about compute heat/flux command
1. Is compute heat/flux command only used for NVE ensemble?
2. variable J equal c_flux[1]/vol:
Is the “vol” always the total volumn of the box?
3. Is the following simulation system can use “compute myStress all stress/atom virial” for the entire box?
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress
┌────┐
│ NVT │ 3 T_low=constant
├────┤
│ NVE │ 2
├────┤
│ NVT │ 1 T_High=constant
└────┘
The ensembles for group 1, 2 and 3 are NVT, NVE and NVT respectively.
The temperature for group 1 and 3 are constant.

about compute heat/flux command
1. Is compute heat/flux command only used for NVE ensemble?

 
If you thermostat you are adding/subtracting energy, so that doesn’t make sense
with what compute heat/flux is doing.
2. variable J equal c_flux[1]/vol:
Is the “vol” always the total volumn of the box

 
it is in that formula  you can use whatever formula you like
3. Is the following simulation system can use “compute myStress all stress/atom virial” for the entire box?
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress

 
I don’t understand this question. If you use group all, then
you’re computing quanties for all atoms in the box.