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