329 lines
18 KiB
Groff
329 lines
18 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 viscosity 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 0.0502552 on 1 procs for 1000 steps with 200 atoms
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Performance: 8596132.389 tau/day, 19898.455 timesteps/s, 3.980 Matom-step/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 | 0.0095071 | 0.0095071 | 0.0095071 | 0.0 | 18.92
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Neigh | 0.0042809 | 0.0042809 | 0.0042809 | 0.0 | 8.52
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Comm | 0.0022049 | 0.0022049 | 0.0022049 | 0.0 | 4.39
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Output | 0.0001259 | 0.0001259 | 0.0001259 | 0.0 | 0.25
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Modify | 0.032467 | 0.032467 | 0.032467 | 0.0 | 64.60
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Other | | 0.00167 | | | 3.32
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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 = 0.006 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 small viscosity 10 x y 50
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fix 4 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 500 dump.dimer.mp
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#dump 1 all image 500 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 25000
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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 1.3421139 3394 0.24797209 20.515424 21.515299 5.9986227 13474 52 52 1 704 16900 5625 3394 1.1328453 0 14 0
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2000 1.3372296 3366 0.24694513 20.429958 21.426194 9.640193 13302 74 74 0 1516 16900 5625 3366 1.1634167 0 14 0
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3000 1.4022742 3360 0.24799552 20.472637 21.517331 5.9446731 13483 47 47 0 2989 16900 5625 3360 1.1774442 0 217 0
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4000 1.6325677 3376 0.25066282 20.532497 21.74876 6.9698781 13206 61 61 2 4198 16900 5625 3376 1.1749717 0 217 0
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5000 2.0992887 3391 0.25484065 20.547279 22.111249 10.648531 13414 62 69 1 6389 16900 5625 3391 1.1862903 0 412 0
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6000 1.7584548 3388 0.25126127 20.490636 21.800684 8.68036 13456 58 58 0 7672 16900 5625 3388 1.1553986 0 412 0
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7000 2.2384486 3343 0.25650382 20.58791 22.255554 12.008146 13187 59 59 0 8879 16900 5625 3343 1.1728994 0 412 0
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8000 2.4981644 3380 0.25734806 20.467672 22.328804 6.7156077 13383 51 51 0 10085 16900 5625 3380 1.156205 0 412 0
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9000 2.4321991 3384 0.25838085 20.606426 22.418415 9.9820399 12847 55 55 0 11445 16900 5625 3384 1.156145 0 412 0
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10000 2.2560205 3387 0.25541566 20.480404 22.161139 10.87418 13022 66 66 0 12863 16900 5625 3387 1.1559136 0 412 0
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11000 2.2321955 3378 0.25533735 20.491359 22.154345 8.510825 13175 70 70 1 14273 16900 5625 3378 1.1470284 0 412 0
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12000 2.2715125 3377 0.25469529 20.40636 22.098637 9.0604601 13146 68 68 0 15742 16900 5625 3377 1.171755 0 412 0
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13000 2.3766974 3364 0.25667348 20.499635 22.270275 10.766786 12829 60 60 1 17214 16900 5625 3364 1.130354 0 412 0
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14000 2.5659704 3347 0.25802994 20.47632 22.387967 8.2568074 13090 66 66 1 18767 16900 5625 3347 1.1609852 0 412 0
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15000 2.3235671 3400 0.25603152 20.483517 22.214574 5.4785711 13389 50 50 0 20173 16900 5625 3400 1.149754 0 412 0
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16000 2.6335413 3373 0.25956137 20.558854 22.520843 4.7121947 13027 58 58 1 21668 16900 5625 3373 1.1308267 0 412 0
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17000 2.5603168 3410 0.25744829 20.430065 22.337501 6.1898616 13218 51 51 1 23170 16900 5625 3410 1.1285699 0 412 0
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18000 2.7801428 3362 0.26002524 20.489884 22.56109 8.9919312 13002 57 57 3 24829 16900 5625 3362 1.1610153 0 412 0
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19000 2.7869738 3364 0.26033026 20.51126 22.587555 9.6539159 13085 46 46 0 26476 16900 5625 3364 1.1431913 0 412 0
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20000 2.678182 3383 0.2586317 20.444934 22.44018 7.3468277 12939 42 42 0 27992 16900 5625 3383 1.143534 0 412 0
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21000 2.8094503 3375 0.26088069 20.542272 22.635313 8.2257869 13449 52 52 0 29570 16900 5625 3375 1.1375499 0 412 0
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22000 3.2220363 3377 0.26464914 20.561866 22.962283 6.6329375 13178 65 65 6 31203 16900 5625 3377 1.1683184 0 412 0
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23000 3.2268368 3339 0.26414495 20.514543 22.918536 4.6879815 12589 51 51 0 32929 16900 5625 3339 1.1378613 0 412 0
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24000 2.6062461 3380 0.25967238 20.588821 22.530474 10.036449 12745 53 54 0 34460 16900 5625 3380 1.1396017 0 412 0
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25000 3.2519674 3373 0.26376614 20.462953 22.885669 7.7592712 12856 52 52 1 36172 16900 5625 3373 1.1858891 0 412 0
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Loop time of 20.7208 on 1 procs for 25000 steps with 17353 atoms
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Performance: 104243.242 tau/day, 1206.519 timesteps/s, 20.937 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 | 0.39343 | 0.39343 | 0.39343 | 0.0 | 1.90
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Neigh | 0.09039 | 0.09039 | 0.09039 | 0.0 | 0.44
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Comm | 0.26483 | 0.26483 | 0.26483 | 0.0 | 1.28
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Output | 0.0021023 | 0.0021023 | 0.0021023 | 0.0 | 0.01
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Modify | 19.785 | 19.785 | 19.785 | 0.0 | 95.49
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Other | | 0.1847 | | | 0.89
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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: 146 ave 146 max 146 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1326 ave 1326 max 1326 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1326
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Ave neighs/atom = 0.0764133
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Neighbor list builds = 1290
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Dangerous builds = 0
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Total wall time: 0:00:21
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