323 lines
14 KiB
Groff
323 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 viscosity 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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2 by 2 by 1 MPI processor grid
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reading atoms ...
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270 atoms
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read_data CPU = 0.001 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) = 5.554 | 5.554 | 5.555 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 0.0311841 on 4 procs for 1000 steps with 270 atoms
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Performance: 13853197.664 tau/day, 32067.587 timesteps/s, 8.658 Matom-step/s
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97.6% 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 | 0.0027957 | 0.0031644 | 0.0035219 | 0.5 | 10.15
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Neigh | 0.001171 | 0.0012862 | 0.0014036 | 0.3 | 4.12
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Comm | 0.0099068 | 0.010544 | 0.011053 | 0.4 | 33.81
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Output | 0.00014281 | 0.00016091 | 0.00020823 | 0.0 | 0.52
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Modify | 0.013319 | 0.013618 | 0.014047 | 0.2 | 43.67
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Other | | 0.002411 | | | 7.73
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Nlocal: 67.5 ave 80 max 54 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 29.75 ave 33 max 26 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Neighs: 104.5 ave 135 max 72 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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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 = 0.003 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 small viscosity 10 x y 50
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fix 4 all enforce2d
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# diagnostics
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uncompute tbig
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compute tbig big temp/sphere
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
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WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp: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.mp
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#dump 1 all image 1000 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
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@Article{Intveld08,
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author = {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) = 14.19 | 14.19 | 14.2 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 1.3506473 8186 0.22968182 37.201018 37.421123 5.6398923 14572 54 54 0 654 42436 11236 8186 1.0228728 0 3 0
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2000 0.99412905 8212 0.22952823 37.234094 37.3961 8.5863689 14257 69 69 0 1394 42436 11236 8212 1.0206297 0 12 0
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3000 1.4469134 8192 0.22970951 37.189841 37.425634 8.0408437 14439 53 53 0 2178 42436 11236 8192 1.0121272 0 12 0
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4000 1.6112802 8172 0.2303679 37.270324 37.532903 8.3379947 14098 57 57 0 2992 42436 11236 8172 1.0171443 0 12 0
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5000 2.0436283 8191 0.23016186 37.166298 37.499334 7.1370191 14030 49 49 0 3804 42436 11236 8191 1.0054513 0 12 0
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6000 2.2894073 8184 0.2303867 37.162878 37.535967 7.6496143 13970 50 50 0 4662 42436 11236 8184 1.0084738 0 12 0
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7000 2.1640822 8183 0.23045121 37.193812 37.546477 7.1526683 13926 56 57 0 5445 42436 11236 8183 1.0046108 0 15 0
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8000 2.8851243 8199 0.23121762 37.201176 37.671344 9.1644504 13849 58 58 0 6237 42436 11236 8199 1.0081629 0 15 0
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9000 2.6422092 8180 0.23070839 37.157795 37.588377 2.4816571 13651 70 70 0 7007 42436 11236 8180 1.0089869 0 15 0
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10000 2.7121051 8189 0.23087145 37.172972 37.614945 11.176036 13901 63 64 0 7845 42436 11236 8189 1.0023484 0 15 0
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Loop time of 6.56969 on 4 procs for 10000 steps with 43990 atoms
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Performance: 131513.146 tau/day, 1522.143 timesteps/s, 66.959 Matom-step/s
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99.1% 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 | 0.037869 | 0.059232 | 0.073664 | 5.4 | 0.90
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Neigh | 0.015688 | 0.017835 | 0.019891 | 1.1 | 0.27
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Comm | 0.22905 | 0.24375 | 0.26098 | 2.3 | 3.71
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Output | 0.00069058 | 0.00071614 | 0.00078869 | 0.0 | 0.01
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Modify | 6.1124 | 6.1385 | 6.1881 | 1.2 | 93.44
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Other | | 0.1096 | | | 1.67
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Nlocal: 10997.5 ave 12305 max 10259 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Nghost: 58.25 ave 73 max 48 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Neighs: 402.75 ave 520 max 207 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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Total # of neighbors = 1611
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Ave neighs/atom = 0.03662196
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:06
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