322 lines
14 KiB
Groff
322 lines
14 KiB
Groff
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# SRD diffusion demo - rigid star 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.star fix molprop NULL Molecules
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Reading data file ...
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orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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270 atoms
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read_data CPU = 0.011 seconds
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set type 1 mass 1.0
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Setting atom values ...
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270 settings made for mass
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group big type 1
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270 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 270 atoms
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.star.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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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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 = 38 38 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) = 5.562 | 5.562 | 5.562 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.3101488 0 0 0.21350573 0.32876464
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100 5.0954142 3.291475 0 4.1218387 1.0087565
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200 13.041252 4.6176595 0 6.7429006 1.5291618
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300 11.912727 7.0921814 0 9.0335147 1.9578844
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400 17.60886 8.3666709 0 11.236263 1.602563
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500 16.786375 10.630838 0 13.366396 1.7725508
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600 18.470347 12.42157 0 15.431552 2.1627885
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700 19.39794 14.349074 0 17.510219 1.9554238
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800 19.082984 16.464746 0 19.574566 2.2424126
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900 20.702091 18.253108 0 21.626782 1.8041661
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1000 18.299191 20.699563 0 23.681654 2.9475408
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Loop time of 0.0585091 on 1 procs for 1000 steps with 270 atoms
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Performance: 7383466.593 tau/day, 17091.358 timesteps/s, 4.615 Matom-step/s
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99.1% 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 | 0.017165 | 0.017165 | 0.017165 | 0.0 | 29.34
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Neigh | 0.0058479 | 0.0058479 | 0.0058479 | 0.0 | 9.99
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Comm | 0.0028221 | 0.0028221 | 0.0028221 | 0.0 | 4.82
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Output | 0.00017384 | 0.00017384 | 0.00017384 | 0.0 | 0.30
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Modify | 0.03015 | 0.03015 | 0.03015 | 0.0 | 51.53
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Other | | 0.00235 | | | 4.02
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Nlocal: 270 ave 270 max 270 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 73 ave 73 max 73 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 418 ave 418 max 418 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 418
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Ave neighs/atom = 1.5481481
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Neighbor list builds = 176
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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 60025 atoms
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using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
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create_atoms CPU = 0.013 seconds
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set type 2 mass 0.1
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Setting atom values ...
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60025 settings made for mass
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group small type 2
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60025 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 0.5
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delete_atoms overlap 0.5 small big
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System init for delete_atoms ...
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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 = 19 19 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:312)
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Deleted 16305 atoms, new total = 43990
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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 270 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:904)
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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:530)
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thermo 1000
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#dump 1 all atom 1000 dump.star
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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 = {in 't Veld, P. J. 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 = {Comput.\ Phys.\ Commut.},
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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{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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@article{Monti2022,
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author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava,
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Ishan and Silbert, Leonardo E. and Grest, Gary S.
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and Lechman, Jeremy B.},
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title = {Large-scale frictionless jamming with power-law particle
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size distributions},
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journal = {Phys. Rev. E},
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volume = {106}
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issue = {3}
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year = {2022}
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}
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- fix srd command: doi:10.1063/1.3419070
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@Article{Petersen10,
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author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
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G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
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title = {Mesoscale Hydrodynamics via Stochastic Rotation
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Dynamics: Comparison with {L}ennard-{J}ones Fluid},
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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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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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SRD info:
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SRD/big particles = 43720 270
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big particle diameter max/min = 1 1
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SRD temperature & lamda = 1 0.063245553
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SRD max distance & max velocity = 0.25298221 12.649111
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SRD grid counts: 106 106 1
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SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
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SRD per actual grid cell = 5.5586635
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SRD viscosity = 0.23558168
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big/SRD mass density ratio = 0.14409881
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WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
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# of rescaled SRD velocities = 0
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ave/max small velocity = 4.1908497 7.725824
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ave/max big velocity = 2.202625 5.4167964
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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 = 26.586808, 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/atomonly/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) = 41.29 | 41.29 | 41.29 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 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
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1000 1.2074332 8227 0.22959643 37.210444 37.407211 7.9007359 14317 47 47 0 649 28900 11236 8227 1.0260288 0 3 0
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2000 1.2044605 8206 0.22945824 37.188414 37.384697 5.8738384 14470 63 63 0 1423 28900 11236 8206 1.018589 0 4 0
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3000 1.1060368 8226 0.22936549 37.189341 37.369584 4.7013136 14255 51 51 0 2207 28900 11236 8226 1.0007203 0 4 0
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4000 1.2395587 8236 0.2294891 37.187723 37.389725 5.7916781 14371 56 56 0 2916 28900 11236 8236 1.0229966 0 4 0
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5000 1.3332555 8236 0.22962818 37.195112 37.412383 10.662157 14373 61 61 0 3740 28900 11236 8236 1.0094713 0 4 0
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6000 1.2991744 8192 0.22957221 37.191547 37.403264 1.2016626 14145 56 58 0 4425 28900 11236 8192 1.0215234 0 4 0
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7000 1.0110737 8147 0.22923336 37.18329 37.348057 6.2493424 14200 59 59 0 5102 28900 11236 8147 1.0163405 0 4 0
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8000 0.79508387 8168 0.22908516 37.194343 37.323912 9.832591 14355 45 45 0 5839 28900 11236 8168 1.0063207 0 4 0
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9000 1.0340542 8207 0.2292515 37.1825 37.351013 11.458942 14220 54 54 0 6606 28900 11236 8207 1.0074421 0 4 0
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10000 0.96342976 8202 0.22912995 37.174206 37.33121 1.7523017 14308 53 53 0 7379 28900 11236 8202 1.0126923 0 4 0
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Loop time of 18.5504 on 1 procs for 10000 steps with 43990 atoms
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Performance: 46575.737 tau/day, 539.071 timesteps/s, 23.714 Matom-step/s
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99.7% 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 | 0.21961 | 0.21961 | 0.21961 | 0.0 | 1.18
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Neigh | 0.055763 | 0.055763 | 0.055763 | 0.0 | 0.30
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Comm | 0.22073 | 0.22073 | 0.22073 | 0.0 | 1.19
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Output | 0.0013822 | 0.0013822 | 0.0013822 | 0.0 | 0.01
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Modify | 17.872 | 17.872 | 17.872 | 0.0 | 96.34
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Other | | 0.1812 | | | 0.98
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Nlocal: 43990 ave 43990 max 43990 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 138 ave 138 max 138 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1587 ave 1587 max 1587 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1587
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Ave neighs/atom = 0.036076381
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:20
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