forked from lijiext/lammps
293 lines
18 KiB
Groff
293 lines
18 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 2d SRD test: big + small particles
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units lj
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atom_style sphere
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atom_modify first big
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dimension 2
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# create big particles with sigma 1.0
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lattice sq 0.4
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Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
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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 -0.790569) to (15.8114 15.8114 0.790569)
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2 by 2 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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Time spent = 0.000455379 secs
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set type 1 mass 1.0
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100 settings made for mass
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set type 1 diameter 1.0
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100 settings made for diameter
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group big type 1
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100 atoms in group big
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 big nve
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fix 2 all enforce2d
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.171 | 4.171 | 4.171 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -0.54272 0 0.88288 -0.041088
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1000 1.8791467 -0.97185784 0 0.8884974 0.61487657
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Loop time of 0.0164104 on 4 procs for 1000 steps with 100 atoms
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Performance: 26324848.583 tau/day, 60937.149 timesteps/s
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94.8% 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 | 0.0017555 | 0.0019422 | 0.0022526 | 0.4 | 11.84
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Neigh | 0.00085735 | 0.00090593 | 0.00096583 | 0.0 | 5.52
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Comm | 0.0088477 | 0.0094896 | 0.0098495 | 0.4 | 57.83
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Output | 2.1935e-05 | 2.3127e-05 | 2.6226e-05 | 0.0 | 0.14
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Modify | 0.00074744 | 0.00088817 | 0.0012014 | 0.0 | 5.41
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Other | | 0.003161 | | | 19.26
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Nlocal: 25 ave 26 max 23 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 47 ave 48 max 46 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 114.75 ave 124 max 100 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Total # of neighbors = 459
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Ave neighs/atom = 4.59
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Neighbor list builds = 129
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Dangerous builds = 0
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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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lattice sq 0.4
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Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
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region plane block 0 10 0 10 -0.001 0.001
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lattice sq 85.0
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Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
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create_atoms 2 region plane
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Created 21316 atoms
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Time spent = 0.00417233 secs
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set type 2 mass 0.01
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21316 settings made for mass
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set type 2 diameter 0.0
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21316 settings made for diameter
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group small type 2
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21316 atoms in group small
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set 1-2 cutoff to non-zero value
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.5
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delete_atoms overlap 0.5 small big
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 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/newton
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bin: standard
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WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:305)
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Deleted 6700 atoms, new total = 14716
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# SRD run
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reset_timestep 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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comm_modify mode multi group big vel yes
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neigh_modify include big
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# no pairwise interactions with small particles
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.0
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# use fix SRD to push small particles out from inside big ones
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timestep 0.001
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fix 1 big nve
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fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
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fix 3 all enforce2d
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# diagnostics
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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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thermo_style custom step temp f_2[7] 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[8] f_2[9] f_2[10]
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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:488)
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thermo 100
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#dump 1 all atom 250 dump.srd.mixture
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#dump 2 all image 250 image.*.jpg type type zoom 1.6
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#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2
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#dump 3 all movie 250 movie.mpg type type zoom 1.6
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#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2
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run 5000
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SRD info:
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SRD/big particles = 14616 100
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big particle diameter max/min = 0.88 0.88
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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: 63 63 1
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SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
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SRD per actual grid cell = 4.86648
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SRD viscosity = 0.463448
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big/SRD mass density ratio = 2.12808
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WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2888)
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# of rescaled SRD velocities = 0
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ave/max small velocity = 13.2944 24.262
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ave/max big velocity = 1.69284 5.10989
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.921 | 5.925 | 5.93 Mbytes
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Step Temp f_2[7] 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[8] f_2[9] f_2[10]
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0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0
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100 1.4044369 3969 0.0030633093 -0.93959598 0.4507966 0.78900119 7464 99 99 0 17 22500 3005 1.028131 0
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200 1.1569383 3969 0.0010543995 -0.99020352 0.15516543 0.50132981 7393 82 82 0 43 22500 2996 1.014347 0
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300 0.97802835 3969 -0.00019991154 -0.99766705 -0.029418982 0.35789515 7411 90 90 0 84 22500 3001 1.0213725 0
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400 1.0992982 3969 0.00055034756 -1.007316 0.080989146 0.35177983 7443 78 78 0 107 22500 2993 1.0451641 0
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500 1.0436705 3969 -7.4779704e-05 -1.0442384 -0.011004581 0.15132448 7504 94 94 0 141 22500 3007 1.0236992 0
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600 1.0216461 3969 -0.00032426678 -1.0591487 -0.047719099 0.2200765 7508 111 111 0 179 22500 3007 1.0304838 0
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700 1.1491339 3969 0.0012328743 -0.95621278 0.18142978 0.80670059 7448 95 95 0 201 22500 2978 1.0099113 0
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800 1.0332166 3969 -0.00040684239 -1.0827554 -0.059870926 0.35939225 7453 113 113 0 235 22500 3024 1.0141565 0
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900 1.0652211 3969 -6.1337025e-06 -1.0554715 -0.00090263566 0.51460169 7447 97 97 0 259 22500 2982 1.0192735 0
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1000 0.92834993 3969 -0.00067681883 -1.0186671 -0.09960066 0.738738 7328 78 78 0 286 22500 2999 1.023841 0
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1100 1.0386338 3969 -0.00018904027 -1.0560666 -0.027819166 0.57129719 7449 96 96 0 325 22500 3012 1.0373885 0
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1200 0.92218024 3969 -0.00077989365 -1.0277276 -0.11476915 0.48613467 7507 100 100 0 355 22500 3003 1.0254889 0
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1300 1.1835318 3969 0.00096836748 -1.0291915 0.14250496 0.62935386 7439 92 92 0 384 22500 2993 1.0289037 0
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1400 1.0895805 3969 0.00022072203 -1.0462033 0.032481455 0.49130771 7492 80 80 0 426 22500 3005 1.0083895 0
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1500 1.0713283 3969 0.00042008247 -0.99879571 0.061819337 0.63979877 7498 87 87 0 457 22500 3000 1.0009934 0
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1600 0.97815063 3969 -0.0005425653 -1.048213 -0.079843909 0.3604669 7533 105 105 0 492 22500 3004 1.0375508 0
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1700 1.1626991 3969 0.00048969595 -1.0790084 0.072063656 0.36261544 7493 87 87 0 519 22500 3014 1.0151507 0
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1800 0.91077627 3969 -0.0012059339 -1.0791337 -0.17746523 0.14204134 7553 77 77 0 554 22500 3001 1.0393648 0
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1900 1.0736324 3969 0.00048053532 -0.99218049 0.070715578 0.56468307 7660 96 96 0 579 22500 2990 1.0071005 0
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2000 1.0529119 3969 -0.00019827686 -1.0715612 -0.029178422 0.28111275 7561 93 93 0 630 22500 3020 1.0201426 0
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2100 0.9995282 3969 -0.00066769217 -1.0877905 -0.09825758 0.22578496 7488 83 83 0 671 22500 2993 1.0246877 0
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2200 1.1492521 3969 0.00093648659 -0.99994625 0.13781337 0.66214341 7481 97 97 0 699 22500 2999 1.0420787 0
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2300 1.174939 3969 0.00098605988 -1.0180811 0.14510857 0.57783443 7414 83 83 0 723 22500 2989 1.004816 0
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2400 1.1382223 3969 0.00050867975 -1.0519828 0.074857312 0.41119597 7601 77 77 0 754 22500 2996 1.007891 0
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2500 0.96793374 3969 -0.00075093709 -1.0687623 -0.1105079 0.12887172 7444 88 88 0 789 22500 2984 1.0268818 0
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2600 1.0064799 3969 -0.00023588466 -1.0311279 -0.034712786 0.38564304 7483 83 83 0 831 22500 3047 1.0199727 0
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2700 1.1198694 3969 0.00019125912 -1.080525 0.028145692 0.35649192 7372 72 72 0 863 22500 2991 0.99989809 0
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2800 1.130996 3969 0.00083301498 -0.99709952 0.12258648 0.76321666 7293 95 95 0 895 22500 2997 1.0077098 0
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2900 1.069281 3969 0.00033771134 -1.0088906 0.049697601 0.60669604 7485 86 86 0 929 22500 3004 1.0105564 0
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3000 1.0864905 3969 5.9065123e-05 -1.0669336 0.0086920235 0.2448914 7367 88 88 0 965 22500 3018 1.0256143 0
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3100 1.2930036 3969 0.0016599457 -1.035796 0.24427761 0.4417485 7502 103 103 0 1002 22500 2996 1.0207648 0
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3200 0.99779215 3969 0.00017970488 -0.96136886 0.02644537 0.48688189 7463 89 89 0 1040 22500 2975 1.0226074 0
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3300 1.1649719 3969 0.00083129956 -1.0309882 0.12233404 0.32895722 7504 92 92 0 1072 22500 2984 1.016696 0
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3400 1.1428122 3969 0.00094373594 -0.99250387 0.13888018 0.62272115 7519 103 103 0 1092 22500 3005 1.0177259 0
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3500 1.1207278 3969 0.00052216214 -1.0326791 0.076841381 0.51325294 7456 71 71 0 1127 22500 2986 1.0290334 0
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3600 0.97869243 3969 -0.00058219044 -1.0545807 -0.085675146 0.44258567 7321 72 72 0 1164 22500 2976 1.031506 0
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3700 1.0853936 3969 -4.3134698e-06 -1.0751745 -0.00063477022 0.37380213 7444 80 80 0 1194 22500 2985 1.0445746 0
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3800 1.0351364 3969 -0.00012682002 -1.0434479 -0.018662834 0.42474168 7503 76 76 0 1226 22500 2986 1.0260769 0
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3900 0.96833719 3969 -0.00039514299 -1.0168031 -0.058149242 0.42237112 7423 79 79 0 1276 22500 3014 1.0160914 0
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4000 1.0465724 3969 0.00016394266 -1.0119808 0.024125802 0.46524856 7502 97 97 0 1299 22500 2984 1.0159361 0
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4100 1.2417361 3969 0.0011421943 -1.0612334 0.16808531 0.39684717 7633 83 83 0 1328 22500 3015 1.0264492 0
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4200 1.0974708 3969 0.00053755453 -1.0073895 0.079106524 0.52996179 7347 86 86 0 1363 22500 3020 1.0215105 0
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4300 1.1082592 3969 0.00034118461 -1.0469679 0.050208728 0.40630088 7470 94 94 0 1400 22500 3012 1.0278618 0
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4400 1.0021274 3969 -0.00027032597 -1.0318873 -0.039781169 0.50493986 7643 77 77 0 1434 22500 3006 1.0236688 0
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4500 0.97643527 3969 -0.00024256014 -1.0023661 -0.03569515 0.55193268 7488 75 75 0 1476 22500 2998 1.0281645 0
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4600 1.0333058 3969 -9.5227766e-05 -1.0369865 -0.014013718 0.37752045 7455 86 86 0 1507 22500 3003 1.0419695 0
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4700 1.1320717 3969 0.00069912511 -1.0178677 0.10288325 0.42203645 7594 80 80 0 1531 22500 2989 1.0343185 0
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4800 1.1326193 3969 0.0010771417 -0.96278098 0.15851217 0.59591984 7504 101 101 0 1560 22500 2998 1.0182951 0
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4900 1.1174294 3969 0.00044360443 -1.0409743 0.065280828 0.30043772 7611 96 96 0 1590 22500 2996 1.0255445 0
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5000 0.93845577 3969 -0.00055722 -1.0110717 -0.082000495 0.41966034 7582 83 83 0 1632 22500 2990 1.0290121 0
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Loop time of 1.15581 on 4 procs for 5000 steps with 14716 atoms
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Performance: 373763.989 tau/day, 4325.972 timesteps/s
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95.1% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.0088997 | 0.011787 | 0.01474 | 1.9 | 1.02
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Neigh | 0.00226 | 0.0025237 | 0.002775 | 0.4 | 0.22
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Comm | 0.077973 | 0.084049 | 0.088172 | 1.3 | 7.27
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Output | 0.0065994 | 0.007837 | 0.011406 | 2.3 | 0.68
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Modify | 0.99157 | 0.99959 | 1.0146 | 0.9 | 86.48
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Other | | 0.05002 | | | 4.33
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Nlocal: 3679 ave 3871 max 3455 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nghost: 46.5 ave 49 max 43 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 118.25 ave 151 max 84 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Total # of neighbors = 473
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Ave neighs/atom = 0.0321419
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Neighbor list builds = 250
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:01
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