006017.1 0 0.10041092 0.097934217 0 0.19834514
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1100 997762.63 0 0.11229742 0.10841547 0 0.22071289
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1200 1011707.8 0 0.12006388 0.1190115 0 0.23907538
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1300 1012099.1 0 0.13097486 0.12996632 0 0.26094117
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1400 997602.43 0 0.14345778 0.13830585 0 0.28176362
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1500 1005358.1 0 0.15441686 0.14927539 0 0.30369225
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1600 1007081.8 0 0.16496828 0.15936363 0 0.3243319
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1700 990284.9 0 0.1747286 0.16818246 0 0.34291106
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1800 969006.97 0 0.18228778 0.17972813 0 0.3620159
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1900 998066.69 0 0.19338277 0.19226121 0 0.38564397
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2000 972300.66 0 0.20352485 0.20145928 0 0.40498413
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2100 985025.88 0 0.21283854 0.21090075 0 0.42373929
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2200 1010964.6 0 0.22279055 0.22110734 0 0.44389789
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2300 975819.44 0 0.23128131 0.23226488 0 0.46354619
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2400 977043.53 0 0.24284105 0.24301689 0 0.48585794
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2500 969708.21 0 0.25415238 0.25354284 0 0.50769522
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2600 981969.5 0 0.26457173 0.26318018 0 0.52775192
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2700 987261.1 0 0.27497004 0.27761213 0 0.55258218
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2800 1005751.1 0 0.28530448 0.28715428 0 0.57245876
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2900 975930.11 0 0.29394811 0.29896948 0 0.59291759
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3000 997388.08 0 0.30674701 0.31193573 0 0.61868274
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Loop time of 1.501 on 1 procs for 3000 steps with 3600 atoms
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Performance: 1726.852 tau/day, 1998.672 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 | 0.00059271 | 0.00059271 | 0.00059271 | 0.0 | 0.04
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Comm | 0.0055437 | 0.0055437 | 0.0055437 | 0.0 | 0.37
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Output | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 0.27
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Modify | 1.3852 | 1.3852 | 1.3852 | 0.0 | 92.28
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Other | | 0.1057 | | | 7.04
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Nlocal: 3600.00 ave 3600 max 3600 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 = 21
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Dangerous builds = 0
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Total wall time: 0:00:01
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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 @@
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LAMMPS (8 Apr 2021)
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using 1 OpenMP thread(s) per MPI task
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##### dynamics of non-interacting point particles in 2D #####
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variable rng string gaussian
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variable seed string 198098
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variable temp string 5.0
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variable gamma_t string 1.0
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variable params string ${rng}_${temp}_${gamma_t}
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variable params string gaussian_${temp}_${gamma_t}
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variable params string gaussian_5.0_${gamma_t}
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variable params string gaussian_5.0_1.0
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units lj
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atom_style atomic
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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 -30 30 -30 30 -0.2 0.2
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create_box 1 box
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Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 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 3600 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 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
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fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
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#initialisation for the main run
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# MSD
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compute msd all msd
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thermo_style custom step ke pe c_msd[*]
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#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
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#dump_modify 1 first yes sort id
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timestep 0.00001
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thermo 100
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# main run
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run 3000
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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) = 2.664 | 2.664 | 2.664 Mbytes
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Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
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0 0.99972222 0 0 0 0 0
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100 1017972.1 0 0.010094052 0.0097502899 0 0.019844342
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200 1004552.1 0 0.020125116 0.01957629 0 0.039701406
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300 1017712.9 0 0.030271373 0.029411656 0 0.059683029
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400 1016693.8 0 0.040610061 0.038605869 0 0.07921593
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500 999527.84 0 0.049451389 0.049042225 0 0.098493614
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600 961157.92 0 0.059691948 0.059033176 0 0.11872512
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700 1006804.9 0 0.071205977 0.069972106 0 0.14117808
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800 1007321.8 0 0.081136977 0.079825976 0 0.16096295
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900 1002801.7 0 0.091236148 0.090833816 0 0.18206996
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1000 1010134.7 0 0.10091362 0.10023906 0 0.20115269
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1100 990246.55 0 0.1118367 0.11141049 0 0.22324719
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1200 1010555.5 0 0.12091736 0.12355456 0 0.24447192
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1300 997117.19 0 0.13099592 0.13292775 0 0.26392367
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1400 1020817.1 0 0.14167961 0.14172898 0 0.28340859
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1500 1015048.1 0 0.15225884 0.15162948 0 0.30388833
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1600 990291.98 0 0.16460973 0.16251919 0 0.32712891
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1700 980848.58 0 0.17380313 0.17351201 0 0.34731513
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1800 1000673.8 0 0.18383991 0.18175453 0 0.36559445
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1900 1009388.9 0 0.19411523 0.19367453 0 0.38778976
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2000 1005935.9 0 0.2015342 0.20585359 0 0.40738779
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2100 985500.56 0 0.21161056 0.21238463 0 0.42399519
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2200 997241.34 0 0.21841986 0.22117922 0 0.43959908
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2300 1011672.3 0 0.22688099 0.23155741 0 0.4584384
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2400 989837.68 0 0.23849839 0.24219 0 0.48068839
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2500 1035706.8 0 0.24541408 0.24947563 0 0.49488971
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2600 992370.08 0 0.25537803 0.25758332 0 0.51296135
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2700 990586.56 0 0.26542605 0.26762286 0 0.53304892
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2800 1002767.3 0 0.27570392 0.27874972 0 0.55445363
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2900 995307.27 0 0.28580946 0.29115624 0 0.5769657
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3000 1024317.7 0 0.29493208 0.30208924 0 0.59702132
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Loop time of 0.413047 on 4 procs for 3000 steps with 3600 atoms
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Performance: 6275.312 tau/day, 7263.093 timesteps/s
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98.0% 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 | 0.00016236 | 0.00016338 | 0.00016403 | 0.0 | 0.04
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Comm | 0.0026367 | 0.0030084 | 0.0031497 | 0.4 | 0.73
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Output | 0.0011849 | 0.0013574 | 0.0018065 | 0.7 | 0.33
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Modify | 0.34447 | 0.35223 | 0.36357 | 1.2 | 85.28
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Other | | 0.05629 | | | 13.63
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Nlocal: 900.000 ave 906 max 891 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 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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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 = 22
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Dangerous builds = 0
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Total wall time: 0:00:00
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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}_${gamma_t}
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||||
variable params string gaussian_5.0_${gamma_t}
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||||
variable params string gaussian_5.0_1.0
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|
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units lj
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||||
atom_style atomic
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||||
dimension 3
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||||
newton off
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||||
|
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lattice sc 0.4
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Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
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region box block -8 8 -8 8 -8 8
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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
|
||||
Reference in New Issue
Block a user