117 lines
4.5 KiB
Plaintext
117 lines
4.5 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units lj
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lattice sc 1.0
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Lattice spacing in x,y,z = 1 1 1
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boundary p p p
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neighbor 1.0 bin
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neigh_modify every 5 delay 0 check yes
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atom_style full
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bond_style harmonic
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#angle_style harmonic
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pair_style lj/cut 2.5
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pair_modify table 0
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special_bonds lj 0.0 1.0 1.0
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read_data quartic_bonds.init
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Scanning data file ...
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6 = max bonds/atom
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Reading data file ...
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orthogonal box = (-6.54473 -6.54473 -6.54473) to (6.54473 6.54473 6.54473)
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1 by 2 by 2 MPI processor grid
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2100 atoms
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2600 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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6 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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16 = max # of 1-4 neighbors
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18 = max # of special neighbors
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special_bonds lj 0.0 1.0 1.0
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bond_coeff 1 100.0 1.0
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pair_coeff * * 1.0 1.0 2.5
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timestep 0.005
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fix NPT all npt temp 1.0 1.0 1.0 iso 0.1 0.1 10.0
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thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz
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thermo_modify flush yes
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thermo 100
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########################################################################
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variable l equal xhi
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region MESH block -$l $l -$l $l -$l $l
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region MESH block -6.5447300000000003806 $l -$l $l -$l $l
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region MESH block -6.5447300000000003806 6.5447300000000003806 -$l $l -$l $l
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region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l -$l $l
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region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -$l $l
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region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l
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region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806
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group MESH region MESH
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2100 atoms in group MESH
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# ID group atc PhysicsType ParameterFile
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fix ATC MESH atc field
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ATC: constructing shape function field estimate
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 5
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fix_modify ATC atom_element_map eulerian 100
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fix_modify ATC fields add mass_density energy stress
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## ID part keywords nx ny nz region
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fix_modify ATC mesh create 4 4 1 MESH p p p
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ATC: created uniform mesh with 50 nodes, 16 unique nodes, and 16 elements
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fix_modify ATC bond_interactions on
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fix_modify ATC pair_interactions on
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fix_modify ATC output nodeset all average energy
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fix_modify ATC output nodeset all average stress
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fix_modify ATC output quartic_bondsFE 100 full_text binary tensor_components
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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#########################################################################
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reset_timestep 0
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dump d1 all custom 10000 config.dmp id type mol x y z ix iy iz
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run 400
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Setting up run ...
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WARNING: Inconsistent image flags (../domain.cpp:607)
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ATC: computing bond matrix ..........done
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Memory usage per processor = 24.4426 Mbytes
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Step Temp TotEng E_vdwl E_bond Pxx Pyy Pzz Lz
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0 0 -4.2793581 -4.9222297 0.64287162 -0.122936 -0.43455241 -0.37510432 13.08946
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ATC: computing bond matrix ..........done
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100 0.51761758 -4.2411444 -5.3350909 0.31788979 -1.8360748 -1.7957803 -1.6501347 13.061394
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ATC: computing bond matrix ..........done
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200 0.55719016 -4.194575 -5.3921735 0.36221126 -0.83902447 -1.0583266 -0.82924205 12.978287
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ATC: computing bond matrix ..........done
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300 0.60702877 -4.114999 -5.4634339 0.43832539 -0.05969492 -0.37357729 0.1227012 12.887908
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ATC: computing bond matrix ..........done
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400 0.67773634 -4.0068285 -5.5021915 0.47924261 0.5562405 0.24275905 0.4181606 12.828709
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Loop time of 19.4332 on 4 procs for 400 steps with 2100 atoms
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Pair time (%) = 0.450128 (2.31628)
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Bond time (%) = 0.01934 (0.0995206)
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Neigh time (%) = 0.101799 (0.523842)
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Comm time (%) = 0.129651 (0.667162)
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Outpt time (%) = 0.00420249 (0.0216253)
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Other time (%) = 18.7281 (96.3716)
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Nlocal: 525 ave 528 max 522 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 3037 ave 3052 max 3022 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Neighs: 45578.5 ave 45912 max 45191 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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FullNghs: 91157 ave 91645 max 90702 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 364628
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Ave neighs/atom = 173.632
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Ave special neighs/atom = 13.3324
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Neighbor list builds = 9
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Dangerous builds = 0
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