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update ASPHERE box/srd example

This commit is contained in:
Axel Kohlmeyer 2021-06-17 10:35:07 -04:00
parent 5a511c2e92
commit a90a48c038
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8 changed files with 1306 additions and 649 deletions
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6
examples/ASPHERE/box/in.box
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@ -7,7 +7,7 @@ dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
fix molprop all property/atom mol ghost yes
read_data data.box fix molprop NULL Molecules
set type 1 mass 1.0
@ -17,7 +17,7 @@ velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
@ -108,4 +108,4 @@ thermo 1000
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 10000

130
examples/ASPHERE/box/in.box.mp
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@ -1,112 +1,112 @@
# SRD viscosity demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.box fix molprop NULL Molecules
fix molprop all property/atom mol ghost yes
read_data data.box fix molprop NULL Molecules
set type 1 mass 1.0
group big type 1
velocity big create 1.44 87287 loop geom
set type 1 mass 1.0
group big type 1
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
fix 2 all enforce2d
fix 1 big rigid molecule
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
#dump 1 all atom 10 dump.box.equil
compute tbig all temp/sphere
thermo_modify temp tbig
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
thermo 100
run 1000
#undump 1
unfix soft
unfix 1
unfix 2
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
create_atoms 2 region plane
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
create_atoms 2 region plane
set type 2 mass 0.1
group small type 2
velocity small create 1.0 593849 loop geom
set type 2 mass 0.1
group small type 2
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
delete_atoms overlap 1.0 small big
# SRD run
reset_timestep 0
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
timestep 0.001
fix 1 big rigid molecule
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
fix 1 big rigid molecule
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
thermo 1000
thermo_modify temp tbig
thermo 1000
#dump 1 all atom 1000 dump.box.mp
#dump 1 all atom 1000 dump.box.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
run 10000

309
examples/ASPHERE/box/log.17Jun21.box.g++.1 Normal file
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@ -0,0 +1,309 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.box fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
420 atoms
read_data CPU = 0.002 seconds
set type 1 mass 1.0
Setting atom values ...
420 settings made for mass
group big type 1
420 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 54 54 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.570 | 5.570 | 5.570 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.4252596 0 0 0.14931291 -8.727261
100 4.7699234 3.4203218 0 3.9200281 0.63667047
200 14.850064 5.3315601 0 6.8872811 0.71533738
300 21.249889 7.2094878 0 9.4356667 1.0710181
400 24.551027 9.2008598 0 11.772872 1.0133205
500 23.999755 11.562353 0 14.076613 1.3275867
600 25.022182 13.731564 0 16.352935 1.0236907
700 26.601942 15.850142 0 18.637012 0.80166569
800 24.154216 18.395444 0 20.925886 1.7521839
900 27.3897 20.3322 0 23.201597 0.65472411
1000 27.381112 22.600716 0 25.469214 0.69152692
Loop time of 0.0920079 on 1 procs for 1000 steps with 420 atoms
Performance: 4695251.138 tau/day, 10868.637 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.029557 | 0.029557 | 0.029557 | 0.0 | 32.12
Neigh | 0.011621 | 0.011621 | 0.011621 | 0.0 | 12.63
Comm | 0.0041208 | 0.0041208 | 0.0041208 | 0.0 | 4.48
Output | 0.00034363 | 0.00034363 | 0.00034363 | 0.0 | 0.37
Modify | 0.042122 | 0.042122 | 0.042122 | 0.0 | 45.78
Other | | 0.004243 | | | 4.61
Nlocal: 420.000 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84.0000 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 562.000 ave 562 max 562 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 562
Ave neighs/atom = 1.3380952
Neighbor list builds = 158
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 124609 atoms
create_atoms CPU = 0.042 seconds
set type 2 mass 0.1
Setting atom values ...
124609 settings made for mass
group small type 2
124609 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 28 28 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308)
Deleted 51030 atoms, new total = 73999
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483)
thermo 1000
#dump 1 all atom 1000 dump.box
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comp.~Phys.~Comm.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Stratford2018,
author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},
title = {Implementation of multi-level contact detection in LAMMPS},
year = {2018}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {DEM simulations of polydisperse media: efficient contact
detection applied to investigate the quasi-static limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
- fix srd command:
@Article{Petersen10,
author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.},
year = 2010,
volume = 132,
pages = {174106}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
SRD info:
SRD/big particles = 73579 420
big particle diameter max/min = 1.0000000 1.0000000
SRD temperature & lamda = 1.0000000 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 153 153 1
SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000
SRD per actual grid cell = 4.0557326
SRD viscosity = 0.22929663
big/SRD mass density ratio = 0.19661407
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1966772 7.7276214
ave/max big velocity = 2.1275716 5.8359099
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 38.289379, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 75.37 | 75.37 | 75.37 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.7986429 16232 0.24173874 42.193535 42.591488 10.849557 10086 45 45 0 1004 51984 23409 16232 0.91196906 0 5 0
2000 1.4227624 16312 0.24027816 42.185099 42.334151 11.114609 10229 28 28 0 1829 51984 23409 16312 0.91266737 0 5 0
3000 1.2870561 16338 0.24012829 42.172911 42.307746 9.1532934 10247 29 29 0 2474 51984 23409 16338 0.92249481 0 5 0
4000 0.99207377 16354 0.23996323 42.174734 42.278665 13.010306 10390 42 42 0 3137 51984 23409 16354 0.93252257 0 5 0
5000 1.2778672 16234 0.24012389 42.1731 42.306972 11.375628 10158 39 39 0 3802 51984 23409 16234 0.93405963 0 7 0
6000 0.92241679 16273 0.23984728 42.161601 42.258235 9.4164757 10190 34 35 0 4514 51984 23409 16273 0.94347665 0 7 0
7000 1.4747828 16291 0.24015741 42.158375 42.312876 11.273642 10208 40 40 0 5231 51984 23409 16291 0.94315382 0 7 0
8000 1.143932 16385 0.23997671 42.1612 42.28104 11.518583 10409 31 31 0 5954 51984 23409 16385 0.94024078 0 7 0
9000 1.123729 16298 0.23981793 42.135341 42.253065 14.210625 10067 51 51 0 6654 51984 23409 16298 0.9463894 0 7 0
10000 1.0362924 16356 0.23977465 42.136875 42.245439 10.19621 10227 33 34 0 7437 51984 23409 16356 0.94188712 0 7 0
Loop time of 41.8379 on 1 procs for 10000 steps with 73999 atoms
Performance: 20651.124 tau/day, 239.018 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.44984 | 0.44984 | 0.44984 | 0.0 | 1.08
Neigh | 0.11618 | 0.11618 | 0.11618 | 0.0 | 0.28
Comm | 0.4757 | 0.4757 | 0.4757 | 0.0 | 1.14
Output | 0.0035887 | 0.0035887 | 0.0035887 | 0.0 | 0.01
Modify | 40.52 | 40.52 | 40.52 | 0.0 | 96.85
Other | | 0.2722 | | | 0.65
Nlocal: 73999.0 ave 73999 max 73999 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 135.000 ave 135 max 135 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2407.00 ave 2407 max 2407 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2407
Ave neighs/atom = 0.032527467
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:45

309
examples/ASPHERE/box/log.17Jun21.box.g++.4 Normal file
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@ -0,0 +1,309 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# SRD diffusion demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.box fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000)
2 by 2 by 1 MPI processor grid
reading atoms ...
420 atoms
read_data CPU = 0.009 seconds
set type 1 mass 1.0
Setting atom values ...
420 settings made for mass
group big type 1
420 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 54 54 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.558 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.4252596 0 0 0.14931291 -8.727261
100 4.7699234 3.4203218 0 3.9200281 0.63667047
200 14.850064 5.3315601 0 6.8872811 0.71533738
300 21.249889 7.2094878 0 9.4356667 1.0710181
400 24.551027 9.2008598 0 11.772872 1.0133205
500 23.999755 11.562353 0 14.076613 1.3275867
600 25.022182 13.731564 0 16.352935 1.0236907
700 26.601942 15.850142 0 18.637012 0.80166569
800 24.154216 18.395444 0 20.925886 1.7521839
900 27.3897 20.3322 0 23.201597 0.65472411
1000 27.381112 22.600716 0 25.469214 0.69152692
Loop time of 0.102477 on 4 procs for 1000 steps with 420 atoms
Performance: 4215597.184 tau/day, 9758.327 timesteps/s
87.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0086884 | 0.011084 | 0.012345 | 1.4 | 10.82
Neigh | 0.0038968 | 0.0042393 | 0.0045272 | 0.4 | 4.14
Comm | 0.028577 | 0.030455 | 0.032476 | 1.0 | 29.72
Output | 0.00028127 | 0.00044494 | 0.0009265 | 0.0 | 0.43
Modify | 0.041755 | 0.042937 | 0.044332 | 0.4 | 41.90
Other | | 0.01332 | | | 13.00
Nlocal: 105.000 ave 130 max 77 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 39.0000 ave 49 max 21 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 140.500 ave 180 max 105 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 562
Ave neighs/atom = 1.3380952
Neighbor list builds = 158
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 124609 atoms
create_atoms CPU = 0.025 seconds
set type 2 mass 0.1
Setting atom values ...
124609 settings made for mass
group small type 2
124609 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 28 28 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308)
Deleted 51030 atoms, new total = 73999
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483)
thermo 1000
#dump 1 all atom 1000 dump.box
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comp.~Phys.~Comm.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Stratford2018,
author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},
title = {Implementation of multi-level contact detection in LAMMPS},
year = {2018}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {DEM simulations of polydisperse media: efficient contact
detection applied to investigate the quasi-static limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
- fix srd command:
@Article{Petersen10,
author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.},
year = 2010,
volume = 132,
pages = {174106}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
SRD info:
SRD/big particles = 73579 420
big particle diameter max/min = 1.0000000 1.0000000
SRD temperature & lamda = 1.0000000 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 153 153 1
SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000
SRD per actual grid cell = 4.0557326
SRD viscosity = 0.22929663
big/SRD mass density ratio = 0.19661407
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1966772 7.7276214
ave/max big velocity = 2.1275716 5.8359099
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 38.289379, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 27.16 | 27.18 | 27.21 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
1000 2.4803865 16183 0.24097572 42.197203 42.457053 10.685486 10313 34 34 0 1010 70756 23409 16183 0.91088084 0 10 0
2000 1.5192587 16288 0.2403558 42.18867 42.34783 12.991827 10247 51 51 0 1780 70756 23409 16288 0.91423542 0 10 0
3000 1.3453745 16254 0.24021083 42.181344 42.322288 10.311263 9901 36 36 0 2457 70756 23409 16254 0.92345925 0 10 0
4000 1.5208981 16348 0.24035467 42.188298 42.347631 11.118817 10195 32 33 2 3117 70756 23409 16348 0.93218296 0 10 0
5000 1.0700659 16291 0.2400755 42.186343 42.298445 9.3784033 10271 35 35 0 3810 70756 23409 16291 0.93211425 0 10 0
6000 1.0488908 16303 0.2400744 42.188368 42.298252 12.777782 10058 50 50 0 4557 70756 23409 16303 0.94151194 0 10 0
7000 1.331013 16244 0.24024721 42.189259 42.328698 10.953939 10388 36 36 0 5276 70756 23409 16244 0.94703063 0 10 0
8000 0.94738473 16321 0.23996282 42.179342 42.278592 11.767946 10161 41 41 0 5967 70756 23409 16321 0.94682195 0 10 0
9000 1.1009209 16291 0.24002765 42.17468 42.290015 8.045595 10584 33 33 0 6751 70756 23409 16291 0.94001295 0 10 0
10000 1.0564033 16282 0.23992848 42.161871 42.272542 12.284202 10257 40 40 0 7488 70756 23409 16282 0.94873736 0 10 0
Loop time of 30.6515 on 4 procs for 10000 steps with 73999 atoms
Performance: 28187.845 tau/day, 326.248 timesteps/s
90.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14666 | 0.20404 | 0.29182 | 13.1 | 0.67
Neigh | 0.040061 | 0.050996 | 0.068192 | 4.8 | 0.17
Comm | 1.087 | 1.2248 | 1.2747 | 7.2 | 4.00
Output | 0.0024737 | 0.0037751 | 0.0060755 | 2.4 | 0.01
Modify | 28.133 | 28.273 | 28.452 | 2.3 | 92.24
Other | | 0.8951 | | | 2.92
Nlocal: 18499.8 ave 20267 max 16093 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 74.5000 ave 90 max 57 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 590.250 ave 907 max 422 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 2361
Ave neighs/atom = 0.031905837
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:32

310
examples/ASPHERE/box/log.17Jun21.box.mp.g++.1 Normal file
View File

@ -0,0 +1,310 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.box fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
420 atoms
read_data CPU = 0.002 seconds
set type 1 mass 1.0
Setting atom values ...
420 settings made for mass
group big type 1
420 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 54 54 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.570 | 5.570 | 5.570 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.4252596 0 0 0.14931291 -8.727261
100 4.7699234 3.4203218 0 3.9200281 0.63667047
200 14.850064 5.3315601 0 6.8872811 0.71533738
300 21.249889 7.2094878 0 9.4356667 1.0710181
400 24.551027 9.2008598 0 11.772872 1.0133205
500 23.999755 11.562353 0 14.076613 1.3275867
600 25.022182 13.731564 0 16.352935 1.0236907
700 26.601942 15.850142 0 18.637012 0.80166569
800 24.154216 18.395444 0 20.925886 1.7521839
900 27.3897 20.3322 0 23.201597 0.65472411
1000 27.381112 22.600716 0 25.469214 0.69152692
Loop time of 0.0830324 on 1 procs for 1000 steps with 420 atoms
Performance: 5202788.685 tau/day, 12043.492 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.027522 | 0.027522 | 0.027522 | 0.0 | 33.15
Neigh | 0.011039 | 0.011039 | 0.011039 | 0.0 | 13.29
Comm | 0.0034208 | 0.0034208 | 0.0034208 | 0.0 | 4.12
Output | 0.00033641 | 0.00033641 | 0.00033641 | 0.0 | 0.41
Modify | 0.037199 | 0.037199 | 0.037199 | 0.0 | 44.80
Other | | 0.003515 | | | 4.23
Nlocal: 420.000 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84.0000 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 562.000 ave 562 max 562 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 562
Ave neighs/atom = 1.3380952
Neighbor list builds = 158
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 124609 atoms
create_atoms CPU = 0.044 seconds
set type 2 mass 0.1
Setting atom values ...
124609 settings made for mass
group small type 2
124609 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 28 28 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308)
Deleted 51030 atoms, new total = 73999
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483)
thermo 1000
#dump 1 all atom 1000 dump.box.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comp.~Phys.~Comm.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Stratford2018,
author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},
title = {Implementation of multi-level contact detection in LAMMPS},
year = {2018}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {DEM simulations of polydisperse media: efficient contact
detection applied to investigate the quasi-static limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
- fix srd command:
@Article{Petersen10,
author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.},
year = 2010,
volume = 132,
pages = {174106}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
SRD info:
SRD/big particles = 73579 420
big particle diameter max/min = 1.0000000 1.0000000
SRD temperature & lamda = 1.0000000 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 153 153 1
SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000
SRD per actual grid cell = 4.0557326
SRD viscosity = 0.22929663
big/SRD mass density ratio = 0.19661407
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1966772 7.7276214
ave/max big velocity = 2.1275716 5.8359099
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 38.289379, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 75.37 | 75.37 | 75.37 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
1000 2.9594916 16137 0.24127616 42.199945 42.509987 10.792325 10296 45 45 0 990 51984 23409 16137 0.90706131 0 10 0
2000 1.7108824 16274 0.24052684 42.198731 42.377967 9.5364607 10320 34 34 0 1741 51984 23409 16274 0.91369719 0 10 0
3000 1.3927232 16271 0.24024605 42.182589 42.328493 9.6211672 10122 29 29 0 2450 51984 23409 16271 0.92150155 0 10 0
4000 1.8264312 16304 0.24052774 42.186783 42.378124 9.2177883 10128 38 40 0 3114 51984 23409 16304 0.92089374 0 10 0
5000 1.6944513 16287 0.24043781 42.184766 42.36228 7.4352852 10198 31 31 0 3833 51984 23409 16287 0.92601496 0 10 0
6000 2.1923757 16301 0.24067781 42.174888 42.404565 11.864868 10340 39 39 0 4537 51984 23409 16301 0.93147673 0 10 0
7000 2.1699734 16292 0.24062985 42.168784 42.396114 9.6780093 9932 23 23 0 5290 51984 23409 16292 0.94127767 0 10 0
8000 2.8026605 16335 0.24100748 42.169037 42.462649 9.1457843 10044 38 38 0 6125 51984 23409 16335 0.93275263 0 10 0
9000 4.1434204 16297 0.24180594 42.169255 42.603328 12.358126 10095 37 37 0 6957 51984 23409 16297 0.9324244 0 10 0
10000 3.6168745 16237 0.24147749 42.166548 42.545459 9.1577014 10270 27 27 0 7779 51984 23409 16237 0.93952778 0 10 0
Loop time of 40.9072 on 1 procs for 10000 steps with 73999 atoms
Performance: 21120.990 tau/day, 244.456 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.44663 | 0.44663 | 0.44663 | 0.0 | 1.09
Neigh | 0.11472 | 0.11472 | 0.11472 | 0.0 | 0.28
Comm | 0.45946 | 0.45946 | 0.45946 | 0.0 | 1.12
Output | 0.0036154 | 0.0036154 | 0.0036154 | 0.0 | 0.01
Modify | 39.618 | 39.618 | 39.618 | 0.0 | 96.85
Other | | 0.2648 | | | 0.65
Nlocal: 73999.0 ave 73999 max 73999 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 126.000 ave 126 max 126 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2406.00 ave 2406 max 2406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2406
Ave neighs/atom = 0.032513953
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:44

310
examples/ASPHERE/box/log.17Jun21.box.mp.g++.4 Normal file
View File

@ -0,0 +1,310 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol ghost yes
read_data data.box fix molprop NULL Molecules
Reading data file ...
orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000)
2 by 2 by 1 MPI processor grid
reading atoms ...
420 atoms
read_data CPU = 0.003 seconds
set type 1 mass 1.0
Setting atom values ...
420 settings made for mass
group big type 1
420 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
compute tbig all temp/sphere
thermo_modify temp tbig
thermo 100
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42
ghost atom cutoff = 1.42
binsize = 0.71, bins = 54 54 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.558 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.4252596 0 0 0.14931291 -8.727261
100 4.7699234 3.4203218 0 3.9200281 0.63667047
200 14.850064 5.3315601 0 6.8872811 0.71533738
300 21.249889 7.2094878 0 9.4356667 1.0710181
400 24.551027 9.2008598 0 11.772872 1.0133205
500 23.999755 11.562353 0 14.076613 1.3275867
600 25.022182 13.731564 0 16.352935 1.0236907
700 26.601942 15.850142 0 18.637012 0.80166569
800 24.154216 18.395444 0 20.925886 1.7521839
900 27.3897 20.3322 0 23.201597 0.65472411
1000 27.381112 22.600716 0 25.469214 0.69152692
Loop time of 0.0821786 on 4 procs for 1000 steps with 420 atoms
Performance: 5256844.414 tau/day, 12168.621 timesteps/s
92.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0096035 | 0.011958 | 0.014498 | 1.7 | 14.55
Neigh | 0.0039157 | 0.0041593 | 0.0045318 | 0.4 | 5.06
Comm | 0.021053 | 0.022374 | 0.024067 | 0.8 | 27.23
Output | 0.00024565 | 0.00085109 | 0.0026608 | 0.0 | 1.04
Modify | 0.031525 | 0.034215 | 0.036481 | 1.2 | 41.63
Other | | 0.008622 | | | 10.49
Nlocal: 105.000 ave 130 max 77 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 39.0000 ave 49 max 21 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 140.500 ave 180 max 105 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 562
Ave neighs/atom = 1.3380952
Neighbor list builds = 158
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms 2 region plane
Created 124609 atoms
create_atoms CPU = 0.020 seconds
set type 2 mass 0.1
Setting atom values ...
124609 settings made for mass
group small type 2
124609 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
System init for delete_atoms ...
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 28 28 1
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/2d
bin: standard
(2) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:308)
Deleted 51030 atoms, new total = 73999
# SRD run
reset_timestep 0
neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
uncompute tbig
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:689)
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483)
thermo 1000
#dump 1 all atom 1000 dump.box.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {P.{\,}J.~in{\,}'t~Veld and S.{\,}J.~Plimpton and G.{\,}S.~Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comp.~Phys.~Comm.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Stratford2018,
author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},
title = {Implementation of multi-level contact detection in LAMMPS},
year = {2018}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {DEM simulations of polydisperse media: efficient contact
detection applied to investigate the quasi-static limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
- fix srd command:
@Article{Petersen10,
author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk},
title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.},
year = 2010,
volume = 132,
pages = {174106}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
SRD info:
SRD/big particles = 73579 420
big particle diameter max/min = 1.0000000 1.0000000
SRD temperature & lamda = 1.0000000 0.063245553
SRD max distance & max velocity = 0.25298221 12.649111
SRD grid counts: 153 153 1
SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000
SRD per actual grid cell = 4.0557326
SRD viscosity = 0.22929663
big/SRD mass density ratio = 0.19661407
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.1966772 7.7276214
ave/max big velocity = 2.1275716 5.8359099
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 38.289379, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 27.16 | 27.18 | 27.21 Mbytes
Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.1072437 16288 0.24129297 42.187428 42.512949 11.859485 10412 35 35 0 1004 70756 23409 16288 0.91643759 0 66 0
2000 2.1718238 16265 0.24069263 42.179651 42.407175 11.539339 10224 48 48 0 1797 70756 23409 16265 0.91071196 0 66 0
3000 1.5732455 16326 0.24032934 42.178352 42.343168 10.457457 10058 45 45 0 2517 70756 23409 16326 0.91928964 0 66 0
4000 2.3482192 16229 0.24085032 42.188956 42.43496 10.606093 10150 43 43 0 3181 70756 23409 16229 0.91913606 0 66 0
5000 2.5996379 16333 0.2410073 42.190274 42.462617 11.204793 10528 38 38 0 3885 70756 23409 16333 0.9241125 0 66 0
6000 2.4105417 16271 0.24084161 42.180891 42.433424 9.8492284 10088 30 30 0 4620 70756 23409 16271 0.93147983 0 66 0
7000 2.2377455 16250 0.24081836 42.194898 42.429329 9.2171742 10091 34 34 0 5351 70756 23409 16250 0.92985862 0 66 0
8000 2.9660933 16303 0.24115329 42.177606 42.48834 9.4008156 10139 39 39 0 6167 70756 23409 16303 0.92973123 0 66 0
9000 2.9430592 16287 0.24114154 42.177948 42.486269 10.347006 10329 41 41 0 6957 70756 23409 16287 0.93491985 0 66 0
10000 2.9059731 16336 0.2410888 42.172541 42.476977 8.1176194 10272 31 31 0 7736 70756 23409 16336 0.94200526 0 66 0
Loop time of 24.5198 on 4 procs for 10000 steps with 73999 atoms
Performance: 35236.804 tau/day, 407.833 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 | 0.14222 | 0.18851 | 0.26138 | 11.1 | 0.77
Neigh | 0.039759 | 0.047049 | 0.058019 | 3.3 | 0.19
Comm | 0.58081 | 0.65008 | 0.68833 | 5.4 | 2.65
Output | 0.0024264 | 0.0030395 | 0.0048751 | 1.9 | 0.01
Modify | 23.123 | 23.276 | 23.388 | 2.3 | 94.93
Other | | 0.3547 | | | 1.45
Nlocal: 18499.8 ave 19805 max 17016 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 71.0000 ave 86 max 62 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Neighs: 604.000 ave 818 max 455 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 2416
Ave neighs/atom = 0.032649090
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:26

290
examples/ASPHERE/box/log.1Feb14.box.g++.8
View File

@ -1,290 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD diffusion demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.box fix molprop NULL Molecules
orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
420 atoms
set type 1 mass 1.0
420 settings made for mass
group big type 1
420 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
thermo 100
run 1000
Memory usage per processor = 0.443012 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 -8.770036
100 0 3.4203218 0 3.4203218 0.49351517
200 0 5.3315601 0 5.3315601 0.26965614
300 0 7.2094878 0 7.2094878 0.43326479
400 0 9.2008598 0 9.2008598 0.27649318
500 0 11.562353 0 11.562353 0.60730421
600 0 13.731564 0 13.731564 0.27272312
700 0 15.850142 0 15.850142 0.0032862218
800 0 18.395444 0 18.395444 1.0272658
900 0 20.3322 0 20.3322 -0.16729762
1000 0 22.600716 0 22.600716 -0.13023705
Loop time of 0.0534293 on 8 procs for 1000 steps with 420 atoms
Pair time (%) = 0.00388658 (7.27425)
Neigh time (%) = 0.0012759 (2.38801)
Comm time (%) = 0.0151907 (28.4315)
Outpt time (%) = 0.000330567 (0.618701)
Other time (%) = 0.0327455 (61.2876)
Nlocal: 52.5 ave 67 max 35 min
Histogram: 1 1 1 0 1 0 0 1 1 2
Nghost: 30.625 ave 41 max 17 min
Histogram: 1 0 0 1 1 1 2 0 1 1
Neighs: 70.25 ave 90 max 44 min
Histogram: 2 0 0 1 1 0 1 0 0 3
Total # of neighbors = 562
Ave neighs/atom = 1.3381
Neighbor list builds = 158
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 124609 atoms
set type 2 mass 0.1
124609 settings made for mass
group small type 2
124609 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
Deleted 51030 atoms, new total = 73999
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 1000 dump.box
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 73579 420
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 153 153 1
SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1
SRD per actual grid cell = 4.05573
SRD viscosity = 0.229297
big/SRD mass density ratio = 0.196614
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19668 7.72762
ave/max big velocity = 2.12757 5.83591
Memory usage per processor = 14.2707 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.4640099 16291 0.24158286 42.201127 42.564024 10.312083 10282 38 38 0 957 90440 23409 16291 0.91054529 0 69 0
2000 1.4820124 16228 0.24022248 42.169082 42.324341 9.5969069 10066 30 30 0 1726 90440 23409 16228 0.91140743 0 69 0
3000 1.3797075 16198 0.24017061 42.170661 42.315202 11.093574 10151 43 43 0 2410 90440 23409 16198 0.91909014 0 69 0
4000 1.3403741 16287 0.24014493 42.170257 42.310677 10.101336 10172 38 38 0 3094 90440 23409 16287 0.92752333 0 69 0
5000 1.0444432 16295 0.2399965 42.175108 42.284525 9.5498999 10375 26 26 0 3799 90440 23409 16295 0.93506273 0 69 0
6000 0.78295352 16299 0.2398933 42.184319 42.266343 9.535916 10090 37 37 0 4563 90440 23409 16299 0.93041308 0 69 0
7000 1.1675613 16333 0.24006565 42.174393 42.296709 11.594065 10426 37 37 0 5266 90440 23409 16333 0.94031182 0 69 0
8000 1.1343357 16302 0.24001364 42.168711 42.287546 9.8091173 9979 39 39 0 5993 90440 23409 16302 0.94116994 0 69 0
9000 1.4165164 16306 0.24010969 42.156072 42.304469 10.736953 10191 38 39 1 6683 90440 23409 16306 0.93957787 0 69 0
10000 0.63657628 16306 0.23958347 42.145066 42.211755 6.3923231 10115 37 37 0 7409 90440 23409 16306 0.9420945 0 69 0
11000 0.9421837 16286 0.23976832 42.145619 42.244324 9.9611184 10079 45 45 0 8122 90440 23409 16286 0.94240902 0 69 0
12000 0.9735159 16295 0.23980202 42.148274 42.250262 11.862106 10345 36 36 0 8854 90440 23409 16295 0.94994179 0 69 0
13000 0.93356977 16392 0.23970059 42.134589 42.232391 11.29915 10321 41 41 0 9607 90440 23409 16392 0.94747955 0 69 0
14000 1.0596151 16306 0.2397451 42.129226 42.240233 12.305503 10075 37 37 0 10323 90440 23409 16306 0.94857373 0 69 0
15000 1.4275311 16285 0.23986502 42.11181 42.261361 8.6785032 9963 43 43 0 11054 90440 23409 16285 0.95130035 0 69 0
16000 1.1798179 16367 0.23973717 42.115236 42.238836 9.7201163 10138 38 38 0 11785 90440 23409 16367 0.94838949 0 69 0
17000 1.2809316 16368 0.23978706 42.113433 42.247626 7.4568393 10239 31 31 0 12545 90440 23409 16368 0.94818482 0 69 0
18000 1.0552359 16355 0.23962676 42.108834 42.219382 11.024507 10270 39 39 0 13350 90440 23409 16355 0.94825339 0 69 0
19000 1.1373204 16343 0.23964456 42.103371 42.222519 9.1505749 10245 37 37 0 14198 90440 23409 16343 0.94776971 0 69 0
20000 0.89607862 16295 0.23962161 42.1246 42.218475 8.377591 10173 48 48 0 14985 90440 23409 16295 0.95836326 0 69 0
21000 0.93823225 16323 0.23958542 42.113808 42.212099 9.9128627 10398 39 39 0 15722 90440 23409 16323 0.94732512 0 69 0
22000 1.0132051 16270 0.23958637 42.106121 42.212267 12.521464 10414 37 37 1 16538 90440 23409 16270 0.94611956 0 69 0
23000 1.2399208 16420 0.2396696 42.097034 42.226931 9.1607507 10169 32 32 0 17263 90440 23409 16420 0.95141771 0 69 0
24000 1.2359103 16395 0.23957354 42.080529 42.210006 10.051289 10225 34 34 1 18057 90440 23409 16395 0.95487046 0 69 0
25000 0.96280337 16322 0.23944374 42.086271 42.187136 11.818136 10183 40 40 0 18818 90440 23409 16322 0.95691179 0 69 0
26000 0.83139747 16344 0.23940306 42.09287 42.179968 10.844701 10090 38 38 0 19555 90440 23409 16344 0.95332651 0 69 0
27000 1.107274 16270 0.23949948 42.080957 42.196957 14.435937 10028 46 46 0 20355 90440 23409 16270 0.95321506 0 69 0
28000 1.0892583 16399 0.23938721 42.063064 42.177177 9.3768225 10011 38 38 0 21195 90440 23409 16399 0.95935372 0 69 0
29000 1.1099534 16320 0.23940855 42.064655 42.180936 8.8044985 9919 34 34 0 22020 90440 23409 16320 0.95465302 0 69 0
30000 1.0119272 16302 0.23934223 42.06324 42.169252 12.13721 10160 47 47 0 22750 90440 23409 16302 0.94922806 0 69 0
31000 0.9567755 16335 0.23916982 42.038642 42.138875 8.3903033 10007 30 30 0 23497 90440 23409 16335 0.95223124 0 69 0
32000 0.86048362 16291 0.23910468 42.037252 42.127398 11.646647 10347 41 41 0 24266 90440 23409 16291 0.95484469 0 69 0
33000 1.1129645 16284 0.23928206 42.042053 42.15865 9.0389494 9909 33 33 0 25073 90440 23409 16284 0.96246044 0 69 0
34000 1.0741874 16303 0.23920774 42.033022 42.145556 12.710332 10125 35 35 0 25845 90440 23409 16303 0.95343962 0 69 0
35000 0.87606515 16293 0.23916564 42.046361 42.138139 13.784203 10044 42 42 0 26569 90440 23409 16293 0.95827172 0 69 0
36000 0.8268686 16315 0.23912916 42.045087 42.131712 13.474499 10240 43 44 0 27324 90440 23409 16315 0.9539089 0 69 0
37000 1.1732368 16336 0.23930076 42.039035 42.161945 8.7392785 9996 34 34 0 28094 90440 23409 16336 0.95672234 0 69 0
38000 1.089263 16323 0.2391967 42.029498 42.143611 9.464664 10104 39 39 0 28856 90440 23409 16323 0.95362271 0 69 0
39000 1.06444 16335 0.23919427 42.03167 42.143183 10.036973 9961 36 36 0 29607 90440 23409 16335 0.95464483 0 69 0
40000 1.1390869 16376 0.23927054 42.037288 42.156621 9.8133871 10206 38 38 0 30409 90440 23409 16376 0.95191201 0 69 0
41000 0.76020035 16347 0.23906101 42.040064 42.119704 10.826738 10406 41 41 0 31195 90440 23409 16347 0.94685002 0 69 0
42000 1.3087439 16311 0.23945151 42.051398 42.188505 11.375199 10219 45 45 0 31938 90440 23409 16311 0.95326292 0 69 0
43000 0.98306175 16313 0.23923796 42.047893 42.15088 10.536429 10269 47 47 0 32660 90440 23409 16313 0.94791465 0 69 0
44000 1.1067947 16299 0.23929754 42.045427 42.161377 10.366386 10166 33 33 0 33471 90440 23409 16299 0.9520033 0 69 0
45000 1.1754605 16269 0.2394174 42.059352 42.182496 7.898603 9985 37 37 0 34245 90440 23409 16269 0.95500544 0 69 0
46000 0.93860976 16272 0.23926541 42.057387 42.155717 11.566786 10108 35 35 0 35050 90440 23409 16272 0.95183186 0 69 0
47000 1.3576761 16315 0.23942 42.040721 42.182954 10.037574 9902 33 33 0 35807 90440 23409 16315 0.95525561 0 69 0
48000 1.3465813 16308 0.23938501 42.035719 42.176789 8.9584586 9830 33 33 0 36625 90440 23409 16308 0.95044669 0 69 0
49000 0.93823974 16340 0.23917669 42.041793 42.140085 10.474409 9930 35 35 0 37393 90440 23409 16340 0.94869206 0 69 0
50000 1.0643183 16332 0.23923523 42.0389 42.1504 8.9372951 9886 43 43 0 38182 90440 23409 16332 0.94865149 0 69 0
51000 0.87518396 16310 0.23914944 42.043598 42.135284 11.284535 9695 40 40 0 38995 90440 23409 16310 0.9560088 0 69 0
52000 1.1910982 16336 0.23929054 42.035364 42.160145 12.437325 9961 44 44 0 39787 90440 23409 16336 0.95735399 0 69 0
53000 1.0023949 16384 0.23923896 42.046043 42.151056 10.386358 9859 36 36 0 40569 90440 23409 16384 0.95693245 0 69 0
54000 0.98715708 16261 0.23921241 42.042962 42.146379 9.9941499 10027 35 35 0 41343 90440 23409 16261 0.951038 0 69 0
55000 1.0004435 16299 0.23914811 42.030241 42.135049 12.345206 9830 47 48 0 42056 90440 23409 16299 0.95562154 0 69 0
56000 1.0479458 16296 0.23914874 42.025377 42.135162 11.587952 9801 39 39 0 42915 90440 23409 16296 0.94868699 0 69 0
57000 0.94369119 16319 0.23902076 42.013749 42.112612 10.195934 9764 46 46 0 43652 90440 23409 16319 0.95438171 0 69 0
58000 1.1549569 16347 0.23924582 42.031269 42.152265 9.511812 9910 41 41 0 44366 90440 23409 16347 0.9484367 0 69 0
59000 0.81453047 16402 0.23895926 42.016445 42.101776 10.359564 9967 46 46 0 45115 90440 23409 16402 0.95256147 0 69 0
60000 0.9253868 16360 0.23897085 42.006873 42.103818 12.308731 9839 44 44 0 45872 90440 23409 16360 0.95753176 0 69 0
61000 0.95173279 16298 0.23908799 42.024752 42.124457 10.985428 9848 45 45 0 46621 90440 23409 16298 0.95937218 0 69 0
62000 1.0168886 16273 0.23910318 42.020603 42.127134 13.493586 9842 41 41 0 47356 90440 23409 16273 0.95720763 0 69 0
63000 0.59853847 16306 0.23888991 42.026854 42.089558 11.654045 10030 47 47 0 48152 90440 23409 16306 0.95164201 0 69 0
64000 0.88165231 16295 0.23904152 42.023907 42.11627 8.6017877 9808 31 31 0 48944 90440 23409 16295 0.95791125 0 69 0
65000 0.83089386 16306 0.23895929 42.014736 42.101782 11.57787 10042 51 51 0 49729 90440 23409 16306 0.95848466 0 69 0
66000 1.1172469 16324 0.23919188 42.025716 42.142761 11.423941 9802 55 55 0 50498 90440 23409 16324 0.94666759 0 69 0
67000 0.97470955 16356 0.23903681 42.013327 42.11544 11.345125 10043 40 40 0 51251 90440 23409 16356 0.95264876 0 69 0
68000 0.90592443 16274 0.23906764 42.025966 42.120872 11.050097 9782 44 44 0 52009 90440 23409 16274 0.95334971 0 69 0
69000 1.0820724 16352 0.23920813 42.032265 42.145625 11.892518 9803 43 43 0 52800 90440 23409 16352 0.95290952 0 69 0
70000 1.0413192 16301 0.23929529 42.051891 42.160982 13.193444 9847 48 48 0 53595 90440 23409 16301 0.95613844 0 69 0
71000 0.95433723 16430 0.23919345 42.04306 42.143038 12.116035 9898 46 46 0 54350 90440 23409 16430 0.95532726 0 69 0
72000 0.80923962 16318 0.23909626 42.041137 42.125915 10.240888 9800 37 37 0 55133 90440 23409 16318 0.95196829 0 69 0
73000 0.93773964 16330 0.23920083 42.046099 42.144338 13.100955 9780 37 37 0 55931 90440 23409 16330 0.95075325 0 69 0
74000 1.0547823 16296 0.23913003 42.021364 42.131865 12.215247 10308 45 45 0 56705 90440 23409 16296 0.95515593 0 69 0
75000 0.74939607 16287 0.23910386 42.048745 42.127253 10.270685 10092 43 43 0 57457 90440 23409 16287 0.95365363 0 69 0
76000 0.95221448 16326 0.23921923 42.047825 42.147581 10.33549 10191 47 47 0 58254 90440 23409 16326 0.95389896 0 69 0
77000 0.94854568 16249 0.23925669 42.054809 42.15418 10.317964 10055 35 35 1 59026 90440 23409 16249 0.95716276 0 69 0
78000 1.2663624 16282 0.23949043 42.062695 42.195362 10.496265 9893 41 41 0 59780 90440 23409 16282 0.94847998 0 69 0
79000 0.98933199 16264 0.2392933 42.056987 42.160631 12.876564 9946 41 41 0 60518 90440 23409 16264 0.95354593 0 69 0
80000 0.8212992 16341 0.23927469 42.07131 42.157351 8.5608431 9838 40 40 0 61296 90440 23409 16341 0.95234534 0 69 0
81000 0.98231967 16339 0.23928757 42.056712 42.159622 11.491156 10104 37 38 0 62061 90440 23409 16339 0.94886686 0 69 0
82000 0.99158973 16299 0.23925843 42.050607 42.154488 9.4538952 10047 37 37 0 62852 90440 23409 16299 0.95656275 0 69 0
83000 1.2341517 16344 0.239348 42.040977 42.170269 10.524371 9784 37 37 0 63608 90440 23409 16344 0.94780456 0 69 0
84000 1.1753084 16288 0.23928447 42.035947 42.159074 9.1748883 9831 37 37 0 64314 90440 23409 16288 0.94217045 0 69 0
85000 0.84912682 16310 0.23915288 42.046935 42.135891 11.43337 9890 42 42 0 64992 90440 23409 16310 0.9423407 0 69 0
86000 0.88939653 16275 0.23909757 42.032971 42.126146 12.34417 9961 46 46 0 65677 90440 23409 16275 0.93887016 0 69 0
87000 1.1303842 16248 0.23922093 42.029458 42.147879 11.934641 9945 47 47 0 66417 90440 23409 16248 0.93840688 0 69 0
88000 1.2294052 16326 0.23916023 42.00839 42.137185 9.7233305 9838 35 36 0 67149 90440 23409 16326 0.94945034 0 69 0
89000 1.0455638 16345 0.23918575 42.032147 42.141682 8.6325214 9871 35 35 0 67855 90440 23409 16345 0.94891424 0 69 0
90000 0.79047982 16288 0.23897011 42.020876 42.103688 10.271997 10053 45 45 0 68551 90440 23409 16288 0.94963234 0 69 0
91000 0.85451256 16320 0.23898107 42.016098 42.105619 12.567859 10053 42 42 0 69246 90440 23409 16320 0.9506585 0 69 0
92000 1.1082033 16363 0.23917252 42.023254 42.139351 11.730554 9858 46 46 0 70046 90440 23409 16363 0.95352701 0 69 0
93000 0.90368051 16312 0.23897927 42.010631 42.105303 10.70167 9793 37 37 0 70824 90440 23409 16312 0.95992717 0 69 0
94000 0.95749706 16350 0.23909592 42.025545 42.125855 10.174353 9970 42 42 0 71646 90440 23409 16350 0.95082103 0 69 0
95000 0.90723392 16298 0.23898239 42.010809 42.105853 11.561525 9938 33 33 0 72414 90440 23409 16298 0.94768554 0 69 0
96000 1.0249944 16288 0.23910408 42.019912 42.127292 10.755062 9945 38 38 0 73184 90440 23409 16288 0.94637131 0 69 0
97000 0.96263604 16339 0.23911151 42.027754 42.128601 9.9303923 9816 36 36 0 73853 90440 23409 16339 0.94851816 0 69 0
98000 0.93105892 16301 0.23897506 42.00702 42.10456 12.088691 9933 39 39 0 74604 90440 23409 16301 0.94785265 0 69 0
99000 1.2448977 16286 0.23920972 42.015487 42.145905 11.565661 10001 51 51 0 75328 90440 23409 16286 0.9483854 0 69 0
100000 0.95492648 16337 0.23919603 42.043453 42.143492 11.223512 9793 32 32 0 76045 90440 23409 16337 0.95143273 0 69 0
Loop time of 51.3335 on 8 procs for 100000 steps with 73999 atoms
Pair time (%) = 0.586967 (1.14344)
Neigh time (%) = 3.95145 (7.69761)
Comm time (%) = 2.97199 (5.78957)
Outpt time (%) = 0.0085291 (0.0166151)
Other time (%) = 43.8145 (85.3528)
Nlocal: 9249.88 ave 10642 max 7533 min
Histogram: 1 0 0 1 1 1 2 0 1 1
Nghost: 57.375 ave 89 max 34 min
Histogram: 1 2 0 1 1 0 2 0 0 1
Neighs: 335.875 ave 616 max 209 min
Histogram: 2 1 0 3 1 0 0 0 0 1
Total # of neighbors = 2687
Ave neighs/atom = 0.0363113
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

291
examples/ASPHERE/box/log.1Feb14.box.mp.g++.8
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@ -1,291 +0,0 @@
LAMMPS (1 Feb 2014)
# SRD viscosity demo - rigid box particles
units lj
atom_style sphere
atom_modify map array first big
dimension 2
# read in clusters of rigid bodies
fix molprop all property/atom mol
read_data data.box fix molprop NULL Molecules
orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
420 atoms
set type 1 mass 1.0
420 settings made for mass
group big type 1
420 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style soft 1.12
pair_coeff 1 1 0.0
pair_coeff 2 2 0.0 0.0
pair_coeff 1 2 0.0 0.0
variable prefactor equal ramp(0,60)
fix soft all adapt 1 pair soft a * * v_prefactor
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.box.equil
thermo 100
run 1000
Memory usage per processor = 0.443012 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 -8.770036
100 0 3.4203218 0 3.4203218 0.49351517
200 0 5.3315601 0 5.3315601 0.26965614
300 0 7.2094878 0 7.2094878 0.43326479
400 0 9.2008598 0 9.2008598 0.27649318
500 0 11.562353 0 11.562353 0.60730421
600 0 13.731564 0 13.731564 0.27272312
700 0 15.850142 0 15.850142 0.0032862218
800 0 18.395444 0 18.395444 1.0272658
900 0 20.3322 0 20.3322 -0.16729762
1000 0 22.600716 0 22.600716 -0.13023705
Loop time of 0.0540034 on 8 procs for 1000 steps with 420 atoms
Pair time (%) = 0.00388333 (7.1909)
Neigh time (%) = 0.0012731 (2.35743)
Comm time (%) = 0.0160792 (29.7743)
Outpt time (%) = 0.000274509 (0.508318)
Other time (%) = 0.0324934 (60.169)
Nlocal: 52.5 ave 67 max 35 min
Histogram: 1 1 1 0 1 0 0 1 1 2
Nghost: 30.625 ave 41 max 17 min
Histogram: 1 0 0 1 1 1 2 0 1 1
Neighs: 70.25 ave 90 max 44 min
Histogram: 2 0 0 1 1 0 1 0 0 3
Total # of neighbors = 562
Ave neighs/atom = 1.3381
Neighbor list builds = 158
Dangerous builds = 0
#undump 1
unfix soft
unfix 1
unfix 2
# add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 124609 atoms
set type 2 mass 0.1
124609 settings made for mass
group small type 2
124609 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 1.0
delete_atoms overlap 1.0 small big
Deleted 51030 atoms, new total = 73999
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule
30 rigid bodies with 420 atoms
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
fix 3 small viscosity 10 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/sphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 1000 dump.box.mp
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 73579 420
big particle diameter max/min = 1 1
SRD temperature & lamda = 1 0.0632456
SRD max distance & max velocity = 0.252982 12.6491
SRD grid counts: 153 153 1
SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1
SRD per actual grid cell = 4.05573
SRD viscosity = 0.229297
big/SRD mass density ratio = 0.196614
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19668 7.72762
ave/max big velocity = 2.12757 5.83591
Memory usage per processor = 14.2707 Mbytes
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
1000 3.0049838 16229 0.24126663 42.1935 42.508307 10.275827 10158 39 39 0 970 90440 23409 16229 0.90908897 0 5 0
2000 2.1454941 16282 0.24068985 42.18192 42.406686 8.3551805 10114 39 39 0 1766 90440 23409 16282 0.91411077 0 5 0
3000 1.7194781 16297 0.24043991 42.182513 42.362649 9.0500757 10293 35 35 0 2454 90440 23409 16297 0.91613392 0 5 0
4000 1.9700398 16189 0.24063155 42.190029 42.396415 11.380017 10043 27 28 0 3083 90440 23409 16189 0.92535621 0 5 0
5000 2.2262815 16301 0.24071918 42.178625 42.411854 10.059361 10169 29 29 0 3730 90440 23409 16301 0.92861813 0 5 0
6000 2.2291507 16232 0.24063671 42.163793 42.397323 7.276142 9899 40 40 0 4445 90440 23409 16232 0.93275834 0 5 0
7000 2.7841984 16212 0.2407729 42.129641 42.421319 10.838996 10144 39 39 0 5148 90440 23409 16212 0.93329636 0 5 0
8000 3.1799279 16294 0.24102189 42.132053 42.465189 9.3204165 10068 31 31 0 5897 90440 23409 16294 0.93229671 0 5 0
9000 3.6101913 16308 0.24126974 42.130646 42.508857 9.9117415 10113 30 30 0 6716 90440 23409 16308 0.93107227 0 5 0
10000 4.1022731 16319 0.24161934 42.140689 42.570451 9.8799373 10205 34 34 0 7480 90440 23409 16319 0.92489062 0 5 0
11000 4.2790298 16269 0.2417129 42.138657 42.586936 10.14836 10002 37 37 2 8283 90440 23409 16269 0.92331323 0 10 0
12000 4.4299614 16323 0.24179577 42.137445 42.601537 11.786696 10068 37 37 1 9085 90440 23409 16323 0.93507414 0 10 0
13000 4.1451629 16263 0.24166347 42.143972 42.578227 7.5907603 9931 27 27 0 9967 90440 23409 16263 0.93269278 0 10 0
14000 5.0478037 16299 0.24222245 42.147894 42.676711 9.616107 10010 39 39 0 10856 90440 23409 16299 0.93132197 0 10 0
15000 4.9761523 16318 0.24208522 42.131222 42.652533 10.028283 10181 45 45 0 11744 90440 23409 16318 0.92914494 0 10 0
16000 5.0281695 16300 0.24209471 42.127445 42.654206 13.025657 10410 38 38 0 12657 90440 23409 16300 0.9322983 0 10 0
17000 6.0553511 16294 0.24278108 42.140765 42.775135 8.3971756 9898 31 31 0 13606 90440 23409 16294 0.93207864 0 10 0
18000 5.8870865 16349 0.24261355 42.128876 42.745619 9.4579631 9872 33 33 0 14510 90440 23409 16349 0.92911772 0 10 0
19000 6.19767 16260 0.2425369 42.082834 42.732114 10.497489 10068 37 37 0 15478 90440 23409 16260 0.9258668 0 10 0
20000 5.0588231 16330 0.24187554 42.085618 42.61559 9.3582625 9935 35 35 0 16470 90440 23409 16330 0.92639501 0 10 0
21000 6.4272357 16337 0.24285051 42.11404 42.78737 11.339789 9973 38 38 0 17363 90440 23409 16337 0.91830732 0 10 0
22000 6.3660195 16301 0.24257121 42.071243 42.738159 10.340724 9855 41 41 0 18300 90440 23409 16301 0.92735973 0 13 0
23000 5.9141967 16265 0.24245321 42.097787 42.71737 10.888473 9874 46 46 0 19294 90440 23409 16265 0.92958577 0 13 0
24000 7.3326392 16305 0.24333743 42.104977 42.873159 8.159204 9831 32 32 0 20337 90440 23409 16305 0.92498949 0 13 0
25000 7.8712498 16317 0.24365329 42.104202 42.928809 13.3861 10107 51 52 0 21343 90440 23409 16317 0.92093733 0 13 0
26000 7.6909446 16302 0.24354679 42.104327 42.910045 9.3626418 10101 45 45 0 22390 90440 23409 16302 0.91881953 0 13 0
27000 7.7525711 16296 0.24366541 42.11877 42.930944 9.3545743 9869 31 31 0 23458 90440 23409 16296 0.92276633 0 13 0
28000 7.8688635 16287 0.24363999 42.102109 42.926466 9.6143934 10023 37 37 0 24515 90440 23409 16287 0.92561111 0 13 0
29000 8.1116441 16298 0.24396496 42.13393 42.983722 9.8457785 10018 37 37 0 25571 90440 23409 16298 0.92896968 0 13 0
30000 7.5432306 16233 0.24356273 42.12261 42.912853 10.484741 9978 33 33 0 26714 90440 23409 16233 0.92084331 0 13 0
31000 7.9849131 16251 0.24395097 42.144741 42.981256 8.728219 9926 36 36 0 27794 90440 23409 16251 0.91985968 0 13 0
32000 8.8200827 16255 0.24461412 42.174088 43.098096 9.4477224 10118 31 31 0 28911 90440 23409 16255 0.92764378 0 13 0
33000 9.0462578 16266 0.24476502 42.176979 43.124682 9.0256529 9948 41 41 0 30010 90440 23409 16266 0.92496675 0 13 0
34000 11.115911 16273 0.24591951 42.163566 43.32809 10.89006 10013 35 35 1 31155 90440 23409 16273 0.9209011 0 59 0
35000 9.5287387 16348 0.24494148 42.157524 43.155772 9.1589486 10058 33 33 0 32262 90440 23409 16348 0.91852697 0 59 0
36000 8.6525285 16271 0.24454224 42.178976 43.085431 9.6115865 9936 39 39 0 33447 90440 23409 16271 0.91738637 0 59 0
37000 9.3244405 16237 0.24490339 42.172216 43.149062 11.766374 10057 49 49 0 34660 90440 23409 16237 0.92209291 0 59 0
38000 9.2952308 16272 0.24496591 42.186292 43.160078 9.5173055 10039 32 32 1 35916 90440 23409 16272 0.91915422 0 59 0
39000 10.12307 16312 0.24550971 42.195376 43.255888 10.678168 9989 43 43 1 37116 90440 23409 16312 0.92499805 0 59 0
40000 11.051307 16266 0.24606279 42.195578 43.353334 10.078073 9867 37 37 0 38363 90440 23409 16266 0.9229677 0 59 0
41000 10.400692 16313 0.24566631 42.193882 43.283479 9.2181368 10040 39 39 0 39612 90440 23409 16313 0.92195363 0 59 0
42000 9.0646248 16277 0.24487452 42.194348 43.143975 8.2531891 10173 37 37 0 40821 90440 23409 16277 0.91941681 0 59 0
43000 9.8646504 16258 0.24532194 42.189366 43.222806 10.34072 10037 37 37 0 42068 90440 23409 16258 0.91264623 0 59 0
44000 10.441846 16296 0.24553053 42.165649 43.259556 12.147264 10299 31 31 0 43277 90440 23409 16296 0.91599514 0 59 0
45000 10.458302 16261 0.24544296 42.148496 43.244128 8.8999271 10208 26 26 0 44492 90440 23409 16261 0.91716968 0 59 0
46000 10.117248 16269 0.24511999 42.127322 43.187224 9.0053892 10132 36 36 0 45691 90440 23409 16269 0.91327538 0 59 0
47000 9.6094606 16247 0.24494761 42.150148 43.156854 11.844069 9936 43 43 0 46930 90440 23409 16247 0.91513796 0 59 0
48000 12.544005 16250 0.24661869 42.137144 43.451278 14.420938 9999 43 43 0 48233 90440 23409 16250 0.91642267 0 59 0
49000 11.948168 16257 0.24628573 42.140902 43.392614 8.653163 10093 38 38 0 49517 90440 23409 16257 0.90604463 0 59 0
50000 12.315254 16233 0.2466687 42.16992 43.460089 9.1125366 10050 39 39 0 50806 90440 23409 16233 0.90490961 0 59 0
51000 11.364234 16265 0.24609762 42.168932 43.359471 9.8694192 9860 37 37 0 52074 90440 23409 16265 0.909623 0 59 0
52000 10.627787 16231 0.24578998 42.191882 43.305269 10.869196 9877 33 33 0 53420 90440 23409 16231 0.90981484 0 59 0
53000 11.809423 16261 0.24656286 42.204263 43.441441 13.38992 9828 39 39 0 54766 90440 23409 16261 0.90710704 0 59 0
54000 10.63283 16251 0.24554697 42.148537 43.262453 10.181102 10098 29 29 0 56085 90440 23409 16251 0.90800902 0 59 0
55000 10.803075 16254 0.24562954 42.145251 43.277002 7.9856721 9964 26 26 0 57451 90440 23409 16254 0.90786888 0 59 0
56000 10.844803 16274 0.2458735 42.183861 43.319983 9.9407901 10031 36 36 0 58695 90440 23409 16274 0.89847818 0 59 0
57000 10.623373 16218 0.24574768 42.184891 43.297816 12.015798 9792 43 43 0 60012 90440 23409 16218 0.90944412 0 59 0
58000 10.679964 16262 0.24583434 42.194231 43.313084 11.651504 9776 45 45 0 61295 90440 23409 16262 0.90511687 0 59 0
59000 10.35931 16278 0.24567475 42.199706 43.284967 10.599471 10069 30 30 1 62506 90440 23409 16278 0.90064789 0 59 0
60000 12.034078 16208 0.24677506 42.218115 43.478828 10.511331 9936 31 31 0 63825 90440 23409 16208 0.90250225 0 59 0
61000 11.915856 16208 0.24666669 42.211407 43.459734 11.982448 10227 34 34 0 65189 90440 23409 16208 0.90006711 0 59 0
62000 11.388719 16269 0.24635856 42.212341 43.405445 8.4867265 9991 29 29 0 66502 90440 23409 16269 0.90418592 0 59 0
63000 10.513272 16243 0.24593174 42.228854 43.330244 9.2843187 10133 39 39 0 67836 90440 23409 16243 0.91282932 0 59 0
64000 11.465761 16203 0.24638806 42.209467 43.410642 8.8736184 10023 38 39 0 69216 90440 23409 16203 0.90742452 0 59 0
65000 9.9798452 16292 0.24547666 42.204557 43.250064 12.475112 9766 36 36 0 70559 90440 23409 16292 0.90921789 0 59 0
66000 12.184131 16177 0.2468175 42.209872 43.486305 8.4442171 10049 33 33 0 71851 90440 23409 16177 0.90771921 0 59 0
67000 11.845593 16250 0.24645726 42.181869 43.422835 8.2359478 9678 33 33 0 73241 90440 23409 16250 0.9069606 0 59 0
68000 10.616202 16220 0.2456631 42.17074 43.282913 7.6844013 9954 28 28 0 74707 90440 23409 16220 0.90830051 0 59 0
69000 11.708481 16174 0.246425 42.190549 43.417152 9.6601201 10019 34 34 0 76143 90440 23409 16174 0.90853993 0 59 0
70000 13.149115 16175 0.24730865 42.195313 43.57284 7.8721271 9794 31 31 0 77520 90440 23409 16175 0.90460472 0 59 0
71000 12.420743 16210 0.24676949 42.176626 43.477846 10.370102 9886 36 36 0 78901 90440 23409 16210 0.90567986 0 59 0
72000 13.424842 16222 0.24726211 42.158228 43.56464 10.837461 9892 36 36 0 80221 90440 23409 16222 0.90896224 0 59 0
73000 12.983985 16177 0.2470467 42.16646 43.526687 7.3246122 9975 31 31 0 81578 90440 23409 16177 0.90172487 0 59 0
74000 11.873207 16217 0.24644792 42.177329 43.421189 11.257297 9937 40 40 0 83004 90440 23409 16217 0.9069376 0 59 0
75000 11.719883 16219 0.24631358 42.169723 43.397521 8.2731229 10281 28 28 0 84503 90440 23409 16219 0.90087971 0 59 0
76000 11.648725 16220 0.24633978 42.181793 43.402136 11.364684 9961 31 31 0 85910 90440 23409 16220 0.90445518 0 59 0
77000 11.315159 16169 0.24618794 42.189986 43.375384 10.639734 9853 35 35 0 87272 90440 23409 16169 0.90967681 0 59 0
78000 11.026923 16262 0.2459278 42.17435 43.329551 9.3461335 10068 36 36 0 88765 90440 23409 16262 0.90250223 0 59 0
79000 11.923316 16205 0.24657893 42.195162 43.444272 8.3200696 9914 29 29 1 90167 90440 23409 16205 0.89792511 0 59 0
80000 12.28723 16233 0.246793 42.194756 43.481989 9.8594414 9898 41 41 0 91543 90440 23409 16233 0.89920018 0 59 0
81000 12.657271 16252 0.24700788 42.193847 43.519847 9.5478351 10045 38 38 0 92888 90440 23409 16252 0.90032559 0 59 0
82000 10.415047 16249 0.24563975 42.1877 43.2788 8.4502786 9729 30 30 0 94355 90440 23409 16249 0.90516702 0 59 0
83000 13.038087 16237 0.24718282 42.184776 43.550671 10.813181 9834 48 48 0 95792 90440 23409 16237 0.90160106 0 59 0
84000 11.994728 16253 0.24664911 42.200046 43.456637 10.907779 9632 48 48 0 97203 90440 23409 16253 0.90075335 0 59 0
85000 11.560331 16253 0.24626448 42.177788 43.38887 9.8019244 9637 27 27 0 98581 90440 23409 16253 0.90204694 0 59 0
86000 12.294346 16214 0.2466302 42.165325 43.453305 8.4731319 9776 30 30 1 100022 90440 23409 16214 0.8976977 0 59 0
87000 11.439691 16227 0.24593937 42.133145 43.331589 11.138197 9408 35 35 0 101446 90440 23409 16227 0.90678956 0 59 0
88000 12.269451 16218 0.24642733 42.132191 43.417562 9.2022903 9627 28 28 0 102882 90440 23409 16218 0.89354177 0 59 0
89000 11.630085 16281 0.24612243 42.145453 43.363843 9.4906584 9713 45 45 0 104390 90440 23409 16281 0.90416008 0 59 0
90000 12.068036 16226 0.24636746 42.142743 43.407014 13.55402 9721 30 30 1 105786 90440 23409 16226 0.90693102 0 59 0
91000 11.423374 16180 0.24593187 42.133533 43.330267 11.12182 9490 33 33 0 107319 90440 23409 16180 0.89908597 0 59 0
92000 11.759782 16253 0.24594059 42.099827 43.331804 8.5785997 9808 36 37 0 108822 90440 23409 16253 0.90323757 0 59 0
93000 12.860286 16203 0.24670999 42.120094 43.467362 9.7352723 9342 32 32 0 110320 90440 23409 16203 0.89837993 0 59 0
94000 12.65067 16201 0.24650827 42.106515 43.431823 11.726981 9708 37 37 0 111721 90440 23409 16201 0.90153973 0 59 0
95000 12.938398 16301 0.2467405 42.117288 43.472739 13.229664 9490 42 42 0 113106 90440 23409 16301 0.89222858 0 59 0
96000 13.125 16243 0.24672164 42.094416 43.469416 11.492955 9666 43 43 0 114441 90440 23409 16243 0.89369219 0 59 0
97000 14.779601 16270 0.24775001 42.102263 43.650602 9.7132418 9517 31 31 0 115831 90440 23409 16270 0.88854614 0 59 0
98000 15.427308 16254 0.24808383 42.093224 43.709418 11.821283 9510 36 37 0 117263 90440 23409 16254 0.88982996 0 59 0
99000 16.212104 16248 0.24846852 42.078784 43.777195 10.786344 9807 37 37 0 118659 90440 23409 16248 0.89136464 0 59 0
100000 15.896 16229 0.24841013 42.101613 43.766908 10.836017 9640 28 28 0 120081 90440 23409 16229 0.90018614 0 59 0
Loop time of 53.3125 on 8 procs for 100000 steps with 73999 atoms
Pair time (%) = 0.559711 (1.04987)
Neigh time (%) = 3.94754 (7.40453)
Comm time (%) = 3.46588 (6.50106)
Outpt time (%) = 0.00787139 (0.0147646)
Other time (%) = 45.3315 (85.0298)
Nlocal: 9249.88 ave 10477 max 8359 min
Histogram: 1 2 1 1 0 1 0 0 0 2
Nghost: 54 ave 65 max 45 min
Histogram: 2 1 0 0 1 1 0 2 0 1
Neighs: 316.875 ave 387 max 170 min
Histogram: 1 0 0 0 1 0 0 4 0 2
Total # of neighbors = 2535
Ave neighs/atom = 0.0342572
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation