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LAMMPS (30 Aug 2013)
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
create_atoms 1 region atomRegion
Created 2304 atoms
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: 3 materials defined from Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 65.169 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4509.8851 0 -4509.8851 26.948349
100 4.7374019e-13 -4509.8851 0 -4509.8851 26.94834
200 9.7683427e-13 -4509.8851 0 -4509.8851 26.94803
300 1.9565172e-11 -4509.8851 0 -4509.8851 26.946439
400 2.6411547e-10 -4509.8852 0 -4509.8852 26.942798
500 1.351766e-09 -4509.8852 0 -4509.8852 26.93773
600 3.6802148e-09 -4509.8852 0 -4509.8852 26.932648
700 6.6530697e-09 -4509.8852 0 -4509.8852 26.928033
800 9.5474556e-09 -4509.8852 0 -4509.8852 26.923147
900 1.2412323e-08 -4509.8852 0 -4509.8852 26.917542
1000 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973
Loop time of 19.6581 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 5.96992 (30.3688)
Neigh time (%) = 2.49911 (12.7129)
Comm time (%) = 6.03219 (30.6855)
Outpt time (%) = 0.000867546 (0.00441317)
Other time (%) = 5.15602 (26.2285)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288910 max 68513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000
Setting up run ...
Memory usage per processor = 65.169 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.5423223e-08 -4509.8852 0 -4509.8852 26.911973
100 1.809994e-08 -4509.8852 0 -4509.8852 26.907429
200 1.9777109e-08 -4509.8852 0 -4509.8852 26.904241
300 2.0275205e-08 -4509.8852 0 -4509.8852 26.902912
400 1.9266773e-08 -4509.8852 0 -4509.8852 26.904281
500 1.6821974e-08 -4509.8851 0 -4509.8851 26.908126
600 1.370661e-08 -4509.8852 0 -4509.8852 26.912761
700 1.0292223e-08 -4509.8852 0 -4509.8852 26.916838
800 6.5498338e-09 -4509.8853 0 -4509.8853 26.920715
900 3.1643856e-09 -4509.8853 0 -4509.8853 26.925094
1000 1.0112513e-09 -4509.8852 0 -4509.8852 26.928958
1100 4.4564547e-10 -4509.8852 0 -4509.8852 26.930177
1200 2.264627e-09 -4509.8852 0 -4509.8852 26.92803
1300 6.3325706e-09 -4509.8853 0 -4509.8853 26.923952
1400 1.1281983e-08 -4509.8853 0 -4509.8853 26.919616
1500 1.5582979e-08 -4509.8852 0 -4509.8852 26.915411
1600 1.8378446e-08 -4509.8852 0 -4509.8852 26.911278
1700 1.9544417e-08 -4509.8852 0 -4509.8852 26.907886
1800 1.993739e-08 -4509.8851 0 -4509.8851 26.905965
1900 1.9956722e-08 -4509.8851 0 -4509.8851 26.905229
2000 1.9225238e-08 -4509.8852 0 -4509.8852 26.905144
2100 1.6580757e-08 -4509.8853 0 -4509.8853 26.906419
2200 1.2058028e-08 -4509.8853 0 -4509.8853 26.910376
2300 7.4549951e-09 -4509.8852 0 -4509.8852 26.916716
2400 4.0264612e-09 -4509.8852 0 -4509.8852 26.923054
2500 1.8321195e-09 -4509.8852 0 -4509.8852 26.92718
2600 5.8894583e-10 -4509.8852 0 -4509.8852 26.92887
2700 1.1822868e-09 -4509.8853 0 -4509.8853 26.928935
2800 4.1199827e-09 -4509.8853 0 -4509.8853 26.927485
2900 8.3401571e-09 -4509.8853 0 -4509.8853 26.924202
3000 1.2795486e-08 -4509.8852 0 -4509.8852 26.91968
3100 1.656454e-08 -4509.8852 0 -4509.8852 26.915184
3200 1.8809835e-08 -4509.8852 0 -4509.8852 26.911167
3300 1.9524689e-08 -4509.8852 0 -4509.8852 26.907277
3400 1.9239653e-08 -4509.8852 0 -4509.8852 26.904028
3500 1.8306513e-08 -4509.8852 0 -4509.8852 26.903155
3600 1.6715381e-08 -4509.8852 0 -4509.8852 26.905573
3700 1.4633381e-08 -4509.8851 0 -4509.8851 26.909896
3800 1.1933216e-08 -4509.8851 0 -4509.8851 26.913983
3900 8.1608505e-09 -4509.8852 0 -4509.8852 26.917338
4000 4.081711e-09 -4509.8853 0 -4509.8853 26.920926
4100 1.5631282e-09 -4509.8853 0 -4509.8853 26.924958
4200 1.2262219e-09 -4509.8853 0 -4509.8853 26.928167
4300 2.985009e-09 -4509.8852 0 -4509.8852 26.929352
4400 6.8933386e-09 -4509.8852 0 -4509.8852 26.928435
4500 1.1278724e-08 -4509.8852 0 -4509.8852 26.925624
4600 1.4438096e-08 -4509.8852 0 -4509.8852 26.920742
4700 1.6779441e-08 -4509.8852 0 -4509.8852 26.914294
4800 1.8690218e-08 -4509.8853 0 -4509.8853 26.908349
4900 1.9317873e-08 -4509.8852 0 -4509.8852 26.905059
5000 1.8273072e-08 -4509.8851 0 -4509.8851 26.904542
Loop time of 97.2827 on 4 procs for 5000 steps with 2304 atoms
Pair time (%) = 29.7789 (30.6107)
Neigh time (%) = 12.5179 (12.8676)
Comm time (%) = 29.2909 (30.109)
Outpt time (%) = 0.00928915 (0.00954861)
Other time (%) = 25.6857 (26.4032)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288957 max 67836 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 500
Dangerous builds = 0
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