creating molecules

Dear all,

I would like to add water and co2 molecules to the current system. The current system was imported via read_data, and then the extra molecules are created, the relevant lines from the log files are listed at the end, which seems working fine. I just wonder if I need to add “extra/special/per/atom” arg for adding molecules in this case, since it already has enough special neighbors (1-2 and 1-3 neighbors) per atom by reading the data file.

Thank you for your time.
Regards,
Pengyu

read_data data.original extra/atom/types 4 extra/bond/types 2 extra/angle/types 2

reading atoms …
48048 atoms
scanning bonds …
3 = max bonds/atom
scanning angles …
6 = max angles/atom
reading bonds …
61534 bonds
reading angles …
119262 angles
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
8 = max # of special neighbors

molecule CO2mol co2.txt offset 4 3 4 0 0
Read molecule CO2mol:
3 atoms with 6 types
2 bonds with 4 types
1 angles with 5 types
0 dihedrals with 0 types
0 impropers with 0 types
molecule H2Omol h2o.txt offset 6 4 5 0 0
Read molecule H2Omol:
3 atoms with 8 types
2 bonds with 5 types
1 angles with 6 types
0 dihedrals with 0 types
0 impropers with 0 types

Dear all,

I would like to add water and co2 molecules to the current system. The
current system was imported via read_data, and then the extra molecules are
created, the relevant lines from the log files are listed at the end, which
seems working fine. I just wonder if I need to add "extra/special/per/atom"
arg for adding molecules in this case, since it already has enough special
neighbors (1-2 and 1-3 neighbors) per atom by reading the data file.

​LAMMPS should fail, if you have not reserved sufficient space for
exclusions. 3-atomic molecules don't need many of those, though.

axel.​