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lammps/examples/USER/atc/molecule/harmonic_bonds.screen
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LAMMPS (30 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 quartic
#angle_style harmonic
pair_style lj/cut 2.5
pair_modify table 0
special_bonds lj 1.0 1.0 1.0
read_data harmonic_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
# k b1 b2 rc U0
bond_coeff 1 1434.3 -0.7589 0.00 1.5 67.2234
pair_coeff * * 1.0 1.0 2.5
timestep 0.005
fix 1 all npt temp 0.3 0.3 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
reset_timestep 0
########################################################################
variable l equal xhi
#region MESH block xlo xhi ylo yhi zlo zhi
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 all atc field
ATC: constructing shape function field estimate
ATC: version 2.0
ATC: peratom PE compute created with ID: 5
fix_modify ATC fields add mass_density energy stress heat_flux
# 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 off
fix_modify ATC output nodeset all average energy
fix_modify ATC output nodeset all average stress
fix_modify ATC output harmonic_bondsFE 100 full_text binary tensor_components
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
########################################################################
dump d1 all custom 1000 config.dmp id type mol x y z ix iy iz
run 1000
Setting up run ...
WARNING: Inconsistent image flags (../domain.cpp:607)
ATC: computing bond matrix ...........done
Memory usage per processor = 22.5059 Mbytes
Step Temp TotEng E_vdwl E_bond Pxx Pyy Pzz Lz
0 0 27.418101 -4.9222297 32.340331 -6.4375188 -5.3652966 -8.8338595 13.08946
ATC: computing bond matrix ...........done
100 2.2145029 25.770666 -4.6618339 27.112327 1.4701161 2.16737 2.7891188 13.107872
ATC: computing bond matrix ...........done
200 1.6441119 24.285276 -4.6100702 26.430353 -0.2111306 0.11829479 -0.34968383 13.21971
ATC: computing bond matrix ...........done
300 1.2519109 23.218023 -4.7073226 26.048373 -0.90980473 -0.55453672 -1.175576 13.280803
ATC: computing bond matrix ...........done
400 1.0087196 22.413664 -4.8800967 25.781401 -0.94622376 -0.72705532 -0.96132435 13.209446
ATC: computing bond matrix ...........done
500 0.85508692 21.781946 -5.1146958 25.614623 -0.25867636 0.45882845 -1.5464988 13.067112
ATC: computing bond matrix ...........done
600 0.72896043 21.277404 -5.3122654 25.496749 -0.23318524 -0.79102184 -0.28592714 12.940731
ATC: computing bond matrix ...........done
700 0.63573201 20.877991 -5.4819279 25.406775 -0.22930105 0.17264694 -0.13977843 12.838254
ATC: computing bond matrix ...........done
800 0.54900117 20.560582 -5.6107452 25.348218 -0.40709766 -0.32952441 -0.39623019 12.765768
ATC: computing bond matrix ...........done
900 0.4864295 20.309827 -5.7089607 25.289491 0.18995702 -0.4389685 0.32204857 12.716563
ATC: computing bond matrix ...........done
1000 0.43059305 20.104384 -5.8079042 25.266707 -0.0082532778 0.34329484 0.20699648 12.673678
Loop time of 2.37561 on 4 procs for 1000 steps with 2100 atoms
Pair time (%) = 1.15772 (48.7335)
Bond time (%) = 0.108688 (4.57518)
Neigh time (%) = 0.317073 (13.347)
Comm time (%) = 0.327571 (13.7889)
Outpt time (%) = 0.0205073 (0.863244)
Other time (%) = 0.444053 (18.6922)
Nlocal: 525 ave 530 max 523 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 3067.75 ave 3080 max 3059 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 48006.5 ave 48692 max 47634 min
Histogram: 1 1 1 0 0 0 0 0 0 1
FullNghs: 96013 ave 97189 max 95320 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 384052
Ave neighs/atom = 182.882
Ave special neighs/atom = 13.3324
Neighbor list builds = 28
Dangerous builds = 0
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