348 lines
16 KiB
Groff
348 lines
16 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 - ellipsoids
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units lj
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atom_style ellipsoid
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atom_modify first big
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dimension 2
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# create big ellipsoidal particles
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lattice sq 0.14
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Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124
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region box block 0 10 0 10 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 region box
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Created 100 atoms
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using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
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create_atoms CPU = 0.000 seconds
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set type 1 mass 1.0
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Setting atom values ...
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100 settings made for mass
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set type 1 shape 3.0 1.0 1.0
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Setting atom values ...
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100 settings made for shape
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group big type 1
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100 atoms in group big
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set group big quat/random 29898
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Setting atom values ...
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100 settings made for quat/random
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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 gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
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pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
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pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
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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 nve/asphere
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fix 2 all enforce2d
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compute rot big temp/asphere
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compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
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#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*]
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#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
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thermo_style custom step temp c_rot epair etotal press
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thermo 100
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run 1000
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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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- pair gayberne command: doi:10.1063/1.3058435
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@Article{Brown09,
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author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest},
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title = {Liquid Crystal Nanodroplets in Solution},
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journal = {J.~Chem.\ Phys.},
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year = 2009,
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volume = 130,
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number = 4,
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pages = {044901}
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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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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 = 4.3
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ghost atom cutoff = 4.3
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binsize = 2.15, bins = 13 13 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair gayberne, 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) = 4.611 | 4.611 | 4.611 Mbytes
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Step Temp c_rot E_pair TotEng Press
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0 1.44 0.95677852 2.7038078 4.1294078 10.518912
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100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
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200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
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300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
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400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
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500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
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600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
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700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
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800 2.7632972 2.9060854 -0.52075351 2.2149107 0.7710678
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900 2.9905597 2.8869667 -0.49099378 2.4696603 0.69616841
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1000 2.8470138 2.9005012 -0.51282088 2.3057228 0.68817567
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Loop time of 0.192844 on 1 procs for 1000 steps with 100 atoms
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Performance: 2240155.241 tau/day, 5185.545 timesteps/s, 518.554 katom-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 | 0.17225 | 0.17225 | 0.17225 | 0.0 | 89.32
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Neigh | 0.0025614 | 0.0025614 | 0.0025614 | 0.0 | 1.33
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Comm | 0.0024746 | 0.0024746 | 0.0024746 | 0.0 | 1.28
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Output | 0.0001406 | 0.0001406 | 0.0001406 | 0.0 | 0.07
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Modify | 0.014112 | 0.014112 | 0.014112 | 0.0 | 7.32
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Other | | 0.001306 | | | 0.68
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Nlocal: 100 ave 100 max 100 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 77 ave 77 max 77 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 369 ave 369 max 369 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 369
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Ave neighs/atom = 3.69
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Neighbor list builds = 174
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Dangerous builds = 0
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#undump 1
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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 120.0
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Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093
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create_atoms 2 region plane
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Created 85849 atoms
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using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062)
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create_atoms CPU = 0.015 seconds
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set type 2 mass 0.01
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Setting atom values ...
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85849 settings made for mass
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group small type 2
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85849 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 2.0
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neigh_modify one 10000
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delete_atoms overlap 1.6 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: 10000, 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 = 20 20 2
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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 71060 atoms, new total = 14889
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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 gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
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pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
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pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 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 0.0005
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fix 1 big nve/asphere
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
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fix 3 small viscosity 20 x y 50
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fix 4 all enforce2d
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# diagnostics
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compute tbig big temp/asphere
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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 c_rot f_2[9] 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 custom 500 dump.ellipsoid id type x y z c_0[*]
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#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
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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 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 = 14789 100
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big particle diameter max/min = 3 1
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SRD temperature & lamda = 1 0.1
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SRD max distance & max velocity = 0.4 40
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SRD grid counts: 107 107 1
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SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124
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SRD per actual grid cell = 1.9275711
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SRD viscosity = 0.68810145
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big/SRD mass density ratio = 1.3736715
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# of rescaled SRD velocities = 0
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ave/max small velocity = 13.30933 24.335888
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ave/max big velocity = 2.0802836 5.05672
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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: 10000, page size: 100000
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master list distance cutoff = 4.3
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ghost atom cutoff = 4.3
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binsize = 26.726124, bins = 1 1 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair gayberne, 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) = 43.23 | 43.23 | 43.23 Mbytes
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Step Temp c_rot f_2[9] 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 2.9005012 2.9005012 0 0.025582147 -0.51282088 3.8089259 0.8986241 0 0 0 0 0 0 0 0 0 0 0 0
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1000 2.3102693 2.3102693 0.82371999 0.019779507 -0.49733043 2.9449709 1.9807143 13954 30 30 0 277 38416 11449 4255 0.82371999 15 50 0
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2000 1.5312119 1.5312119 0.90846884 0.008532096 -1.011162 1.2703438 0.58038663 14523 37 37 0 439 38416 11449 4257 0.90846884 20 50 0
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3000 1.3603443 1.3603443 0.95241399 0.0085403252 -0.75534393 1.271569 1.2262133 14864 34 35 0 599 38416 11449 4287 0.95241399 20 50 0
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4000 2.2408861 2.2408861 0.99089404 0.016876315 -0.82620566 2.5127146 1.2664088 15457 35 35 0 809 38416 11449 4272 0.99089404 21 50 0
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5000 1.7110067 1.7110067 0.99729333 0.011146301 -0.88982716 1.6595728 0.97334407 15555 36 36 0 1026 38416 11449 4324 0.99729333 24 50 0
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6000 1.684666 1.684666 1.0235606 0.009751253 -1.0582882 1.4518641 0.62435255 15752 45 46 0 1256 38416 11449 4303 1.0235606 24 50 0
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7000 2.1142261 2.1142261 1.0160206 0.014786886 -0.94857757 2.2016194 0.7761903 16144 30 30 0 1492 38416 11449 4401 1.0160206 27 50 0
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8000 2.5622926 2.5622926 1.0125365 0.019933518 -0.84991443 2.9679015 0.93716383 16302 43 43 0 1720 38416 11449 4346 1.0125365 27 50 0
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9000 2.6593623 2.6593623 1.0110535 0.020725053 -0.87669675 3.0857531 0.97818336 16856 44 44 0 2000 38416 11449 4298 1.0110535 30 50 0
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10000 2.7567851 2.7567851 1.0379053 0.021598993 -0.8917358 3.2158741 0.74950846 16770 50 53 0 2284 38416 11449 4316 1.0379053 30 50 0
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Loop time of 9.02679 on 1 procs for 10000 steps with 14889 atoms
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Performance: 47857.551 tau/day, 1107.814 timesteps/s, 16.494 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 | 1.8454 | 1.8454 | 1.8454 | 0.0 | 20.44
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Neigh | 0.018708 | 0.018708 | 0.018708 | 0.0 | 0.21
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Comm | 0.059853 | 0.059853 | 0.059853 | 0.0 | 0.66
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Output | 0.00081453 | 0.00081453 | 0.00081453 | 0.0 | 0.01
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Modify | 7.0469 | 7.0469 | 7.0469 | 0.0 | 78.07
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Other | | 0.05507 | | | 0.61
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Nlocal: 14889 ave 14889 max 14889 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 75 ave 75 max 75 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 382 ave 382 max 382 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 382
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Ave neighs/atom = 0.025656525
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Neighbor list builds = 500
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Dangerous builds = 0
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Total wall time: 0:00:11
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