Dear
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