344 lines
15 KiB
Groff
344 lines
15 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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# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
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units lj
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atom_style tri
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atom_modify first big map yes
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read_data data.tri.srd
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Reading data file ...
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orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1500 atoms
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1500 triangles
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read_data CPU = 0.013 seconds
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# add small particles as hi density lattice
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lattice sc 0.4
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Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
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region box block INF INF INF INF INF INF
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lattice sc 20.0
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Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
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create_atoms 2 region box
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Created 91125 atoms
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using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
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create_atoms CPU = 0.014 seconds
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group big type 1
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1500 atoms in group big
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group small type 2
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91125 atoms in group small
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set group small mass 0.01
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Setting atom values ...
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91125 settings made for mass
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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 1.5
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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
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delete_atoms overlap 1.5 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 = 1.8
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ghost atom cutoff = 1.8
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binsize = 0.9, bins = 19 19 19
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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/3d
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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/3d
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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 76354 atoms, new total = 16271
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# SRD run
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reset_timestep 0
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velocity small create 1.44 87287 loop geom
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neighbor 0.3 multi
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude molecule/intra big include big
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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 tri/lj 3.5
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pair_coeff 1 1 0.1 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/small molecule #langevin 1.0 1.0 0.1 12398
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create bodies CPU = 0.000 seconds
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125 rigid bodies with 1500 atoms
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1.8601881 = max distance from body owner to body atom
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fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore
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fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
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# diagnostics
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compute tsmall small temp/deform
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compute tbig big temp
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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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compute_modify tbig extra/dof -4500
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compute 1 big erotate/asphere
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compute 2 all ke
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compute 3 all pe
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variable toteng equal (c_1+c_2+c_3)/atoms
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thermo 100
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thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4]
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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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compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
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#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
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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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- 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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WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
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WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
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SRD info:
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SRD/big particles = 14771 1500
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big particle diameter max/min = 2.9202881 0.87320391
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SRD temperature & lamda = 1 0.2
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SRD max distance & max velocity = 0.8 40
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SRD grid counts: 17 17 17
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SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
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SRD per actual grid cell = -3.9971745
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SRD viscosity = -34.162587
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big/SRD mass density ratio = -3.3753691
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WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
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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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WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
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# of rescaled SRD velocities = 0
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ave/max small velocity = 19.970837 35.150443
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ave/max big velocity = 0 0
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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 = 3.8
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ghost atom cutoff = 3.8
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binsize = 16.874681, bins = 1 1 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tri/lj, 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/3d
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bin: multi
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Per MPI rank memory allocation (min/avg/max) = 381.8 | 381.8 | 381.8 Mbytes
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Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
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0 0 1.4502537 0 -0.15976045 0 0
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100 0.41802172 1.152223 0.27557714 1.0421065 1.1470081 283
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200 0.79710339 1.0669332 0.5813323 0.97699684 1.0361619 534
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300 1.3739181 1.0275476 1.0869716 0.81001536 1.0211312 658
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400 1.9355117 1.0155457 1.5813236 1.7798798 0.99354559 831
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500 2.8557382 1.0005021 2.267698 3.3903849 0.98597972 927
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600 4.7851916 1.0156689 3.730334 2.838776 0.99140534 1053
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700 5.3647697 1.0176657 3.9593121 5.1189107 0.9972029 1218
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800 8.23688 1.0268086 5.899689 6.8199153 0.99310516 1349
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900 9.9330758 1.0356047 7.0260595 7.2596589 0.98360014 1607
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1000 9.8719995 1.043178 6.9903792 10.05101 1.0045416 1805
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Loop time of 79.2664 on 1 procs for 1000 steps with 16271 atoms
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Performance: 1089.995 tau/day, 12.616 timesteps/s, 205.270 katom-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 | 57.961 | 57.961 | 57.961 | 0.0 | 73.12
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Neigh | 0.34589 | 0.34589 | 0.34589 | 0.0 | 0.44
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Comm | 0.28615 | 0.28615 | 0.28615 | 0.0 | 0.36
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Output | 0.0022784 | 0.0022784 | 0.0022784 | 0.0 | 0.00
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Modify | 20.644 | 20.644 | 20.644 | 0.0 | 26.04
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Other | | 0.02724 | | | 0.03
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Nlocal: 16271 ave 16271 max 16271 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4612 ave 4612 max 4612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 99463 ave 99463 max 99463 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 99463
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Ave neighs/atom = 6.1129003
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Neighbor list builds = 72
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Dangerous builds = 0
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#undump 1
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#undump 2
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unfix 3
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change_box all triclinic
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Changing box ...
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triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
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fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore
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#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
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fix 3 all deform 1 xy erate 0.05 units box remap v
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run 2000
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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 = 14771 1500
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big particle diameter max/min = 2.9202881 0.87320391
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SRD temperature & lamda = 1 0.2
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SRD max distance & max velocity = 0.8 40
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SRD grid counts: 13 13 13
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SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
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SRD per actual grid cell = -2.775698
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SRD viscosity = -12.180602
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big/SRD mass density ratio = -5.5653033
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WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
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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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WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832)
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# of rescaled SRD velocities = 3
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ave/max small velocity = 16.23763 40
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ave/max big velocity = 1.9825234 5.257255
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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 = 3.8
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ghost atom cutoff = 3.8
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binsize = 13.499745, bins = 1 1 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tri/lj, perpetual
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attributes: half, newton on
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pair build: half/multi/atomonly/newton/tri
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stencil: half/multi/3d/tri
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bin: multi
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Per MPI rank memory allocation (min/avg/max) = 278.4 | 278.4 | 278.4 Mbytes
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Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
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1000 9.8719995 1.0317167 6.98982 4.0948969 0 0
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1100 7.6460335 1.0028444 5.2446585 6.6348814 1 1320
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1200 6.2789381 1.0012003 4.5257435 6.3278972 1 1024
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1300 5.5060209 1.002182 3.7063549 7.0004503 1 794
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1400 5.4107119 1.002291 3.594515 7.9511695 1 621
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1500 5.072582 1.0001037 3.2501353 8.6993671 1 503
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1600 4.7912016 0.99982803 3.1208274 6.464157 1 416
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1700 4.5518848 1.0030059 2.9084074 6.3278992 1 346
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1800 4.368682 1.000831 2.807184 6.7382017 1 282
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1900 4.458655 1.0012568 2.7966515 6.0124309 1 246
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2000 4.1256128 1.0004032 2.763649 6.3707442 1 208
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2100 3.7040346 1.0004125 2.4398152 5.4213931 1 181
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2200 4.2347861 1.002625 2.6206986 6.6832437 1 151
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2300 4.254984 1.0028871 2.6794167 7.1661525 1 127
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2400 4.1017692 1.0028508 2.6371178 8.388599 1 105
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2500 3.9285571 1.0002888 2.5002741 6.0806187 1 95
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2600 3.6239964 1.0012152 2.2573993 6.7863124 1 80
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2700 3.4085702 1.0023974 2.1179914 6.7351139 1 68
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2800 3.1399303 1.0005349 2.0163219 6.4502765 1 61
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2900 3.1277562 1.0004013 2.0453134 6.6485498 1 51
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3000 3.0737732 1.0022962 1.997382 6.797214 1 44
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Loop time of 206.387 on 1 procs for 2000 steps with 16271 atoms
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Performance: 837.264 tau/day, 9.691 timesteps/s, 157.675 katom-step/s
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99.3% 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 | 173.6 | 173.6 | 173.6 | 0.0 | 84.12
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Neigh | 1.0077 | 1.0077 | 1.0077 | 0.0 | 0.49
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Comm | 0.58656 | 0.58656 | 0.58656 | 0.0 | 0.28
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Output | 0.0042824 | 0.0042824 | 0.0042824 | 0.0 | 0.00
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Modify | 31.128 | 31.128 | 31.128 | 0.0 | 15.08
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Other | | 0.05664 | | | 0.03
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Nlocal: 16271 ave 16271 max 16271 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4521 ave 4521 max 4521 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 94777 ave 94777 max 94777 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 94777
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Ave neighs/atom = 5.8249032
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Neighbor list builds = 100
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Dangerous builds = 0
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Total wall time: 0:04:47
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