LAMMPS (30 Aug 2013)
units		metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
variable V equal 0.00010000000000000000479*$L
variable V equal 0.00010000000000000000479*10
# END -----------------------------------

atom_style atomic
lattice    diamond  1.0
Lattice spacing in x,y,z = 1 1 1
boundary   f p p
region	box block -$L $L 0 1 0 1
region	box block -10 $L 0 1 0 1
region	box block -10 10 0 1 0 1
create_box 1 box
Created orthogonal box = (-10 0 0) to (10 1 1)
  4 by 1 by 1 MPI processor grid
group	box region box
0 atoms in group box
atom_modify  sort 0 1
timestep     0.0
mass         *  12.01

# coupling
### NOTE ATC:  material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix         AtC box  atc electrostatic-equilibrium CNT.mat
ATC: constructing equilibrium electrostatic coupling with parameter file CNT.mat
 ATC: version 2.0
 ATC: peratom PE compute created with ID: 3
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: 7 materials defined from CNT.mat
 ATC: creating electrostatic extrinsic model
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: 7 materials defined from CNT.mat
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: computed mass density : 96.08
 ATC: 7 materials defined from CNT.mat
fix_modify  AtC internal_quadrature off
#fix_modify  AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify  AtC atom_weight constant box 1.0
fix_modify  AtC omit atomic_charge
fix_modify  AtC mesh create $e  1  1  box f p p
fix_modify  AtC mesh create 4  1  1  box f p p
 ATC: created uniform mesh with 20 nodes, 5 unique nodes, and 4 elements
#fix_modify  AtC control  momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
 ATC: created elementset all with 4 elements

# bcs/ics conditions
fix_modify AtC  fix 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  fix velocity x all 0.0
fix_modify AtC  fix velocity y all 0.0
fix_modify AtC  fix velocity z all 0.0

fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
 ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc  10  10 INF INF INF INF
 ATC: created nodeset rbc with 1 nodes
fix_modify AtC  fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC  fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 $V
fix_modify AtC  fix electric_potential lbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208
 ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0)
fix_modify AtC  fix electric_potential rbc linear 0 0 0 $E 0 0 $V
fix_modify AtC  fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 $V
fix_modify AtC  fix electric_potential rbc linear 0 0 0 0.00010000000000000000479 0 0 0.0010000000000000000208
 ATC: created function : 0.001 + 0.0001(x-0)+0(y-0)+0(z-0)

# run
thermo_style    custom step cpu etotal ke
thermo          $s
thermo          1
fix_modify      AtC  output electron_densityFE $s text
fix_modify      AtC  output electron_densityFE 1 text
 ATC: Warning : text output can create _LARGE_ files
 ATC: output custom names:

fix_modify      AtC  output index step
log electron_density.log

# run default material
print "default material - table linear"
default material - table linear
run   	        $s
run   	        1
Setting up run ...
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: all initial conditions for electron_density have not been defined and the undefined are assumed zero
 ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng 
       0            0            0           -0 
       1 0.0053369999            0           -0 
Loop time of 0.00535321 on 4 procs for 1 steps with 0 atoms

Pair  time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm  time (%) = 2.563e-06 (0.0478778)
Outpt time (%) = 0.000362277 (6.76747)
Other time (%) = 0.00498837 (93.1847)

Nlocal:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

# run CNT1 material
print "CNT1 material - analytical linear"
CNT1 material - analytical linear
fix_modify AtC material all CNT1
run   	        $s
run   	        1
Setting up run ...
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng 
       1            0            0           -0 
       2  0.001543045            0           -0 
Loop time of 0.0015552 on 4 procs for 1 steps with 0 atoms

Pair  time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm  time (%) = 7.15256e-07 (0.0459911)
Outpt time (%) = 0.00018543 (11.9232)
Other time (%) = 0.00136906 (88.0308)

Nlocal:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

# run CNT2 material
print "CNT2 material - analytical exponetial"
CNT2 material - analytical exponetial
fix_modify AtC material all CNT2
run   	        $s
run   	        1
Setting up run ...
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng 
       2            0            0           -0 
       3 0.0015628338            0           -0 
Loop time of 0.0015763 on 4 procs for 1 steps with 0 atoms

Pair  time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm  time (%) = 1.78814e-06 (0.113439)
Outpt time (%) = 0.000164747 (10.4515)
Other time (%) = 0.00140977 (89.4351)

Nlocal:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

# run CNT material
print "CNT material - table DOS"
CNT material - table DOS
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC  fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC  fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run   	        $s
run   	        1
Setting up run ...
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt-exp] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null 
 ATC: WARNING: material: [cnt] cannot find body_force
 ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null 
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng 
       3            0            0           -0 
       4  0.001554966            0           -0 
Loop time of 0.00156641 on 4 procs for 1 steps with 0 atoms

Pair  time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm  time (%) = 1.49012e-06 (0.0951294)
Outpt time (%) = 0.000194073 (12.3896)
Other time (%) = 0.00137085 (87.5152)

Nlocal:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Neighbor list builds = 0
Dangerous builds = 0

