# needs description
#AtC Two temperature Coupling
# DESCRIPTION:
# delete elements from the mesh
# heating and then relaxation

echo both
units    metal
variable INF equal 1000

variable T equal 20

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
#create_atoms 1 region MD
#group   internal region FREE
#mass    1 39.95 
#read_data cutout.data
#pair_coeff * * .238 3.405 13.5
#velocity  internal create 40 87287 mom yes loop geom
#fix NVE internal nve
#thermo 100
#dump CONFIG all atom 100 cutout.dump
##run 1000
#unfix NVE 
#write_restart cutout.rst

pair_style lj/cut 13.5
read_data cutout.init
group   internal region FREE
group   ghost subtract all internal

timestep  0.002
thermo  20

# allow initial state to relax
fix NVT internal nvt temp $T $T 10 drag 0.2
fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0
run 200
unfix RESCALE
run 800
unfix NVT

#          ID  group atc PhysicsType ParameterFile
fix        AtC internal  atc two_temperature  Ar_ttm.mat

#          ID  part keywords    nx ny nz region
fix_modify AtC mesh  create 8 6  1  FE f f p

fix_modify AtC mesh create_elementset wire  -4 4 -INF  0 -INF INF
fix_modify AtC mesh create_nodeset    gap   -4 4 -0  INF -INF INF
fix_modify AtC mesh create_elementset gap   -4 4 -0  INF -INF INF
fix_modify AtC mesh delete_elements gap

fix_modify  AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF
fix_modify  AtC  control thermal flux faceset bndy

# fix a temperature
fix_modify AtC  initial temperature          all 20.0
fix_modify AtC  initial electron_temperature all 30.0
fix_modify AtC  initial temperature          gap  0.0

# relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC  output   cutoutFE 10 text
fix_modify AtC extrinsic electron_integration implicit

# heating
fix_modify AtC mesh create_nodeset lbc -8  -8 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc  8   8 -INF INF -INF INF
fix_modify AtC  fix electron_temperature lbc 20. 
fix_modify AtC  fix electron_temperature rbc 20.
fix_modify AtC  source electron_temperature wire 0.001
run    200

# relaxation
fix_modify AtC  remove_source electron_temperature wire
run    200
