311 lines
13 KiB
Groff
311 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 viscosity 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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1 by 1 by 1 MPI processor grid
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reading atoms ...
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420 atoms
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read_data CPU = 0.002 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) = 5.570 | 5.570 | 5.570 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 0.0830324 on 1 procs for 1000 steps with 420 atoms
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Performance: 5202788.685 tau/day, 12043.492 timesteps/s
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99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.027522 | 0.027522 | 0.027522 | 0.0 | 33.15
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Neigh | 0.011039 | 0.011039 | 0.011039 | 0.0 | 13.29
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Comm | 0.0034208 | 0.0034208 | 0.0034208 | 0.0 | 4.12
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Output | 0.00033641 | 0.00033641 | 0.00033641 | 0.0 | 0.41
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Modify | 0.037199 | 0.037199 | 0.037199 | 0.0 | 44.80
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Other | | 0.003515 | | | 4.23
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Nlocal: 420.000 ave 420 max 420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 84.0000 ave 84 max 84 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 562.000 ave 562 max 562 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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 = 0.044 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 small viscosity 10 x y 50
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fix 4 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.mp
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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) = 75.37 | 75.37 | 75.37 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 2.9594916 16137 0.24127616 42.199945 42.509987 10.792325 10296 45 45 0 990 51984 23409 16137 0.90706131 0 10 0
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Loop time of 40.9072 on 1 procs for 10000 steps with 73999 atoms
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Performance: 21120.990 tau/day, 244.456 timesteps/s
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99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.44663 | 0.44663 | 0.44663 | 0.0 | 1.09
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Neigh | 0.11472 | 0.11472 | 0.11472 | 0.0 | 0.28
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Comm | 0.45946 | 0.45946 | 0.45946 | 0.0 | 1.12
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Output | 0.0036154 | 0.0036154 | 0.0036154 | 0.0 | 0.01
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Modify | 39.618 | 39.618 | 39.618 | 0.0 | 96.85
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Other | | 0.2648 | | | 0.65
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Nlocal: 73999.0 ave 73999 max 73999 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 126.000 ave 126 max 126 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2406.00 ave 2406 max 2406 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2406
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Ave neighs/atom = 0.032513953
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:44
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