Proofing RHEO package
This commit is contained in:
jtclemm
@ -71,5 +71,5 @@ compute nbond all nbond/atom
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thermo 200
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thermo_style custom step time ke press atoms
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dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
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#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
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run 30000
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382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
382
examples/rheo/balloon/log.17Apr2024.balloon.g++.4
Normal file
@ -0,0 +1,382 @@
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LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified)
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# ------ 2D water balloon ------ #
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dimension 2
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units lj
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atom_style hybrid rheo bond
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boundary m m p
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comm_modify vel yes
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newton off
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region box block -40 40 0 80 -0.01 0.01 units box
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create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
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Created orthogonal box = (-40 0 -0.01) to (40 80 0.01)
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2 by 2 by 1 MPI processor grid
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region fluid sphere -10 40 0 30 units box side in
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lattice hex 1.0
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Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
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create_atoms 1 region fluid
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Created 2830 atoms
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using lattice units in orthogonal box = (-40 0 -0.01) to (40 80 0.01)
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create_atoms CPU = 0.001 seconds
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region shell sphere -10 40 0 27 units box side out
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group shell region shell
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544 atoms in group shell
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set group shell rheo/status 1
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Setting atom values ...
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544 settings made for rheo/status
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set group all vx 0.005 vy -0.04
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Setting atom values ...
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2830 settings made for vx
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2830 settings made for vy
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# ------ Model parameters ------#
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variable cut equal 3.0
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variable n equal 1.0
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variable rho0 equal 1.0
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variable cs equal 1.0
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variable mp equal ${rho0}/${n}
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variable mp equal 1/${n}
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variable mp equal 1/1
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variable zeta equal 0.05
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variable kappa equal 0.01*${rho0}/${mp}
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variable kappa equal 0.01*1/${mp}
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variable kappa equal 0.01*1/1
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variable dt_max equal 0.1*${cut}/${cs}/3
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variable dt_max equal 0.1*3/${cs}/3
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variable dt_max equal 0.1*3/1/3
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variable eta equal 0.05
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variable Cv equal 1.0
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variable L equal 1.0
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variable Tf equal 1.0
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mass * ${mp}
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mass * 1
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timestep 0.1
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pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
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pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
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pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
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pair_coeff * * rheo
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pair_coeff * * rheo/solid 1.0 1.0 1.0
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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0 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds many shell shell 1 0 1.5
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Generated 0 of 0 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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 49 49 1
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3 neighbor lists, perpetual/occasional/extra = 2 1 0
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(1) command create_bonds, occasional
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attributes: full, newton off
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pair build: full/bin
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stencil: full/bin/2d
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bin: standard
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(2) pair rheo, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: full/bin/2d
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bin: standard
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(3) pair rheo/solid, perpetual, trim from (2)
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attributes: half, newton off, cut 1.3
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pair build: trim
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stencil: none
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bin: none
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Added 1263 bonds, new total = 1263
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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6 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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bond_style bpm/spring
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bond_coeff 1 1.0 1.0 1.0
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# A lower critical strain allows the balloon to pop
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#bond_coeff 1 1.0 0.05 1.0
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# ------ Drop balloon ------#
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fix 1 all rheo ${cut} quintic 0 shift surface/detection coordination 22 8
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fix 1 all rheo 3 quintic 0 shift surface/detection coordination 22 8
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fix 2 all rheo/viscosity * constant ${eta}
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fix 2 all rheo/viscosity * constant 0.05
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fix 3 all rheo/pressure * linear
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fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
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fix 5 all enforce2d
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compute rho all rheo/property/atom rho
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compute phase all rheo/property/atom phase
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compute nbond all nbond/atom
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# ------ Output & Run ------ #
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thermo 200
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thermo_style custom step time ke press atoms
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dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_nbond c_rho
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run 30000
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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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- BPM bond style: doi:10.1039/D3SM01373A
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@Article{Clemmer2024,
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author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
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title = {A soft departure from jamming: the compaction of deformable
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granular matter under high pressures},
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journal = {Soft Matter},
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year = 2024,
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volume = 20,
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number = 8,
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pages = {1702--1718}
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}
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- @article{PalermoInPrep,
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journal = {in prep},
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title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
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year = {2024},
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author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
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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 0 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 = 3.3
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ghost atom cutoff = 3.3
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binsize = 1.65, bins = 49 49 1
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6 neighbor lists, perpetual/occasional/extra = 6 0 0
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(1) pair rheo, perpetual, half/full from (3)
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attributes: half, newton off
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pair build: halffull/newtoff
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stencil: none
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bin: none
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(2) pair rheo/solid, perpetual, trim from (1)
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attributes: half, newton off, cut 1.3
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pair build: trim
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stencil: none
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bin: none
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(3) compute RHEO/KERNEL, perpetual
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attributes: full, newton off
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pair build: full/bin
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stencil: full/bin/2d
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bin: standard
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(4) compute RHEO/GRAD, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(5) compute RHEO/VSHIFT, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(6) compute RHEO/SURFACE, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 17.63 | 17.64 | 17.65 Mbytes
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Step Time KinEng Press Atoms
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0 0 0.0008125 0.00035927734 2830
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200 20 0.0008125 0.00035927734 2830
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400 40 0.0008125 0.00035927734 2830
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600 60 0.0008125 0.00035927734 2830
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800 80 0.0008125 0.00035927734 2830
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1000 100 0.0008125 0.00035927734 2830
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1200 120 0.0008125 0.00035927734 2830
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1400 140 0.0008125 0.00035927734 2830
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1600 160 0.0008125 0.00035927734 2830
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1800 180 0.0008125 0.00035927734 2830
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2000 200 0.0008125 0.00035927734 2830
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2200 220 0.0008125 0.00035927734 2830
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2400 240 0.00079033569 0.00043037861 2830
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2600 260 0.0007549229 0.00045188383 2830
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2800 280 0.00072808836 0.00031695003 2830
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3000 300 0.0007017958 1.6121754e-05 2830
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3200 320 0.00067479047 -0.00015725514 2830
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3400 340 0.00064762254 -0.00023361314 2830
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3600 360 0.00061960255 -0.00033837679 2830
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3800 380 0.0005857206 -0.00051770716 2830
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4000 400 0.00055061733 -0.00070309251 2830
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4200 420 0.00051884719 -0.0008247795 2830
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4400 440 0.00049022236 -0.00099918413 2830
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4600 460 0.00046060011 -0.0010923159 2830
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4800 480 0.00042900173 -0.0011524571 2830
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5000 500 0.00039751503 -0.0012586358 2830
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5200 520 0.00036620054 -0.0013973543 2830
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5400 540 0.00033130023 -0.0015185231 2830
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5600 560 0.00030565892 -0.0016159836 2830
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5800 580 0.00028209836 -0.0016925198 2830
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6000 600 0.00024695044 -0.0017796892 2830
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6200 620 0.00021190635 -0.0018706272 2830
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6400 640 0.0001947093 -0.0019146643 2830
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6600 660 0.00018903936 -0.0019146199 2830
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6800 680 0.00017753371 -0.0019390155 2830
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7000 700 0.00015170593 -0.0020247472 2830
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7200 720 0.00011509692 -0.0021222209 2830
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7400 740 7.9861785e-05 -0.0022033181 2830
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7600 760 6.1350463e-05 -0.0022511971 2830
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7800 780 6.5269523e-05 -0.0022222806 2830
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8000 800 8.5709569e-05 -0.0021089664 2830
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8200 820 0.00011746348 -0.0019351493 2830
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8400 840 0.00015698134 -0.0017079928 2830
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8600 860 0.00019758065 -0.0014618965 2830
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8800 880 0.00023338199 -0.0012365832 2830
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9000 900 0.00026282353 -0.0010348527 2830
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||||
9200 920 0.00028604776 -0.00085287884 2830
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9400 940 0.00030388767 -0.000681122 2830
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||||
9600 960 0.000317589 -0.00052203521 2830
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9800 980 0.00032716728 -0.00037501187 2830
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10000 1000 0.00033270692 -0.00025576132 2830
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10200 1020 0.00033485986 -0.00016554207 2830
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10400 1040 0.00033476763 -9.8525417e-05 2830
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10600 1060 0.00033351922 -5.1166347e-05 2830
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10800 1080 0.00033161645 -2.0773965e-05 2830
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11000 1100 0.00032913022 2.2384421e-07 2830
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11200 1120 0.00032618376 1.2304773e-05 2830
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11400 1140 0.00032310409 1.3725982e-05 2830
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11600 1160 0.0003202128 9.0431945e-06 2830
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||||
11800 1180 0.00031760386 -5.3537879e-07 2830
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||||
12000 1200 0.00031518884 -1.331708e-05 2830
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||||
12200 1220 0.00031283958 -3.0838612e-05 2830
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||||
12400 1240 0.0003104901 -5.0038548e-05 2830
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||||
12600 1260 0.00030811597 -6.9699925e-05 2830
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||||
12800 1280 0.00030555782 -8.9972287e-05 2830
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||||
13000 1300 0.00030256671 -0.00011712941 2830
|
||||
13200 1320 0.00029907961 -0.00015495826 2830
|
||||
13400 1340 0.00029504656 -0.00020292633 2830
|
||||
13600 1360 0.0002905184 -0.00024892421 2830
|
||||
13800 1380 0.00028564542 -0.000295085 2830
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||||
14000 1400 0.00028073246 -0.00034571956 2830
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||||
14200 1420 0.00027611457 -0.00039341977 2830
|
||||
14400 1440 0.00027217382 -0.0004281012 2830
|
||||
14600 1460 0.00026919129 -0.00045342545 2830
|
||||
14800 1480 0.00026727674 -0.00047323419 2830
|
||||
15000 1500 0.0002663482 -0.00048423944 2830
|
||||
15200 1520 0.00026616663 -0.0004816085 2830
|
||||
15400 1540 0.00026634862 -0.00047573486 2830
|
||||
15600 1560 0.0002664314 -0.00046803192 2830
|
||||
15800 1580 0.00026603348 -0.00045753668 2830
|
||||
16000 1600 0.00026511015 -0.00044676105 2830
|
||||
16200 1620 0.00026373403 -0.00044075794 2830
|
||||
16400 1640 0.00026217342 -0.00043684036 2830
|
||||
16600 1660 0.0002607038 -0.00042774771 2830
|
||||
16800 1680 0.00025951097 -0.00041603026 2830
|
||||
17000 1700 0.00025869088 -0.00040302996 2830
|
||||
17200 1720 0.00025825588 -0.00038415247 2830
|
||||
17400 1740 0.00025818373 -0.00035742127 2830
|
||||
17600 1760 0.00025843381 -0.00032854722 2830
|
||||
17800 1780 0.00025897836 -0.00029821183 2830
|
||||
18000 1800 0.00025981472 -0.00026108907 2830
|
||||
18200 1820 0.00026095775 -0.00021731058 2830
|
||||
18400 1840 0.00026239688 -0.00017030825 2830
|
||||
18600 1860 0.00026404432 -0.00011868778 2830
|
||||
18800 1880 0.00026574247 -5.9556286e-05 2830
|
||||
19000 1900 0.00026729563 2.3014881e-06 2830
|
||||
19200 1920 0.00026852418 6.2100169e-05 2830
|
||||
19400 1940 0.00026929086 0.00012090325 2830
|
||||
19600 1960 0.0002695407 0.00017904223 2830
|
||||
19800 1980 0.00026929677 0.00023112254 2830
|
||||
20000 2000 0.00026863577 0.0002756697 2830
|
||||
20200 2020 0.00026765699 0.0003158399 2830
|
||||
20400 2040 0.00026646841 0.00035200747 2830
|
||||
20600 2060 0.00026516938 0.00038018442 2830
|
||||
20800 2080 0.00026383495 0.00040179111 2830
|
||||
21000 2100 0.00026252489 0.00042030921 2830
|
||||
21200 2120 0.00026128616 0.00043466976 2830
|
||||
21400 2140 0.00026014896 0.00044221445 2830
|
||||
21600 2160 0.00025912325 0.00044531883 2830
|
||||
21800 2180 0.00025821515 0.00044661709 2830
|
||||
22000 2200 0.00025742576 0.00044409089 2830
|
||||
22200 2220 0.00025674938 0.00043634999 2830
|
||||
22400 2240 0.00025617111 0.00042630344 2830
|
||||
22600 2260 0.0002556791 0.00041561603 2830
|
||||
22800 2280 0.00025525963 0.00040166735 2830
|
||||
23000 2300 0.00025489538 0.00038430419 2830
|
||||
23200 2320 0.00025456861 0.0003669402 2830
|
||||
23400 2340 0.00025426747 0.00034972373 2830
|
||||
23600 2360 0.00025398353 0.0003302242 2830
|
||||
23800 2380 0.00025370842 0.00030993088 2830
|
||||
24000 2400 0.00025344084 0.00029143258 2830
|
||||
24200 2420 0.00025318683 0.00027421708 2830
|
||||
24400 2440 0.0002529591 0.00025603123 2830
|
||||
24600 2460 0.0002527713 0.00023950245 2830
|
||||
24800 2480 0.00025264228 0.00022644812 2830
|
||||
25000 2500 0.00025259021 0.00021540748 2830
|
||||
25200 2520 0.00025262892 0.00020544201 2830
|
||||
25400 2540 0.00025276229 0.00019845807 2830
|
||||
25600 2560 0.0002529876 0.00019449958 2830
|
||||
25800 2580 0.00025329374 0.00019082606 2830
|
||||
26000 2600 0.00025366066 0.00018700064 2830
|
||||
26200 2620 0.00025406164 0.00018426061 2830
|
||||
26400 2640 0.00025446737 0.00018098339 2830
|
||||
26600 2660 0.00025484714 0.00017471869 2830
|
||||
26800 2680 0.00025516604 0.00016565557 2830
|
||||
27000 2700 0.00025538911 0.00015493626 2830
|
||||
27200 2720 0.00025548177 0.00014075592 2830
|
||||
27400 2740 0.00025541168 0.00012205573 2830
|
||||
27600 2760 0.00025514889 0.00010039772 2830
|
||||
27800 2780 0.00025467547 7.7069215e-05 2830
|
||||
28000 2800 0.0002539915 5.1158042e-05 2830
|
||||
28200 2820 0.00025312083 2.3468384e-05 2830
|
||||
28400 2840 0.00025211323 -3.2184465e-06 2830
|
||||
28600 2860 0.00025104366 -2.7726301e-05 2830
|
||||
28800 2880 0.00025000263 -5.0202987e-05 2830
|
||||
29000 2900 0.00024907814 -6.9244776e-05 2830
|
||||
29200 2920 0.00024833815 -8.2874516e-05 2830
|
||||
29400 2940 0.0002478155 -9.1854992e-05 2830
|
||||
29600 2960 0.00024750313 -9.766055e-05 2830
|
||||
29800 2980 0.00024735538 -9.9681291e-05 2830
|
||||
30000 3000 0.00024730191 -9.818759e-05 2830
|
||||
Loop time of 177.982 on 4 procs for 30000 steps with 2830 atoms
|
||||
|
||||
Performance: 1456330.235 tau/day, 168.557 timesteps/s, 477.016 katom-step/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 22.913 | 27.061 | 34.594 | 87.2 | 15.20
|
||||
Bond | 0.22386 | 0.26159 | 0.30792 | 6.0 | 0.15
|
||||
Neigh | 0.84412 | 0.84509 | 0.8462 | 0.1 | 0.47
|
||||
Comm | 0.50015 | 0.55579 | 0.60346 | 5.2 | 0.31
|
||||
Output | 0.65854 | 0.69412 | 0.72473 | 2.8 | 0.39
|
||||
Modify | 133.13 | 136 | 137.38 | 14.5 | 76.41
|
||||
Other | | 12.57 | | | 7.06
|
||||
|
||||
Nlocal: 707.5 ave 1576 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 164.75 ave 239 max 94 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 12307.8 ave 27380 max 983 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
FullNghs: 23517 ave 53040 max 1502 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 94068
|
||||
Ave neighs/atom = 33.239576
|
||||
Ave special neighs/atom = 0.89257951
|
||||
Neighbor list builds = 783
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:58
|
||||
Reference in New Issue
Block a user