LAMMPS (30 Aug 2013)
units    real
atom_style  atomic

lattice         fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
region     mdRegion   block -12 12 -3 3 -3 3
region     mdInternal block -10 10 -3 3 -3 3

# create atoms
boundary  f p p
create_box  1 mdRegion
Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
  4 by 1 by 1 MPI processor grid
create_atoms  1 region mdRegion
Created 3456 atoms
mass    1 39.95
pair_style  lj/cut 13.5
pair_coeff    1 1 .238 3.405 13.5

# specify interal/ghost atoms
group    internal region mdInternal
2880 atoms in group internal
velocity  internal create 40 87287 mom yes loop geom # <<< NOTE

neighbor  5. bin
neigh_modify  every 10 delay 0 check no

#               ID  group atc PhysicsType ParameterFile
fix             AtC internal   atc two_temperature  Ar_ttm.mat
ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat
 ATC: version 2.0
 ATC: peratom PE compute created with ID: 3
 ATC: 2 materials defined from Ar_ttm.mat
 ATC: creating two_temperature extrinsic model
 ATC: 2 materials defined from Ar_ttm.mat

fix_modify      AtC mesh read gaussianIC1d_hex.mesh
 ATC: read 44 nodes
 ATC: read 10 HEX8 elements
 ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive

# fix a temperature
fix_modify AtC  fix temperature          all 20.0
fix_modify AtC  initial temperature      all 20.0
fix_modify AtC  initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC  fix electron_temperature     all gaussian 0 0 0 1 0 0 5 20 20

# turn on thermostat
fix_modify AtC extrinsic exchange off
fix_modify AtC  control thermal rescale 10

# equilibrate MD field
timestep  5.0
thermo    10

#output
fix_modify      AtC  output        gaussianIC1d_hexFE 10 text
 ATC: Warning : text output can create _LARGE_ files
 ATC: output custom names:


# change thermostat
fix_modify AtC  unfix          temperature all
fix_modify AtC  unfix electron_temperature all
fix_modify AtC  control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10

# run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0
run     100 # 400
Setting up run ...
Memory usage per processor = 52.9302 Mbytes
Step Temp PotEng AtC[2] AtC[4] 
       0    33.331404   -6667.7177           20    21.852118 
      10    29.605914   -6628.8617    15.526061    21.823928 
      20    20.144352   -6529.8249    4.1452637    21.728037 
      30    10.661516   -6429.3908   -7.2917185    21.537517 
      40    7.6716875   -6394.7484   -10.961235     21.28913 
      50    11.012891   -6425.2214   -7.0020953    21.050343 
      60    15.276591   -6465.7767   -1.8390571     20.85387 
      70     17.15209   -6482.1581   0.55215503    20.688207 
      80    17.028137   -6478.0796   0.55504167    20.530699 
      90    16.865355   -6473.5664   0.41999569    20.372106 
     100    17.920474    -6481.673    1.6267665    20.219157 
Loop time of 4.19774 on 4 procs for 100 steps with 3456 atoms

Pair  time (%) = 0.896439 (21.3553)
Neigh time (%) = 0.408064 (9.72104)
Comm  time (%) = 0.161891 (3.85662)
Outpt time (%) = 0.00701588 (0.167135)
Other time (%) = 2.72433 (64.9)

Nlocal:    864 ave 864 max 864 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    6741 ave 7924 max 5558 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:    272828 ave 288265 max 257696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs:  545657 ave 575527 max 515800 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 2182628
Ave neighs/atom = 631.547
Neighbor list builds = 10
Dangerous builds = 0
