Dear LAMMPS Users,
I need to group and save atoms of my simulation in cylindrical bins. For this purpose, I used the command of “compute chunk/atom” to define cylindrical bins as follows:
“compute cc7 mobile chunk/atom bin/cylinder z lower 24.14 0 0 0.0 5.45719351276 200 bound z 33.065 57.205 units box”
My question is that which LAMMPS output (Thermo_style, dump or fix ave/chunk) do I have to use so that I can save id, type, positions, and velocities of atoms in each cylindrical bin at each 4ft?
I appreciate your help and time.
Best Regards,
Hamed.
Dear LAMMPS Users,
I need to group and save atoms of my simulation in cylindrical bins. For this purpose, I used the command of "compute chunk/atom" to define cylindrical bins as follows:
"compute cc7 mobile chunk/atom bin/cylinder z lower 24.14 0 0 0.0 5.45719351276 200 bound z 33.065 57.205 units box"
My question is that which LAMMPS output (Thermo_style, dump or fix ave/chunk) do I have to use so that I can save id, type, positions, and velocities of atoms in each cylindrical bin at each 4ft?
you can use dump. i would not use separate dump files, but simply
output the chunk/atom compute data as one field. then you can select
atoms by bin and still have only one file.
otherwise, you can use the dump_modify thresh keyword to output only
selected atoms based on an equal style variable, that compares the
chunk id to a given value.
axel.
Dear Prof. Kohlmeyer,
Thank you for your advice. If it is possible would you please explain more on how to use dump command to output the chunk/atom compute data? The manual says: “The c_ID and c_ID[I] attributes allow local vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script.” Based on that I wrote down the following commands to save id, type, positions and velocities at each 4ft:
compute cc7 mobile chunk/atom bin/cylinder z lower 24.14 0 0 0.0 5.45719351276 200 bound z 33.065 57.205 units box
dump 1 mobile custom 4 traj_nvt.lammpstrj id type c_cc7[xu] c_cc7[yu] c_cc7[zu] c_cc7[vx] c_cc7[vy] c_cc7[vz]
However, I am getting wrong data and I need your advising help to correct it.
Best Regards,
Hamed.
Dear Prof. Kohlmeyer,
Thank you for your advice. If it is possible would you please explain more on how to use dump command to output the chunk/atom compute data? The manual says: "The c_ID and c_ID[I] attributes allow local vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script." Based on that I wrote down the following commands to save id, type, positions and velocities at each 4ft:
compute cc7 mobile chunk/atom bin/cylinder z lower 24.14 0 0 0.0 5.45719351276 200 bound z 33.065 57.205 units box
dump 1 mobile custom 4 traj_nvt.lammpstrj id type c_cc7[xu] c_cc7[yu] c_cc7[zu] c_cc7[vx] c_cc7[vy] c_cc7[vz]
However, I am getting wrong data and I need your advising help to correct it.
no, you need to read the documentation more carefully and not make up a syntax.
there are examples given in the documentation and in the examples tree
of the LAMMPS distribution.
axel.
I.e. you cannot say c_cc7[xu]. You have to replace xu by 1 or 5 or whatever.
The compute explains which column is which.
Steve
Dear Dr. Plimpton,
Thank you for your advice. I will get back to you if I have more question.
Regards,
Hamed.
Dear Dr. Plimpton,
I used the compute chunk/atom command to group atoms of my simulation in a cylindrical bin. The manual says this compute calculates an integer chunk for each atom. My question is that if it is possible, how can I define columns of positions and velocities of atoms (xu,yu,zu,vx,vy,vz) using this compute? I need to define them to be used by the dump command in next line.
compute cc7 mobile chunk/atom bin/cylinder z lower 24.14 0 0 0.0 5.45719351276 200 bound z 33.065 57.205
dump 1 all custom 4 traj_nvt.lammpstrj id type c_cc7[1] c_cc7[2] c_cc7[3] c_cc7[4] c_cc7[5] c_cc7[6]
I appreciate your advice and help.
Regards,
Hamed.
Dear Dr. Plimpton,
I used the compute chunk/atom command to group atoms of my simulation in a cylindrical bin. The manual says this compute calculates an integer chunk for each atom. My question is that if it is possible, how can I define columns of positions and velocities of atoms (xu,yu,zu,vx,vy,vz) using this compute? I need to define them to be used by the dump command in next line.
compute cc7 mobile chunk/atom bin/cylinder z lower 24.14 0 0 0.0 5.45719351276 200 bound z 33.065 57.205
dump 1 all custom 4 traj_nvt.lammpstrj id type c_cc7[1] c_cc7[2] c_cc7[3] c_cc7[4] c_cc7[5] c_cc7[6]
I appreciate your advice and help.
i already gave you advice and help which still applies. you need to spend some more time to better understanding how things work in LAMMPS. there is extensive and detailed documentation.
the chunk/atom compute computes a chunk-id. you can just output it as a per-atom property (using c_cc7 without any brackets).
that identifies for each atom to which chunk (i.e. bin) it belongs and you output all other per-atom properties with it.
if rather you want one file of coordinates for each bin (or chunk), use dump_modify to select only atoms where the chunk-id has a desired value.
please note, it is you that has to understand how things work in LAMMPS, and then figure out how to do what you want.
but not the other way around, where you make up how LAMMPS should work and then ask for the commands, which you are now doing for the second time.
axel.