# needs description
#AtC drift diffusion Coupling
# DESCRIPTION:
# electric potential solved over whole domain
# all others only over the lower half
# temperature is fixed over whole domain

# NOTE the vacuum can fully masked out by making the material 
# have null electron_density in Ar_ddm.mat

echo both
units    metal

variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W   equal 1000

atom_style  atomic

lattice   fcc 5.405 origin 0.25 0.25 0.25
region    FE block   -8 8 -6 6 0 3
region    MD block   -7 7 -6 0 0 3
region    FREE block -4 4 -6 0 0 3

boundary  f f p

# create atoms
create_box  1 FE
mass    1 39.95 
atom_modify     sort 0 1

timestep  0.002
thermo  $s

#          ID  group atc PhysicsType ParameterFile
fix        AtC all  atc drift_diffusion  Ar_ddm.mat

#          ID  part keywords    nx ny nz region
fix_modify AtC mesh  create 4 4  1  FE f f p

variable a   equal $W+${tol}
fix_modify AtC mesh create_elementset wire  -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap   -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset
variable a   equal $W-${tol}
fix_modify AtC mesh create_nodeset    void -$a $a  ${tol}  INF -INF INF
fix_modify AtC mesh output   null_material_ddmMESH binary

fix_modify  AtC control thermal none

# fix a temperature
fix_modify AtC  initial temperature          all $T
fix_modify AtC  initial electron_temperature all $T
fix_modify AtC  initial electron_density     all $n
fix_modify AtC  initial electric_potential   all 0.0
fix_modify AtC  initial temperature          void 0.0
fix_modify AtC  initial electron_density     void 0.0
fix_modify AtC  initial electric_potential   void 0.0

# create vacuum
fix_modify AtC material gap Vacuum

thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC  output          null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit

# 
fix_modify AtC mesh create_nodeset lbc -8.1  -7.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc  7.9   8.1 -INF INF -INF INF
fix_modify AtC  fix electron_temperature lbc $T
fix_modify AtC  fix electron_temperature rbc $T
fix_modify AtC  fix electron_density     lbc $n
fix_modify AtC  fix electric_potential lbc 0.0

variable m equal $s*10
run    $m