310 lines
13 KiB
Groff
310 lines
13 KiB
Groff
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
|