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

region		simRegion block -12 12 -3 3 -3 3
region		mdRegion block -8 8 -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 mdRegion
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

# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style	lj/cut 13.
#pair_coeff	1 1 0.010323166 3.405 13.
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
fix_modify	AtC boundary ghosts

#               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
fix_modify      AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF  INF outward
 ATC: created faceset obndy with 2 faces
fix_modify      AtC internal_quadrature off
fix_modify  AtC  internal_atom_integrate off
fix iNVE internal nve

# initial conditions
fix_modify  AtC  initial displacement x all 0.0
fix_modify  AtC  fix displacement y all 0.0
fix_modify  AtC  fix displacement z all 0.0
fix_modify  AtC  initial velocity x all 0.0
fix_modify  AtC  fix velocity y all 0.0
fix_modify  AtC  fix velocity z all 0.0

# 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.
#fix_modify  AtC  fix displacement x rbc 0.
fix_modify  AtC  fix displacement x lbc 0.
fix_modify  AtC  fix velocity x lbc 0.

# turn on multiscale
fix_modify      AtC control momentum ghost_flux

# new boundary conditions
fix_modify  AtC  fix velocity x rbc 0.00000004


#fix_modify      AtC  output follow_ex.fe 50
#fix_modify	AtC  localized_lambda on
#fix_modify	AtC  momentum control glc_velocity
#fix_modify	AtC  momentum control flux faceset obndy
#fix_modify     AtC control momentum flux
#fix_modify	AtC control momentum ghost_flux
#fix_modify      AtC  filter scale 1000.0

# run to extension
compute		myTemp internal temp
compute		atomStress internal stress/atom
compute		avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable	myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style	custom step c_myTemp v_myPres pe
fix_modify      AtC  output bar1d_ghost_fluxFE 500 text
 ATC: Warning : text output can create _LARGE_ files
 ATC: output custom names:

#dump            D1 all atom 100 bar1d_ghost_flux.dmp
timestep	5
thermo		100
run 		1000
Setting up run ...
Memory usage per processor = 65.6268 Mbytes
Step myTemp myPres PotEng 
       0            0 -0.00072339042   -4509.8851 
     100 7.1225566e-14 -0.00069609188   -4509.8851 
     200 3.7853133e-13 -0.00065829543   -4509.8851 
     300 1.6363911e-11 -0.00093014878   -4509.8851 
     400 2.6679578e-10 -0.0022162027   -4509.8852 
     500 1.616056e-09 -0.0053039586   -4509.8852 
     600 5.0333459e-09 -0.010270696   -4509.8852 
     700 9.7370581e-09 -0.016093983   -4509.8852 
     800 1.3809125e-08 -0.021486202   -4509.8852 
     900 1.6783957e-08 -0.026147268   -4509.8852 
    1000 1.9615527e-08 -0.030744945   -4509.8852 
Loop time of 18.3775 on 4 procs for 1000 steps with 2304 atoms

Pair  time (%) = 5.94283 (32.3375)
Neigh time (%) = 2.46573 (13.4171)
Comm  time (%) = 6.00265 (32.663)
Outpt time (%) = 0.00820392 (0.044641)
Other time (%) = 3.95812 (21.5378)

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 288581 max 68542 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

# change nodes to fixed
fix_modify      AtC  unfix velocity x rbc
#fix_modify	AtC  fix displacement x rbc 0.0002

#fix_modify      AtC  output bar1d_fluxFE 500 text binary

# run to equilibrium
timestep        5
thermo		100
run 		3000
Setting up run ...
Memory usage per processor = 66.0846 Mbytes
Step myTemp myPres PotEng 
    1000 1.9615527e-08 -0.030744945   -4509.8852 
    1100 2.3080841e-08 -0.035570103   -4509.8852 
    1200 2.6803382e-08 -0.039749355   -4509.8852 
    1300 2.8836885e-08 -0.041881649   -4509.8852 
    1400 2.7038886e-08  -0.04118176   -4509.8852 
    1500 2.247439e-08 -0.037776265   -4509.8852 
    1600 1.8021787e-08 -0.032491325   -4509.8852 
    1700 1.4774855e-08 -0.026754505   -4509.8852 
    1800 1.2061023e-08 -0.022034601   -4509.8852 
    1900 8.5768539e-09 -0.018709001   -4509.8852 
    2000 3.6373058e-09 -0.016114748   -4509.8852 
    2100 5.3669536e-10 -0.014163462   -4509.8853 
    2200 3.2454928e-09 -0.014205399   -4509.8853 
    2300 1.030702e-08 -0.017492992   -4509.8853 
    2400 1.6038797e-08 -0.023210717   -4509.8852 
    2500 1.7061988e-08 -0.029013462   -4509.8851 
    2600 1.9296258e-08  -0.03339452   -4509.8852 
    2700 2.2816944e-08 -0.036626152   -4509.8852 
    2800 2.6944075e-08 -0.039307649   -4509.8852 
    2900 2.8170813e-08 -0.040972921   -4509.8852 
    3000 2.7256286e-08 -0.040327211   -4509.8852 
    3100 2.445985e-08 -0.036617618   -4509.8852 
    3200 1.8787648e-08  -0.03049195   -4509.8852 
    3300 1.4750104e-08 -0.023629006   -4509.8852 
    3400 1.3515772e-08 -0.017473229   -4509.8852 
    3500 1.157919e-08 -0.012114855   -4509.8851 
    3600 9.6213234e-09 -0.0064144434   -4509.8851 
    3700 9.1781574e-09 0.00062376196   -4509.8851 
    3800 9.0938842e-09 0.0087100206    -4509.885 
    3900 7.7454581e-09  0.016669158    -4509.885 
    4000 9.3314606e-09  0.023405906    -4509.885 
Loop time of 54.728 on 4 procs for 3000 steps with 2304 atoms

Pair  time (%) = 17.812 (32.5465)
Neigh time (%) = 7.39237 (13.5075)
Comm  time (%) = 17.7536 (32.4397)
Outpt time (%) = 0.0253569 (0.0463326)
Other time (%) = 11.7446 (21.46)

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 288933 max 68141 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 = 300
Dangerous builds = 0
