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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2 by 2 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) = 5.553 | 5.553 | 5.553 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 6.5773093
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Loop time of 0.0424792 on 4 procs for 1000 steps with 200 atoms
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Performance: 10169676.521 tau/day, 23540.918 timesteps/s, 4.708 Matom-step/s
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98.0% 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 | 0.0022758 | 0.0023448 | 0.002442 | 0.1 | 5.52
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Neigh | 0.0011082 | 0.0011236 | 0.0011582 | 0.1 | 2.64
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Comm | 0.0099484 | 0.010092 | 0.010247 | 0.1 | 23.76
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Output | 9.551e-05 | 0.00010604 | 0.00013381 | 0.0 | 0.25
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Modify | 0.026025 | 0.026222 | 0.026405 | 0.1 | 61.73
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Other | | 0.00259 | | | 6.10
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Nlocal: 50 ave 55 max 47 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Nghost: 33.75 ave 38 max 32 min
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Histogram: 2 1 0 0 0 0 0 0 0 1
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Neighs: 68.75 ave 77 max 64 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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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 = 0.002 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 7.1846103
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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) = 13.2 | 13.21 | 13.22 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 4.0555746 0 0 0 0 0 0 0 0 0 0 0 0
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1000 1.1648085 3389 0.24643931 20.514525 21.382307 5.5927686 13390 59 59 0 1015 28224 5625 3389 1.1513276 0 111 0
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2000 1.1870311 3385 0.24701637 20.548037 21.432375 5.9269821 13271 57 57 2 1878 28224 5625 3385 1.1619099 0 111 0
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3000 1.1362839 3365 0.24577276 20.477942 21.324474 5.1621045 13244 59 60 1 2778 28224 5625 3365 1.1807679 0 111 0
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4000 1.3023748 3390 0.24679509 20.442907 21.413176 5.6127077 13413 65 65 1 3705 28224 5625 3390 1.1726946 0 111 0
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5000 1.195496 3387 0.2458055 20.43667 21.327314 6.1843476 13248 51 51 1 4638 28224 5625 3387 1.1730279 0 111 0
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6000 1.2389419 3387 0.24546635 20.374876 21.297888 5.5909826 13184 54 54 1 5494 28224 5625 3387 1.1859134 0 111 0
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7000 1.2068912 3378 0.24564722 20.414447 21.313581 8.5604547 13188 57 57 1 6428 28224 5625 3378 1.1499181 0 111 0
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8000 1.1014154 3374 0.24514746 20.449665 21.270219 7.3483529 13179 63 63 0 7591 28224 5625 3374 1.1769322 0 121 0
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9000 1.356464 3388 0.24749513 20.463349 21.473915 7.6809833 13138 50 50 2 8485 28224 5625 3388 1.1448659 0 121 0
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10000 1.1632951 3402 0.24560819 20.44354 21.310195 9.5738599 13323 64 67 0 9304 28224 5625 3402 1.1550136 0 121 0
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Loop time of 2.47185 on 4 procs for 10000 steps with 17353 atoms
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Performance: 349536.432 tau/day, 4045.561 timesteps/s, 70.203 Matom-step/s
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99.4% 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 | 0.037524 | 0.039903 | 0.042215 | 1.1 | 1.61
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Neigh | 0.01053 | 0.010805 | 0.011068 | 0.2 | 0.44
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Comm | 0.14536 | 0.14822 | 0.15102 | 0.6 | 6.00
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Output | 0.00051847 | 0.00054674 | 0.0006272 | 0.0 | 0.02
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Modify | 2.2276 | 2.2334 | 2.2381 | 0.3 | 90.35
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Other | | 0.03895 | | | 1.58
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Nlocal: 4338.25 ave 4488 max 4277 min
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Histogram: 2 1 0 0 0 0 0 0 0 1
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Nghost: 76.75 ave 85 max 69 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 331.25 ave 355 max 306 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 1325
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Ave neighs/atom = 0.076355673
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Neighbor list builds = 507
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Dangerous builds = 0
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Total wall time: 0:00:02
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