Dear Lammps users,
I’m using Lammps version 30Apr15 to analyze clustering of groups of molecules. I’m interested in the number of clusters as time goes by, and therefore using the command compute cluster aggregate/atom +cutoff . Since the size of clusters increases as simulation time goes by. I have to increase the cut-off for different time frames. An example is given below:
read_restart restart.sucess
compute cluster all aggregate/atom 4.8
dump calc_agg all custom 10000 aggregate_1_0_seed3.dat id c_cluster
dump_modify calc_agg sort id
rerun traj_equib0_min.lammpstrj first 0 last 50000 dump x y z box yes wrapped no
uncompute cluster
undump calc_agg
compute cluster all aggregate/atom 5.0
dump calc_agg all custom 10000 aggregate_1_1_seed3.dat id c_cluster
dump_modify calc_agg sort id
rerun traj_equib0_min.lammpstrj first 60000 last 110000 dump x y z box yes wrapped no
uncompute cluster
undump calc_agg
However, only result from time step 0 to 50000 are showed. Neither the file aggregate_1_1_seed3.dat nor anything showed up for 60000 to 110000 time step.
I also got an error of BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES in output file.
If I remove the second rerun command, the error message goes away. So, I believe it is the issue of rerun. But I have no idea why it happens.
Appreciate for any help.
Thank you,
Edward
Compute aggregate/atom was added on 1-Sep-2017 and is not available in your 30Apr15 version.
Ray
Dear Lammps users,
I’m using Lammps version 30Apr15 to analyze clustering of groups of molecules. I’m interested in the number of clusters as time goes by, and therefore using the command compute cluster aggregate/atom +cutoff . Since the size of clusters increases as simulation time goes by. I have to increase the cut-off for different time frames. An example is given below:
read_restart restart.sucess
compute cluster all aggregate/atom 4.8
dump calc_agg all custom 10000 aggregate_1_0_seed3.dat id c_cluster
dump_modify calc_agg sort id
rerun traj_equib0_min.lammpstrj first 0 last 50000 dump x y z box yes wrapped no
uncompute cluster
undump calc_agg
compute cluster all aggregate/atom 5.0
dump calc_agg all custom 10000 aggregate_1_1_seed3.dat id c_cluster
dump_modify calc_agg sort id
rerun traj_equib0_min.lammpstrj first 60000 last 110000 dump x y z box yes wrapped no
uncompute cluster
undump calc_agg
However, only result from time step 0 to 50000 are showed. Neither the file aggregate_1_1_seed3.dat nor anything showed up for 60000 to 110000 time step.
I also got an error of BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES in output file.
If I remove the second rerun command, the error message goes away. So, I believe it is the issue of rerun. But I have no idea why it happens.
you are using a version of LAMMPS that is 3.5 years old. please verify with a current version, if this issue persists. there is a good chance, that you are observing an issue, that has already been corrected.
axel.
Thank you Ray for response.
I forgot to mention that I added manually compute_aggregate.cpp and compute_aggregate.h in src file.