313 lines
14 KiB
Groff
313 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 - dimer 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.dimer fix molprop NULL Molecules
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Reading data file ...
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orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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200 atoms
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read_data CPU = 0.001 seconds
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set type 1 mass 1.0
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Setting atom values ...
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200 settings made for mass
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group big type 1
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200 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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fix 1 big rigid molecule
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100 rigid bodies with 200 atoms
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.dimer.equil
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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 = 27 27 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 | 5.557 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3.4028231 0 0 0.83369167 -0.55065517
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100 9.5167872 2.392105 0 4.7237178 2.8319556
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200 13.564465 3.0352634 0 6.3585572 3.6388732
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300 13.133051 4.3835112 0 7.6011086 4.060051
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400 14.576837 5.5141059 0 9.0854309 4.422762
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500 15.227825 6.6472106 0 10.378028 4.8598912
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600 16.93219 7.454865 0 11.603251 5.2908894
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700 16.573769 8.7323442 0 12.792918 5.3544684
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800 17.482599 9.7221047 0 14.005341 5.6200973
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900 18.548144 10.739353 0 15.283649 4.7817995
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1000 18.068079 12.058417 0 16.485096 6.5773091
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Loop time of 0.0511113 on 1 procs for 1000 steps with 200 atoms
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Performance: 8452141.519 tau/day, 19565.142 timesteps/s, 3.913 Matom-step/s
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99.6% 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 | 0.0095507 | 0.0095507 | 0.0095507 | 0.0 | 18.69
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Neigh | 0.0042239 | 0.0042239 | 0.0042239 | 0.0 | 8.26
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Comm | 0.002203 | 0.002203 | 0.002203 | 0.0 | 4.31
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Output | 8.8531e-05 | 8.8531e-05 | 8.8531e-05 | 0.0 | 0.17
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Modify | 0.03336 | 0.03336 | 0.03336 | 0.0 | 65.27
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Other | | 0.001685 | | | 3.30
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Nlocal: 200 ave 200 max 200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 64 ave 64 max 64 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 275 ave 275 max 275 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 275
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Ave neighs/atom = 1.375
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Neighbor list builds = 193
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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 29929 atoms
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using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5)
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create_atoms CPU = 0.007 seconds
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set type 2 mass 0.1
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Setting atom values ...
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29929 settings made for mass
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group small type 2
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29929 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 = 14 14 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 12776 atoms, new total = 17353
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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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100 rigid bodies with 200 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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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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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.dimer
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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 = 17153 200
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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: 75 75 1
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SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1
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SRD per actual grid cell = 5.544404
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SRD viscosity = 0.23553122
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big/SRD mass density ratio = 0.14250828
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# of rescaled SRD velocities = 0
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ave/max small velocity = 4.191188 7.6900178
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ave/max big velocity = 2.6813242 7.1846104
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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 = 18.683304, 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) = 26.77 | 26.77 | 26.77 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 6.8392143 0 0.297476 20.71529 25.810505 4.0555741 0 0 0 0 0 0 0 0 0 0 0 0
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1000 1.2285566 3375 0.24673495 20.492683 21.407958 5.237464 13477 54 54 1 652 16900 5625 3375 1.1653557 0 15 0
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2000 1.3561011 3395 0.24763991 20.476182 21.486477 9.2878509 13435 67 67 0 1504 16900 5625 3395 1.1651182 0 15 0
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3000 1.2445369 3352 0.24713723 20.515681 21.442861 8.0289529 13186 62 63 2 2379 16900 5625 3352 1.1746721 0 15 0
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4000 1.1058201 3389 0.24596239 20.51709 21.340926 10.003266 13466 66 66 0 3264 16900 5625 3389 1.1671415 0 15 0
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5000 1.0584198 3407 0.24539623 20.503281 21.291804 9.1119405 13254 64 64 0 4189 16900 5625 3407 1.1687685 0 15 0
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6000 1.3335611 3360 0.24737788 20.470239 21.463742 8.6885126 13281 62 62 1 5031 16900 5625 3360 1.1568996 0 15 0
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7000 1.1384759 3401 0.24570869 20.47075 21.318914 9.1801119 13059 47 47 1 5878 16900 5625 3401 1.182474 0 15 0
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8000 1.2982334 3397 0.24667224 20.435333 21.402517 6.5904007 13405 56 56 0 6729 16900 5625 3397 1.169017 0 24 0
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9000 1.0456752 3381 0.24504517 20.482316 21.261344 10.497413 13205 81 81 2 7706 16900 5625 3381 1.1694675 0 24 0
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10000 1.2222547 3394 0.24653264 20.479825 21.390405 8.7495888 13296 68 68 1 8581 16900 5625 3394 1.1613437 0 24 0
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Loop time of 7.18514 on 1 procs for 10000 steps with 17353 atoms
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Performance: 120248.165 tau/day, 1391.761 timesteps/s, 24.151 Matom-step/s
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99.8% 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 | 0.14497 | 0.14497 | 0.14497 | 0.0 | 2.02
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Neigh | 0.031835 | 0.031835 | 0.031835 | 0.0 | 0.44
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Comm | 0.094201 | 0.094201 | 0.094201 | 0.0 | 1.31
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Output | 0.00082765 | 0.00082765 | 0.00082765 | 0.0 | 0.01
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Modify | 6.8507 | 6.8507 | 6.8507 | 0.0 | 95.35
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Other | | 0.06259 | | | 0.87
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Nlocal: 17353 ave 17353 max 17353 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1334 ave 1334 max 1334 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1334
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Ave neighs/atom = 0.076874316
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:07
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