NEMDcal.lammps

region block1 block INF INF 5 15 INF INF
group pore1 dynamic H2O region block1

#com
compute alltypealkane  alkane chunk/atom type 
compute alltypeben     ben    chunk/atom type 
compute alltypenon     non    chunk/atom type 
compute alltypeoxy     oxy    chunk/atom type 
compute alltypeoil     oil    chunk/atom type 

compute centeralkane alkane com/chunk  alltypealkane
compute centerben    ben    com/chunk  alltypeben   
compute centernon    non    com/chunk  alltypenon   
compute centeroxy    oxy    com/chunk  alltypeoxy   
compute centeroil    oil    com/chunk  alltypeoil   

fix y0alkane all ave/time 10000 1 10000 c_centeralkane[*] file ./com/y0alkane mode vector 
fix y0ben    all ave/time 10000 1 10000 c_centerben[*]    file ./com/y0ben    mode vector 
fix y0non    all ave/time 10000 1 10000 c_centernon[*]    file ./com/y0non    mode vector 
fix y0oxy    all ave/time 10000 1 10000 c_centeroxy[*]    file ./com/y0oxy    mode vector 
fix y0oil    all ave/time 10000 1 10000 c_centeroil[*]    file ./com/y0oil    mode vector 

compute density_dyH2O    H2O    chunk/atom bin/1d y lower 0.2
fix dyH2O  H2O      ave/chunk 1 1 10000 density_dyH2O      density/mass density/number ave one file ./dyH2O 

fix 2 pore nvt temp 383 383 100.0 
compute xtemp pore temp/partial 1 0 1
fix_modify 2 temp xtemp
fix poreadd pore1 addforce 0 0.00727 0.0