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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4934 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -49,6 +49,7 @@ prd: parallel replica dynamics of a vacancy diffusion in bulk Si
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reax: RDX and TATB models using the ReaxFF
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void
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srd: stochastic rotation dynamics (SRD) particles as solvent
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Here is how you might run and visualize one of the sample problems:
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@ -0,0 +1,102 @@
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# 2d SRD test: big + small particles
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units lj
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atom_style colloid
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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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region box block 0 10 0 10 -0.5 0.5
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create_box 2 box
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create_atoms 1 region box
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mass 1 1.0
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mass 2 0.01
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shape 1 1.0 1.0 1.0
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shape 2 0.0 0.0 0.0
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group big type 1
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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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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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region plane block 0 10 0 10 -0.001 0.001
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lattice sq 85.0
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create_atoms 2 region plane
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group small type 2
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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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# 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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communicate 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 &
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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 &
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f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
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f_2[6] f_2[8] f_2[9] f_2[10]
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thermo_modify temp tbig
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thermo 100
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dump 1 all atom 250 dump.srd.mixture
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run 5000
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@ -0,0 +1,46 @@
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# 2d SRD only test
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units lj
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atom_style atomic
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atom_modify first empty
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dimension 2
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# create box with big lattice
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lattice sq 0.4
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region box block 0 10 0 10 -0.5 0.5
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create_box 1 box
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# add SRD particles as hi density lattice
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lattice sq 0.4
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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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create_atoms 1 region plane
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group empty type 2
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mass 1 0.01
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velocity all create 1.0 593849 loop geom
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# settings - need dummy empty group to enable no communication
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neighbor 0.3 bin
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neigh_modify delay 1 every 1 check no
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communicate single group empty
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# timestep is big and SRD frequency is 1
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timestep 0.02
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fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
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fix 2 all enforce2d
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# diagnostics
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thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
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thermo 100
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dump 1 all atom 250 dump.srd.pure
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run 5000
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@ -0,0 +1,220 @@
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LAMMPS (1 Oct 2010)
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# 2d SRD test: big + small particles
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units lj
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atom_style colloid
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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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1 by 1 by 1 processor grid
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create_atoms 1 region box
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Created 100 atoms
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mass 1 1.0
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mass 2 0.01
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shape 1 1.0 1.0 1.0
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shape 2 0.0 0.0 0.0
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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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Memory usage per processor = 2.1298 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 0.61487656
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Loop time of 0.0272841 on 1 procs for 1000 steps with 100 atoms
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Pair time (%) = 0.0153759 (56.3545)
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Neigh time (%) = 0.00355697 (13.0368)
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Comm time (%) = 0.00313544 (11.4918)
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Outpt time (%) = 2.7895e-05 (0.102239)
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Other time (%) = 0.00518799 (19.0147)
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Nlocal: 100 ave 100 max 100 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 88 ave 88 max 88 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 459 ave 459 max 459 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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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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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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communicate 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
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thermo 100
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dump 1 all atom 250 dump.srd.mixture
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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
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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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Memory usage per processor = 9.18853 Mbytes
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Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
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0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0
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100 1.1854519 3969 0.0020564907 -0.8709642 0.30263317 0.89895867 7567 82 82 0 0 12996 3018 1.0025076 0
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200 1.0912203 3969 0.00077322095 -0.96652094 0.11378719 0.53220883 7617 91 91 0 0 12996 3019 1.0315077 0
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300 0.99609974 3969 -8.9958107e-05 -0.99937698 -0.013238235 0.30744437 7686 92 92 0 0 12996 3014 1.0224789 0
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400 0.97378829 3969 -1.0310777e-06 -0.96420214 -0.00015173339 0.29401458 7517 104 104 0 0 12996 3015 1.0354258 0
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500 1.0704853 3969 0.00045875378 -0.99227027 0.067510207 0.23723623 7507 90 90 0 0 12996 3013 1.0255432 0
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600 0.98490603 3969 -0.00036594295 -1.0289091 -0.053852164 0.17457127 7475 84 84 0 0 12996 2994 1.0362491 0
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700 1.1128816 3969 0.00061003578 -1.0119799 0.089772865 0.44497962 7680 97 97 0 0 12996 3017 1.0076201 0
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800 0.96861977 3969 -0.00069285411 -1.060894 -0.10196041 0.3497781 7534 74 74 0 0 12996 3008 1.0271614 0
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900 1.0407967 3969 0.00047726289 -0.9601547 0.070234006 0.70144271 7521 97 97 0 0 12996 2988 1.0115957 0
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1000 1.0543264 3969 7.8805118e-05 -1.0321862 0.011596961 0.41617549 7499 82 82 0 0 12996 3022 1.0039293 0
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1100 0.79276143 3969 -0.0014999076 -1.0055602 -0.22072641 0.38874703 7333 100 100 0 0 12996 3013 1.0389616 0
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1200 1.084432 3969 0.00068593846 -0.97264494 0.1009427 0.60176004 7348 81 81 0 0 12996 2999 1.0009925 0
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1300 1.0487612 3969 0.00032122262 -0.9910025 0.047271121 0.49732554 7551 94 94 0 0 12996 2988 1.0221747 0
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1400 1.0098443 3969 4.0826801e-05 -0.99373776 0.006008072 0.51403259 7619 89 89 0 0 12996 3007 1.0344942 0
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1500 1.218401 3969 0.00097129173 -1.0632817 0.14293529 0.38730792 7414 87 87 0 0 12996 3015 1.0519305 0
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1600 1.1501145 3969 0.00047446251 -1.0687914 0.069821903 0.35607234 7383 80 80 0 0 12996 3014 1.0203142 0
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1700 0.94258444 3969 -0.0007994931 -1.050812 -0.1176534 0.40572317 7597 92 92 0 0 12996 3002 1.0469204 0
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1800 1.1205745 3969 0.00014712615 -1.0877177 0.021651085 0.37897578 7585 82 82 0 0 12996 2991 1.0389588 0
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1900 0.95430392 3969 -0.0010155747 -1.0942129 -0.14945198 0.24556839 7703 85 85 0 0 12996 3001 1.0246638 0
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2000 0.92246887 3969 -0.0011696335 -1.0853675 -0.17212327 0.23953568 7636 100 100 0 0 12996 3022 1.0204788 0
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2100 0.91529221 3969 -0.0012601691 -1.0915858 -0.18544648 0.22735286 7481 80 80 0 0 12996 3026 1.0280942 0
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2200 0.89505853 3969 -0.00064151149 -0.98051277 -0.094404831 0.51723842 7418 87 87 0 0 12996 3000 1.027661 0
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2300 0.98485557 3969 -0.00075152689 -1.0856017 -0.1105947 0.24927644 7590 80 80 0 0 12996 2999 1.0258603 0
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2400 0.91841201 3969 -0.0010505855 -1.0638321 -0.15460417 0.23326098 7587 103 103 0 0 12996 3001 1.0282876 0
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2500 1.0358998 3969 6.5299645e-05 -1.0159313 0.0096094958 0.34899097 7452 93 93 0 0 12996 2975 1.0426326 0
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2600 0.94743566 3969 -0.00053875484 -1.0172445 -0.079283162 0.22735975 7560 66 66 0 0 12996 2996 1.0211493 0
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2700 0.87106832 3969 -0.0010996524 -1.0241825 -0.16182485 0.25604039 7329 83 83 0 0 12996 3005 1.0305366 0
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2800 1.0803159 3969 0.00030634738 -1.0244307 0.045082081 0.45643311 7418 108 108 0 0 12996 3023 1.0340188 0
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2900 1.1283591 3969 0.00084010869 -0.99344512 0.12363039 0.83746145 7308 91 91 0 0 12996 2981 1.0189882 0
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3000 1.1876657 3969 0.0016273526 -0.93630787 0.23948121 0.97168782 7453 87 87 0 0 12996 2979 1.0166656 0
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3100 1.0004566 3969 -0.00032761995 -1.0386645 -0.048212552 0.61341839 7470 87 87 0 0 12996 3031 1.017823 0
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3200 1.2257669 3969 0.00099290366 -1.0673936 0.1461157 0.61730027 7545 86 86 0 1 12996 2963 1.0419479 0
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3300 1.0483473 3969 -0.00031074739 -1.0835934 -0.045729586 0.52991291 7442 84 84 0 0 12996 3010 1.015561 0
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3400 1.1060909 3969 0.00030818848 -1.049677 0.045353017 0.7068218 7459 87 87 0 0 12996 3002 1.0231151 0
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3500 1.0538669 3969 -0.00036380882 -1.0968664 -0.053538106 0.45965228 7648 81 81 0 0 12996 3020 1.0228882 0
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3600 0.9403379 3969 -0.00095052032 -1.0708131 -0.13987857 0.29232958 7731 104 104 0 0 12996 3015 1.0308016 0
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3700 0.87576431 3969 -0.0013620431 -1.0674449 -0.20043826 0.20807819 7570 93 93 0 0 12996 2999 1.027521 0
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3800 1.0214205 3969 -0.00025908571 -1.0493333 -0.038127053 0.35110253 7480 95 95 0 0 12996 3023 1.0189546 0
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3900 1.0399628 3969 -0.0004657163 -1.098098 -0.068534811 0.14477785 7597 84 84 0 0 12996 3001 1.0391639 0
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4000 0.96223871 3969 -0.00087553027 -1.0814594 -0.12884303 0.32672058 7506 91 91 0 0 12996 3026 1.0273983 0
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4100 0.9978966 3969 -0.00014719261 -1.0095785 -0.021660865 0.54900472 7553 89 89 0 0 12996 3008 1.0214976 0
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4200 0.99324797 3969 -0.00014342613 -1.0044221 -0.02110659 0.5121817 7423 77 77 0 0 12996 3008 1.0621727 0
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4300 0.90689211 3969 -0.00089523015 -1.0295653 -0.13174207 0.41794731 7614 77 77 0 0 12996 3009 1.0361369 0
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4400 0.94201541 3969 -0.00126231 -1.1183568 -0.18576154 0.16778284 7600 91 91 0 0 12996 3004 1.035561 0
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4500 0.97003803 3969 -0.00090250856 -1.0931508 -0.13281316 0.37787471 7505 96 96 0 0 12996 2998 1.0335568 0
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4600 0.96052354 3969 -0.00093721969 -1.0888396 -0.13792125 0.48917838 7532 72 72 0 0 12996 2999 1.0124728 0
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4700 0.95086208 3969 -0.00076105324 -1.0533501 -0.11199659 0.60704145 7429 104 104 0 0 12996 2988 1.0095829 0
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4800 0.94826516 3969 -0.0010878926 -1.0988768 -0.16009427 0.50867751 7351 93 93 0 0 12996 2968 1.0212405 0
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4900 1.0540371 3969 -4.230244e-06 -1.0441192 -0.00062252271 0.6999864 7454 91 91 0 0 12996 2998 1.0019459 0
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5000 0.94814157 3969 -0.0007896491 -1.0548649 -0.11620476 0.61244147 7362 76 76 0 0 12996 2976 1.0250728 0
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Loop time of 5.65139 on 1 procs for 5000 steps with 14716 atoms
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Pair time (%) = 0.0861783 (1.5249)
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Neigh time (%) = 0.310817 (5.49982)
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Comm time (%) = 0.0628221 (1.11162)
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Outpt time (%) = 0.457241 (8.09077)
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Other time (%) = 4.73433 (83.7729)
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Nlocal: 14716 ave 14716 max 14716 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 87 ave 87 max 87 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 480 ave 480 max 480 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 480
|
||||
Ave neighs/atom = 0.0326176
|
||||
Neighbor list builds = 250
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,220 @@
|
|||
LAMMPS (1 Oct 2010)
|
||||
# 2d SRD test: big + small particles
|
||||
|
||||
units lj
|
||||
atom_style colloid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with sigma 1.0
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
mass 1 1.0
|
||||
mass 2 0.01
|
||||
|
||||
shape 1 1.0 1.0 1.0
|
||||
shape 2 0.0 0.0 0.0
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.12925 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.54272 0 0.88288 -0.041088
|
||||
1000 1.8791467 -0.97185784 0 0.8884974 0.61487657
|
||||
Loop time of 0.032092 on 4 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.00402153 (12.5312)
|
||||
Neigh time (%) = 0.000997305 (3.10764)
|
||||
Comm time (%) = 0.0206033 (64.2007)
|
||||
Outpt time (%) = 8.10027e-05 (0.252408)
|
||||
Other time (%) = 0.0063889 (19.9081)
|
||||
|
||||
Nlocal: 25 ave 26 max 23 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 47 ave 48 max 46 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 114.75 ave 124 max 100 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 459
|
||||
Ave neighs/atom = 4.59
|
||||
Neighbor list builds = 129
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region plane block 0 10 0 10 -0.001 0.001
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 21316 atoms
|
||||
|
||||
group small type 2
|
||||
21316 atoms in group small
|
||||
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 6700 atoms, new total = 14716
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
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]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all
|
||||
thermo 100
|
||||
dump 1 all atom 250 dump.srd.mixture
|
||||
|
||||
run 5000
|
||||
SRD info:
|
||||
SRD/big particles = 14616 100
|
||||
big particle diameter max/min = 0.88 0.88
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 63 63 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
|
||||
SRD per actual grid cell = 4.86648
|
||||
SRD viscosity = 0.463448
|
||||
big/SRD mass density ratio = 2.12808
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.2944 24.262
|
||||
ave/max big velocity = 1.69284 5.10989
|
||||
Memory usage per processor = 4.74632 Mbytes
|
||||
Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
|
||||
0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0
|
||||
100 1.3582446 3969 0.0026789295 -0.95043087 0.39423126 0.73581726 7479 87 87 0 0 22500 2999 1.0285157 0
|
||||
200 1.2572907 3969 0.0019616669 -0.95603884 0.28867891 0.62749376 7394 98 98 0 0 22500 2994 1.0253343 0
|
||||
300 1.12798 3969 0.00057755533 -1.0317072 0.084993042 0.30262448 7311 88 88 0 0 22500 2997 1.022263 0
|
||||
400 1.1466105 3969 0.00088785773 -1.0044873 0.13065714 0.40537124 7467 82 82 0 0 22500 2993 1.0139003 0
|
||||
500 1.0151043 3969 -0.00021014381 -1.0358781 -0.030924763 0.19673928 7587 81 81 0 0 22500 2994 1.0145019 0
|
||||
600 0.99210691 3969 -0.0002577968 -1.0201232 -0.037937377 0.2625174 7449 92 92 0 0 22500 2968 0.98574736 0
|
||||
700 0.92572874 3969 -0.00067753277 -1.0161772 -0.099705722 0.19520999 7537 78 78 0 0 22500 2998 1.0064032 0
|
||||
800 0.94627244 3969 -0.0003639106 -0.9903628 -0.053553084 0.22241336 7602 79 79 0 1 22500 3010 1.0134331 0
|
||||
900 0.92523394 3969 -0.00080502966 -1.0344498 -0.11846816 0.18846804 7576 72 72 0 1 22500 3015 1.0136704 0
|
||||
1000 1.0322972 3969 -0.00037569219 -1.0772611 -0.055286863 0.13263626 7601 88 88 0 0 22500 3000 1.0224061 0
|
||||
1100 0.9726161 3969 -0.00041776377 -1.0243681 -0.061478117 0.3120931 7425 87 87 0 0 22500 2991 1.0216981 0
|
||||
1200 0.9785542 3969 -0.00036217362 -1.0220661 -0.053297471 0.37956001 7634 94 94 0 0 22500 3022 1.0055215 0
|
||||
1300 1.102684 3969 0.00056306573 -1.0087964 0.082860753 0.50039902 7380 94 94 0 0 22500 3011 1.0298198 0
|
||||
1400 1.2416072 3969 0.0016380507 -0.98813558 0.24105553 0.6709785 7532 95 95 0 0 22500 3005 1.0272106 0
|
||||
1500 1.1009579 3969 0.00041059416 -1.0295252 0.060423037 0.4271012 7443 86 86 0 0 22500 2990 1.0322439 0
|
||||
1600 0.97932726 3969 -0.00044406974 -1.0348833 -0.065349303 0.23710215 7541 85 85 0 0 22500 3005 1.0504545 0
|
||||
1700 1.07156 3969 0.0003309407 -1.0121432 0.048701233 0.32615222 7660 90 90 0 1 22500 3010 1.0192163 0
|
||||
1800 0.94379054 3969 -0.00060529206 -1.0234274 -0.08907478 0.28437994 7706 92 92 0 0 22500 2983 1.0197247 0
|
||||
1900 1.1935542 3969 0.001087796 -1.0215386 0.16008006 0.32082985 7633 102 102 0 0 22500 3026 1.0227294 0
|
||||
2000 1.0794535 3969 0.00017035747 -1.0435892 0.025069805 0.12933714 7547 76 76 0 0 22500 3028 1.0339312 0
|
||||
2100 1.11728 3969 0.001197717 -0.92985122 0.17625603 0.4877601 7424 88 88 0 0 22500 2986 1.0268223 0
|
||||
2200 1.022726 3969 -0.00017383526 -1.0380804 -0.025581597 0.18522494 7414 92 92 0 0 22500 3004 1.0254694 0
|
||||
2300 1.2289681 3969 0.0014918151 -0.99714295 0.21953551 0.56571933 7669 90 90 0 0 22500 3008 1.0265701 0
|
||||
2400 1.0261081 3969 0.00016550325 -0.99149158 0.024355459 0.53332928 7499 83 83 0 0 22500 3019 1.0160353 0
|
||||
2500 1.0155015 3969 -0.00056230464 -1.0880952 -0.082748751 0.22398562 7712 79 79 0 0 22500 3017 1.03801 0
|
||||
2600 0.8756954 3969 -0.0014956069 -1.087032 -0.22009351 0.10400097 7542 85 85 0 0 22500 2985 1.024091 0
|
||||
2700 0.97964461 3969 -0.00075911535 -1.0815596 -0.11171141 0.27927544 7449 86 86 0 0 22500 2993 1.0166909 0
|
||||
2800 0.97102332 3969 -0.00081115436 -1.0806826 -0.11936948 0.36647698 7662 85 85 0 0 22500 3014 1.0148134 0
|
||||
2900 1.1405082 3969 0.00078035444 -1.0142661 0.11483696 0.73653576 7451 82 82 0 0 22500 3007 1.0296379 0
|
||||
3000 1.0460256 3969 -0.00031837206 -1.082417 -0.046851633 0.25310003 7494 83 83 0 0 22500 3013 1.043192 0
|
||||
3100 1.128752 3969 0.00043203186 -1.0538867 0.063577808 0.37101933 7458 89 89 0 1 22500 2981 1.0082866 0
|
||||
3200 1.0546223 3969 0.00023156986 -1.0099982 0.034077821 0.66191884 7451 92 92 0 0 22500 2988 1.0254862 0
|
||||
3300 1.0859707 3969 -5.4375056e-05 -1.0831128 -0.0080018333 0.3552947 7441 74 74 0 0 22500 2978 1.0252244 0
|
||||
3400 0.90831095 3969 -0.0011506108 -1.0685517 -0.16932389 0.26027658 7478 76 76 0 0 22500 2997 1.0306308 0
|
||||
3500 1.0971397 3969 0.00047675241 -1.0160094 0.070158884 0.39394719 7510 87 87 0 0 22500 2999 1.0303505 0
|
||||
3600 1.0758592 3969 5.1451605e-05 -1.057529 0.0075716182 0.23217468 7505 98 98 0 0 22500 3022 1.0133265 0
|
||||
3700 0.99184036 3969 -0.00051911023 -1.0583142 -0.076392262 0.2659259 7566 104 104 0 0 22500 3006 1.0284719 0
|
||||
3800 0.86950687 3969 -0.0014525295 -1.074566 -0.21375425 0.27380224 7552 80 80 0 0 22500 3013 1.0351337 0
|
||||
3900 0.86286132 3969 -0.0010595017 -1.010149 -0.15591627 0.56043933 7547 104 104 0 0 22500 2992 1.0313609 0
|
||||
4000 0.76083626 3969 -0.0014009914 -0.9593978 -0.2061699 0.64813923 7448 101 101 0 0 22500 3032 1.0109258 0
|
||||
4100 1.0071575 3969 -0.00018734554 -1.0246557 -0.027569769 0.55964495 7489 76 76 0 0 22500 3016 1.0175384 0
|
||||
4200 0.88374612 3969 -0.0010981928 -1.0365187 -0.16161005 0.41352036 7481 92 92 0 0 22500 2995 1.0123735 0
|
||||
4300 0.98819505 3969 -0.00066821798 -1.0766481 -0.098334958 0.41489158 7557 79 79 0 0 22500 2998 1.0400745 0
|
||||
4400 1.1772685 3969 0.0010725317 -1.007662 0.15783376 0.7912903 7522 76 76 0 0 22500 2991 1.0176624 0
|
||||
4500 1.0836741 3969 0.00021867511 -1.0406572 0.032180229 0.58489302 7800 93 93 0 0 22500 2997 1.0023484 0
|
||||
4600 1.0334731 3969 -0.00015378918 -1.04577 -0.022631616 0.53872329 7542 94 94 0 0 22500 2996 0.98823241 0
|
||||
4700 1.2126127 3969 0.0011423373 -1.0323802 0.16810636 0.49583696 7387 81 81 0 0 22500 3001 1.0425378 0
|
||||
4800 1.1593219 3969 0.0010239969 -0.99703726 0.15069139 0.37192735 7374 80 80 0 1 22500 2988 1.0278368 0
|
||||
4900 0.87223689 3969 -0.00099601272 -1.0100878 -0.14657323 0.11585542 7448 89 89 0 0 22500 3000 1.0267238 0
|
||||
5000 0.87426493 3969 -0.0010817587 -1.0247139 -0.15919161 0.15322481 7587 100 100 0 0 22500 2988 1.0030228 0
|
||||
Loop time of 1.93728 on 4 procs for 5000 steps with 14716 atoms
|
||||
|
||||
Pair time (%) = 0.0232192 (1.19854)
|
||||
Neigh time (%) = 0.0877846 (4.53133)
|
||||
Comm time (%) = 0.182241 (9.40704)
|
||||
Outpt time (%) = 0.381904 (19.7134)
|
||||
Other time (%) = 1.26213 (65.1497)
|
||||
|
||||
Nlocal: 3679 ave 3872 max 3379 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 48.25 ave 51 max 45 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 118 ave 167 max 87 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 472
|
||||
Ave neighs/atom = 0.0320739
|
||||
Neighbor list builds = 250
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (1 Oct 2010)
|
||||
# 2d SRD only test
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify first empty
|
||||
dimension 2
|
||||
|
||||
# create box with big lattice
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
|
||||
1 by 1 by 1 processor grid
|
||||
|
||||
# add SRD particles as hi density lattice
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region plane block 0 10 0 10 -0.001 0.001
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 1 region plane
|
||||
Created 21316 atoms
|
||||
|
||||
group empty type 2
|
||||
0 atoms in group empty
|
||||
|
||||
mass 1 0.01
|
||||
velocity all create 1.0 593849 loop geom
|
||||
|
||||
# settings - need dummy empty group to enable no communication
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 1 every 1 check no
|
||||
|
||||
communicate single group empty
|
||||
|
||||
# timestep is big and SRD frequency is 1
|
||||
|
||||
timestep 0.02
|
||||
|
||||
fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
|
||||
fix 2 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
|
||||
thermo 100
|
||||
dump 1 all atom 250 dump.srd.pure
|
||||
|
||||
run 5000
|
||||
SRD info:
|
||||
SRD/big particles = 21316 0
|
||||
big particle diameter max/min = 0 1e+20
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 63 63 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
|
||||
SRD per actual grid cell = 5.37062
|
||||
SRD viscosity = 0.439647
|
||||
big/SRD mass density ratio = 0
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max all velocity = 13.2735 24.2873
|
||||
Memory usage per processor = 4.2049 Mbytes
|
||||
Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6]
|
||||
0 1 0 0.99995309 85.26 0 0 0
|
||||
100 1 3969 0.99995309 85.26 0 0 0
|
||||
200 1 3969 0.99995309 85.26 0 0 0
|
||||
300 1 3969 0.99995309 85.26 0 0 0
|
||||
400 1 3969 0.99995309 85.26 0 0 0
|
||||
500 1 3969 0.99995309 85.26 0 0 0
|
||||
600 1 3969 0.99995309 85.26 0 0 0
|
||||
700 1 3969 0.99995309 85.26 0 0 0
|
||||
800 1 3969 0.99995309 85.26 0 0 0
|
||||
900 1 3969 0.99995309 85.26 0 0 0
|
||||
1000 1 3969 0.99995309 85.26 0 0 0
|
||||
1100 1 3969 0.99995309 85.26 0 0 0
|
||||
1200 1 3969 0.99995309 85.26 0 0 0
|
||||
1300 1 3969 0.99995309 85.26 0 0 0
|
||||
1400 1 3969 0.99995309 85.26 0 0 0
|
||||
1500 1 3969 0.99995309 85.26 0 0 0
|
||||
1600 1 3969 0.99995309 85.26 0 0 0
|
||||
1700 1 3969 0.99995309 85.26 0 0 0
|
||||
1800 1 3969 0.99995309 85.26 0 0 0
|
||||
1900 1 3969 0.99995309 85.26 0 0 0
|
||||
2000 1 3969 0.99995309 85.26 0 0 0
|
||||
2100 1 3969 0.99995309 85.26 0 0 0
|
||||
2200 1 3969 0.99995309 85.26 0 0 0
|
||||
2300 1 3969 0.99995309 85.26 0 0 0
|
||||
2400 1 3969 0.99995309 85.26 0 0 0
|
||||
2500 1 3969 0.99995309 85.26 0 0 0
|
||||
2600 1 3969 0.99995309 85.26 0 0 0
|
||||
2700 1 3969 0.99995309 85.26 0 0 0
|
||||
2800 1 3969 0.99995309 85.26 0 0 0
|
||||
2900 1 3969 0.99995309 85.26 0 0 0
|
||||
3000 1 3969 0.99995309 85.26 0 0 0
|
||||
3100 1 3969 0.99995309 85.26 0 0 0
|
||||
3200 1 3969 0.99995309 85.26 0 0 0
|
||||
3300 1 3969 0.99995309 85.26 0 0 0
|
||||
3400 1 3969 0.99995309 85.26 0 0 0
|
||||
3500 1 3969 0.99995309 85.26 0 0 0
|
||||
3600 1 3969 0.99995309 85.26 0 0 0
|
||||
3700 1 3969 0.99995309 85.26 0 0 0
|
||||
3800 1 3969 0.99995309 85.26 0 0 0
|
||||
3900 1 3969 0.99995309 85.26 0 0 0
|
||||
4000 1 3969 0.99995309 85.26 0 0 0
|
||||
4100 1 3969 0.99995309 85.26 0 0 0
|
||||
4200 1 3969 0.99995309 85.26 0 0 0
|
||||
4300 1 3969 0.99995309 85.26 0 0 0
|
||||
4400 1 3969 0.99995309 85.26 0 0 0
|
||||
4500 1 3969 0.99995309 85.26 0 0 0
|
||||
4600 1 3969 0.99995309 85.26 0 0 0
|
||||
4700 1 3969 0.99995309 85.26 0 0 0
|
||||
4800 1 3969 0.99995309 85.26 0 0 0
|
||||
4900 1 3969 0.99995309 85.26 0 0 0
|
||||
5000 1 3969 0.99995309 85.26 0 0 0
|
||||
Loop time of 10.4217 on 1 procs for 5000 steps with 21316 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Neigh time (%) = 5.80617 (55.7125)
|
||||
Comm time (%) = 0.917962 (8.80821)
|
||||
Outpt time (%) = 0.66245 (6.35647)
|
||||
Other time (%) = 3.03508 (29.1228)
|
||||
|
||||
Nlocal: 21316 ave 21316 max 21316 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (1 Oct 2010)
|
||||
# 2d SRD only test
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify first empty
|
||||
dimension 2
|
||||
|
||||
# create box with big lattice
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
|
||||
2 by 2 by 1 processor grid
|
||||
|
||||
# add SRD particles as hi density lattice
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region plane block 0 10 0 10 -0.001 0.001
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 1 region plane
|
||||
Created 21316 atoms
|
||||
|
||||
group empty type 2
|
||||
0 atoms in group empty
|
||||
|
||||
mass 1 0.01
|
||||
velocity all create 1.0 593849 loop geom
|
||||
|
||||
# settings - need dummy empty group to enable no communication
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 1 every 1 check no
|
||||
|
||||
communicate single group empty
|
||||
|
||||
# timestep is big and SRD frequency is 1
|
||||
|
||||
timestep 0.02
|
||||
|
||||
fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
|
||||
fix 2 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
|
||||
thermo 100
|
||||
dump 1 all atom 250 dump.srd.pure
|
||||
|
||||
run 5000
|
||||
SRD info:
|
||||
SRD/big particles = 21316 0
|
||||
big particle diameter max/min = 0 1e+20
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 63 63 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
|
||||
SRD per actual grid cell = 5.37062
|
||||
SRD viscosity = 0.439647
|
||||
big/SRD mass density ratio = 0
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max all velocity = 13.2735 24.2873
|
||||
Memory usage per processor = 1.31651 Mbytes
|
||||
Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6]
|
||||
0 1 0 0.99995309 85.26 0 0 0
|
||||
100 1 3969 0.99995309 85.26 0 0 0
|
||||
200 1 3969 0.99995309 85.26 0 0 0
|
||||
300 1 3969 0.99995309 85.26 0 0 0
|
||||
400 1 3969 0.99995309 85.26 0 0 0
|
||||
500 1 3969 0.99995309 85.26 0 0 0
|
||||
600 1 3969 0.99995309 85.26 0 0 0
|
||||
700 1 3969 0.99995309 85.26 0 0 0
|
||||
800 1 3969 0.99995309 85.26 0 0 0
|
||||
900 1 3969 0.99995309 85.26 0 0 0
|
||||
1000 1 3969 0.99995309 85.26 0 0 0
|
||||
1100 1 3969 0.99995309 85.26 0 0 0
|
||||
1200 1 3969 0.99995309 85.26 0 0 0
|
||||
1300 1 3969 0.99995309 85.26 0 0 0
|
||||
1400 1 3969 0.99995309 85.26 0 0 0
|
||||
1500 1 3969 0.99995309 85.26 0 0 0
|
||||
1600 1 3969 0.99995309 85.26 0 0 0
|
||||
1700 1 3969 0.99995309 85.26 0 0 0
|
||||
1800 1 3969 0.99995309 85.26 0 0 0
|
||||
1900 1 3969 0.99995309 85.26 0 0 0
|
||||
2000 1 3969 0.99995309 85.26 0 0 0
|
||||
2100 1 3969 0.99995309 85.26 0 0 0
|
||||
2200 1 3969 0.99995309 85.26 0 0 0
|
||||
2300 1 3969 0.99995309 85.26 0 0 0
|
||||
2400 1 3969 0.99995309 85.26 0 0 0
|
||||
2500 1 3969 0.99995309 85.26 0 0 0
|
||||
2600 1 3969 0.99995309 85.26 0 0 0
|
||||
2700 1 3969 0.99995309 85.26 0 0 0
|
||||
2800 1 3969 0.99995309 85.26 0 0 0
|
||||
2900 1 3969 0.99995309 85.26 0 0 0
|
||||
3000 1 3969 0.99995309 85.26 0 0 0
|
||||
3100 1 3969 0.99995309 85.26 0 0 0
|
||||
3200 1 3969 0.99995309 85.26 0 0 0
|
||||
3300 1 3969 0.99995309 85.26 0 0 0
|
||||
3400 1 3969 0.99995309 85.26 0 0 0
|
||||
3500 1 3969 0.99995309 85.26 0 0 0
|
||||
3600 1 3969 0.99995309 85.26 0 0 0
|
||||
3700 1 3969 0.99995309 85.26 0 0 0
|
||||
3800 1 3969 0.99995309 85.26 0 0 0
|
||||
3900 1 3969 0.99995309 85.26 0 0 0
|
||||
4000 1 3969 0.99995309 85.26 0 0 0
|
||||
4100 1 3969 0.99995309 85.26 0 0 0
|
||||
4200 1 3969 0.99995309 85.26 0 0 0
|
||||
4300 1 3969 0.99995309 85.26 0 0 0
|
||||
4400 1 3969 0.99995309 85.26 0 0 0
|
||||
4500 1 3969 0.99995309 85.26 0 0 0
|
||||
4600 1 3969 0.99995309 85.26 0 0 0
|
||||
4700 1 3969 0.99995309 85.26 0 0 0
|
||||
4800 1 3969 0.99995309 85.26 0 0 0
|
||||
4900 1 3969 0.99995309 85.26 0 0 0
|
||||
5000 1 3969 0.99995309 85.26 0 0 0
|
||||
Loop time of 3.48791 on 4 procs for 5000 steps with 21316 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Neigh time (%) = 1.4364 (41.1823)
|
||||
Comm time (%) = 0.740496 (21.2303)
|
||||
Outpt time (%) = 0.541988 (15.5391)
|
||||
Other time (%) = 0.769027 (22.0483)
|
||||
|
||||
Nlocal: 5329 ave 5381 max 5260 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
Loading…
Reference in New Issue