Summary
As discussed, the nufeb/volume compute has been updated to be able to use the group-id setting to calculate cell volumes based on their group.
Related Issues
This was forked from a slightly early than current commit in the main branch, due to the current build issues.
Licensing
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
Backward Compatibility
No breakages.
Implementation Notes
Used the standard mask and groupbit in the compute. Checked the total volume from the new run against an older version of NUFEB which only produced total volumes. Also, the system uses two hetertrophs and their summed volumes is close to the total, which is expected.
Further Information, Files, and Links
The examples-nufeb/biofilm-het case now includes an additional Inputscript and atom file which serve to illustrate and test this functionality. In addition, it shows how to create a csv file of caculated volumes using fix/print.
Summary As discussed, the nufeb/volume compute has been updated to be able to use the group-id setting to calculate cell volumes based on their group.
Related Issues
This was forked from a slightly early than current commit in the main branch, due to the current build issues.
Licensing
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
Backward Compatibility
No breakages.
Implementation Notes
Used the standard mask and groupbit in the compute. Checked the total volume from the new run against an older version of NUFEB which only produced total volumes. Also, the system uses two hetertrophs and their summed volumes is close to the total, which is expected.
Further Information, Files, and Links
The examples-nufeb/biofilm-het case now includes an additional Inputscript and atom file which serve to illustrate and test this functionality. In addition, it shows how to create a csv file of caculated volumes using fix/print.