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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
|
