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 2 by 2 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 = 0.010 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 = 0.005 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) = 184.3 | 184.9 | 185.4 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 -0.15949051 0 0
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100 0.39689465 1.1495173 0.26931663 1.0004927 1.1170389 279
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200 0.82155086 1.0684809 0.60689485 0.81307973 1.0433122 467
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300 1.3210872 1.0334277 1.0368935 1.0853416 0.99443391 621
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400 1.9755695 1.0149146 1.6438403 1.7258285 0.9925525 788
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500 3.0111365 1.0121291 2.4285289 2.5210058 0.99688885 922
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600 4.5413799 1.014305 3.4727946 3.8290233 0.99002027 1063
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700 6.6071849 1.0062952 4.9025772 3.9595327 0.99573591 1186
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800 7.6256618 1.0151252 5.3662442 5.0088255 0.99640985 1371
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900 8.1578206 1.0148959 5.7716683 6.6059298 0.96053165 1555
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1000 10.749617 1.0282309 7.6209538 11.277602 1.0012602 1844
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Loop time of 28.4136 on 4 procs for 1000 steps with 16271 atoms
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Performance: 3040.793 tau/day, 35.194 timesteps/s, 572.647 katom-step/s
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98.7% 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 | 12.454 | 15.242 | 17.781 | 48.4 | 53.64
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Neigh | 0.093078 | 0.094516 | 0.097759 | 0.6 | 0.33
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Comm | 0.48732 | 2.9927 | 5.7363 | 107.5 | 10.53
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Output | 0.00080706 | 0.0008431 | 0.00086933 | 0.0 | 0.00
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Modify | 10.015 | 10.063 | 10.111 | 1.4 | 35.42
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Other | | 0.02046 | | | 0.07
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Nlocal: 4067.75 ave 4467 max 3606 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Nghost: 2313.5 ave 2327 max 2296 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Neighs: 24883 ave 26066 max 24145 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Total # of neighbors = 99532
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Ave neighs/atom = 6.1171409
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Neighbor list builds = 70
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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 = 16.10299 40
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ave/max big velocity = 2.0311414 11.34118
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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) = 148.8 | 149.5 | 150 Mbytes
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Step f_1 c_tsmall Temp Press f_2[9] f_2[4]
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1000 10.749616 1.0167438 7.6203704 5.4893075 0 0
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1100 9.0727748 1.003438 6.1822573 8.6707036 1 1339
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1200 7.1960998 1.0003968 4.8077632 6.7809972 1 1039
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1300 6.2680889 1.0011134 4.3139658 8.2260362 1 861
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1400 5.8199503 1.0024475 3.9876867 7.0322957 1 692
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1500 5.399935 0.99757802 3.4552534 7.905565 1 577
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1600 5.0830248 1.0023727 3.1330433 7.6897887 1 479
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1700 4.8728937 1.0027203 3.0838267 7.606406 1 389
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1800 4.8443541 1.0018057 3.115321 7.4547572 1 317
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1900 5.0622362 1.0007126 2.9336473 6.514338 1 268
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2000 5.022699 1.0030275 3.1244763 7.2999286 1 223
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2100 4.4605894 1.0019457 2.9262733 8.3475145 1 196
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2200 4.6544992 1.0023701 3.0140329 7.3670747 1 164
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2300 4.1954825 1.0012089 2.5802739 7.5553707 1 142
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2400 4.0806819 1.0000292 2.6492187 7.5648723 1 122
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2500 3.7437189 0.99949605 2.3660722 8.2155316 1 104
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2600 4.2333926 1.0002823 2.5704515 7.2839635 1 106
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2700 3.7542455 1.001394 2.4146222 6.3785983 1 86
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2800 3.4011329 0.99832028 2.141193 6.3869497 1 78
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2900 3.4579019 1.0007319 2.1839274 6.241817 1 64
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3000 3.6128019 1.0017345 2.2982426 5.8975992 1 55
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Loop time of 67.0194 on 4 procs for 2000 steps with 16271 atoms
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Performance: 2578.358 tau/day, 29.842 timesteps/s, 485.561 katom-step/s
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98.8% 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 | 36.774 | 43.583 | 50.126 | 71.5 | 65.03
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Neigh | 0.29299 | 0.3134 | 0.32399 | 2.2 | 0.47
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Comm | 0.75102 | 7.2688 | 14.075 | 174.8 | 10.85
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Output | 0.0016347 | 0.0017229 | 0.0018802 | 0.2 | 0.00
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Modify | 15.794 | 15.808 | 15.828 | 0.3 | 23.59
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Other | | 0.04379 | | | 0.07
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Nlocal: 4067.75 ave 4560 max 3583 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 2256.75 ave 2292 max 2241 min
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Histogram: 2 1 0 0 0 0 0 0 0 1
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Neighs: 23706 ave 24669 max 22450 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Total # of neighbors = 94824
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Ave neighs/atom = 5.8277918
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Neighbor list builds = 108
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Dangerous builds = 0
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Total wall time: 0:01:36
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