Query on AtC command

I recently started to work on fixAtC command.However,When I read the input stream below,I have some questions about this command.The red part in the input stream is my question .I wish you can help me.Thank you very much!
Input :
units real
atom_style atomic

create domain

#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)

NOTE following 3 lines added for restart

boundary f p p
pair_style lj/cut 13.5
read_data temp.init
lattice fcc 5.405 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3

create atoms, NOTE commented out for restart

#region mdRegion block -5 5 -3 3 -3 3
#boundary f p p
#create_box 1 mdRegion
#create_atoms 1 region mdRegion
#mass 1 39.95

specify interal/ghost atoms

region mdInternal block -4 4 -3 3 -3 3
group internal region mdInternal
group ghost subtract all internal

velocities have Vcm = 0, NOTE next four lines commented out for restart

#velocity internal create 40. 87287 mom yes loop geom

#pair_style lj/cut 13.5
##pair_coeff 1 1 0.010323166 3.405 13.5
#pair_coeff 1 1 .238 3.405 13.5

neighbor 5. bin
neigh_modify every 10 delay 0 check no

ID group atc PhysicsType ParameterFile

fix AtC internal atc thermal Ar_thermal.mat

ID part keywords nx ny nz region

#fix_modify AtC fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 12 1 1 simRegion f p p

specify atom types

#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost

fix a temperature

fix_modify AtC transfer fix temperature all 20.

turn on thermostat

fix_modify AtC transfer thermal control rescale 10

equilibrate MD field

#dump D1 all atom 100 dump.bar1d
#fix_modify AtC transfer output bar1dfe 100
timestep 5
variable xdof equal 3*count(ghost)
compute_modify thermo_temp extra ${xdof}
thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] Q1: What is the AtC[1] 、temp and AtC[2]?
thermo_modify format 1 %6i format 2 %7.2g
thermo 100
run 400

change thermostat to hoover

fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control hoover
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0 Q2: What is meaning of the scale 10000?
fix_modify AtC transfer filter on
fix_modify AtC transfer internal_quadrature off

add nodesets

ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax

fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.

initialize filter

#thermo 1
run 100 Q3:Why it is must initialize filter?

set up output, should be before a “run”

fix_modify AtC transfer output bar1dFE 100 text Q4:What kind of files the command will creat?What kind of software can open the files?

ouput command

#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1dMD 100

run with FE

reset_timestep 0
thermo 100
run 10000

Maybe Reese or Jeremy can answer these Qs.
I assume these commands are discussed in the documentation
of the AtC package which is quite large.