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lammps/examples/USER/atc/molecule/quartic_bonds.screen
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quartic_bonds.screen
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LAMMPS (24 Aug 2013)
units lj
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
boundary p p p
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style full
bond_style harmonic
#angle_style harmonic
pair_style lj/cut 2.5
pair_modify table 0
special_bonds lj 0.0 1.0 1.0
read_data quartic_bonds.init
Scanning data file ...
6 = max bonds/atom
Reading data file ...
orthogonal box = (-6.54473 -6.54473 -6.54473) to (6.54473 6.54473 6.54473)
1 by 2 by 2 MPI processor grid
2100 atoms
2600 bonds
Finding 1-2 1-3 1-4 neighbors ...
6 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
18 = max # of special neighbors
special_bonds lj 0.0 1.0 1.0
bond_coeff 1 100.0 1.0
pair_coeff * * 1.0 1.0 2.5
timestep 0.005
fix NPT all npt temp 1.0 1.0 1.0 iso 0.1 0.1 10.0
thermo_style custom step temp etotal evdwl ebond pxx pyy pzz lz
thermo_modify flush yes
thermo 100
########################################################################
variable l equal xhi
region MESH block -$l $l -$l $l -$l $l
region MESH block -6.5447300000000003806 $l -$l $l -$l $l
region MESH block -6.5447300000000003806 6.5447300000000003806 -$l $l -$l $l
region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l -$l $l
region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -$l $l
region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 $l
region MESH block -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806 -6.5447300000000003806 6.5447300000000003806
group MESH region MESH
2100 atoms in group MESH
# ID group atc PhysicsType ParameterFile
fix ATC MESH atc field
ATC: constructing shape function field estimate
ATC: version 2.0
ATC: peratom PE compute created with ID: 5
fix_modify ATC atom_element_map eulerian 100
fix_modify ATC fields add mass_density energy stress
## ID part keywords nx ny nz region
fix_modify ATC mesh create 4 4 1 MESH p p p
ATC: created uniform mesh with 50 nodes, 16 unique nodes, and 16 elements
fix_modify ATC bond_interactions on
fix_modify ATC pair_interactions on
fix_modify ATC output nodeset all average energy
fix_modify ATC output nodeset all average stress
fix_modify ATC output quartic_bondsFE 100 full_text binary tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
#########################################################################
reset_timestep 0
dump d1 all custom 10000 config.dmp id type mol x y z ix iy iz
run 400
Setting up run ...
WARNING: Inconsistent image flags (../domain.cpp:607)
ATC: computing bond matrix ..........done
Memory usage per processor = 24.4426 Mbytes
Step Temp TotEng E_vdwl E_bond Pxx Pyy Pzz Lz
0 0 -4.2793581 -4.9222297 0.64287162 -0.122936 -0.43455241 -0.37510432 13.08946
ATC: computing bond matrix ..........done
100 0.51761758 -4.2411444 -5.3350909 0.31788979 -1.8360748 -1.7957803 -1.6501347 13.061394
ATC: computing bond matrix ..........done
200 0.55719016 -4.194575 -5.3921735 0.36221126 -0.83902447 -1.0583266 -0.82924205 12.978287
ATC: computing bond matrix ..........done
300 0.60702877 -4.114999 -5.4634339 0.43832539 -0.05969492 -0.37357729 0.1227012 12.887908
ATC: computing bond matrix ..........done
400 0.67773634 -4.0068285 -5.5021915 0.47924261 0.5562405 0.24275905 0.4181606 12.828709
Loop time of 20.5487 on 4 procs for 400 steps with 2100 atoms
Pair time (%) = 0.466344 (2.26946)
Bond time (%) = 0.021544 (0.104843)
Neigh time (%) = 0.106401 (0.517798)
Comm time (%) = 0.196994 (0.958666)
Outpt time (%) = 0.00453418 (0.0220655)
Other time (%) = 19.7529 (96.1272)
Nlocal: 525 ave 528 max 522 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 3037 ave 3052 max 3022 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 45578.5 ave 45912 max 45191 min
Histogram: 1 0 0 1 0 0 0 0 1 1
FullNghs: 91157 ave 91645 max 90702 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 364628
Ave neighs/atom = 173.632
Ave special neighs/atom = 13.3324
Neighbor list builds = 9
Dangerous builds = 0
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