Creating 0 atoms

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1

The simulation runs fine, except that every time I run it, 0 atoms for co2 is created and I can’t figure out why.
Here’s my code to create my region and atoms.

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

2

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.

3

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.

4

this is just as useless. please do read the “guidelines” and specifically follow points 3 and 9. otherwise your chances of getting help will be very close to zero.

thanks,
axel.