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

# NOTE following 3 lines added for restart
boundary        f p p
pair_style      lj/cut 13.
read_data       temp.init
Reading data file ...
  orthogonal box = (-47.3241 -15.7747 -15.7747) to (47.3241 15.7747 15.7747)
  4 by 1 by 1 MPI processor grid
  2304 atoms
  2304 velocities
region		simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region		mdRegion block -8 8 -3 3 -3 3
#boundary	f p p
#region		mdBox block -9 9 -3 3 -3 3
#create_box	1 mdBox
#create_atoms	1 region mdRegion
#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
#velocity	internal create 40. 87287 mom yes loop geom
#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
#write_restart  tinit.dat

# zero initial momentum
fix             AtC internal   atc elastic     Ar_thermo_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_thermo_elastic.mat
 ATC: version 2.0
 ATC: peratom PE compute created with ID: 3
 ATC: computed mass density : 1.09915
 ATC: 1 materials defined from Ar_thermo_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
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 fix displacement x all 0.
fix_modify      AtC fix displacement y all 0.
fix_modify      AtC fix displacement z all 0.
fix_modify      AtC fix velocity x all 0.
fix_modify      AtC fix velocity y all 0.
fix_modify      AtC fix velocity z all 0.
fix_modify      AtC control momentum glc_velocity
#fix_modify      AtC  output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep        0
thermo          1
run             1
Setting up run ...
Memory usage per processor = 56.6533 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    29.995658   -4509.8851            0   -4303.9707    135.84496 
       1    29.920966   -4509.8851            0   -4304.4835    135.59617 
Loop time of 0.0227802 on 4 procs for 1 steps with 2304 atoms

Pair  time (%) = 0.00607026 (26.6471)
Neigh time (%) = 0 (0)
Comm  time (%) = 0.00152951 (6.71423)
Outpt time (%) = 8.60691e-05 (0.377825)
Other time (%) = 0.0150943 (66.2608)

Nlocal:    576 ave 648 max 504 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:    5677 ave 7126 max 4228 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:    178632 ave 218376 max 138456 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs:  357264 ave 436752 max 277776 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 0
Dangerous builds = 0
unfix AtC

# define  layer
#               ID  group atc PhysicsType ParameterFile
fix             AtC internal   atc thermo_elastic     Ar_thermo_elastic.mat
ATC: constructing thermo-mechanical coupling with parameter file Ar_thermo_elastic.mat
 ATC: version 2.0
 ATC: peratom PE compute created with ID: 3
 ATC: computed mass density : 1.09915
 ATC: 1 materials defined from Ar_thermo_elastic.mat
fix_modify	AtC boundary ghosts
ERROR: Illegal fix_modify command (../fix.cpp:104)
