read_restart restart.*
----------------- Init Section -----------------
include “system.in.init”
----------------- Atom Definition Section -----------------
read_data “system.data”
----------------- Settings Section -----------------
include “system.in.settings”
----------------- Charges Section -----------------
----------------- Run Section -----------------
region total block INF INF INF INF INF INF units box
region mid block INF INF INF INF 600 800 units box
molecule c14 c14.data
molecule co2 co2.data boff 1
#lattice fcc 30 origin 1 0.4 0.4
neigh_modify delay 0 every 1 check yes
delete_atoms group all
create_atoms 1 random 1246 102486 total mol c14 102486
create_atoms 2 random 1246 80000 total mol co2 80000
group c14 type 1
group co2 type 2
group dummy type 3
group flow union co2 c14
thermo 100
restart 50000 restart.*
compute Tflow all temp/com
compute temprof all temp/profile 1 1 1 z 20 out bin
compute tflow all temp/partial 0 0 1
timestep 0.1
compute pres all pressure tflow
compute pres2 all pressure thermo_temp
#fix freeze dummy setforce 0.0 0.0 0.0
dump 1 all atom 1000 traj_poiseulle.lammpstrj
thermo_style custom step atoms temp press density vol etotal c_tflow c_pres[1] c_pres2[1] c_pres[2] c_pres2[2] c_pres[3] c_pres2[3]
minimize 1.0e-20 1.0e-25 50000 50000
timestep 1
fix NVT3 flow nvt temp 900 900 100
run 10000
delete_atoms group dummy
unfix NVT3
timestep 0.1
fix NVT3 all npt temp 344.3 344.3 10 iso 109.2818 109.2818 100
run 20000
unfix NVT3
timestep 5
fix NVT3 all nvt temp 344.3 344.3 500
compute cc16 c14 chunk/atom bin/1d z lower 4.0
fix roc16 c14 ave/chunk 100 10 1000 cc16 density/mass norm all ave running overwrite file roc14.profile
fix roc16w c14 ave/chunk 100 10 1000 cc16 density/mass norm all ave window 50 file roc14w.profile
compute cco2 co2 chunk/atom bin/1d z lower 4.0
fix roco2 co2 ave/chunk 100 10 1000 cco2 density/mass norm all ave running overwrite file roco2.profile
fix roco2w co2 ave/chunk 100 10 1000 cco2 density/mass norm all ave window 50 file roco2w.profile
compute call all chunk/atom bin/1d z lower 4.0
fix roall all ave/chunk 100 10 1000 call density/mass norm all ave running overwrite file roall.profile
fix roallw all ave/chunk 100 10 1000 call density/mass norm all ave window 50 file roallw.profile
run 50000
This is the entire code
The simulation runs fine, except that every time I run it, 0 atoms for co2 is created and I can’t figure out why.
how should anybody else without a crystal ball? there is not enough information here to say anything, let alone reproduce what you are seeing in order to try and understand.
please have a look at https://lammps.sandia.gov/guidelines.html before sending emails to this list.
axel.