Hello,
I am using the following LAMMPS version, which includes packages such as VTK, and supports the sphere atom style:
===== information of LAMMPS =====
Large-scale Atomic/Molecular Massively Parallel Simulator - 29 Aug 2024 - Maintenance
Git info (maintenance / stable_29Aug2024_update1-26-g89e442dac1-modified)
OS: Linux "Ubuntu 24.04.1 LTS" 6.8.0-51-generic x86_64
Compiler: GNU C++ 13.3.0 with OpenMP 4.5
C++ standard: C++11
MPI v3.1: Open MPI v5.0.6, package: Open MPI hp-z8@HP-Z8 Distribution, ident: 5.0.6, repo rev: v5.0.6, Nov 15, 2024
Accelerator configuration:
GPU package API: CUDA
GPU package precision: mixed
OPENMP package API: OpenMP
OPENMP package precision: double
OpenMP standard: OpenMP 4.5
Compatible GPU present: yes
Installed packages:
GPU GRANULAR OPENMP VTK
List of individual style options included in this LAMMPS executable
* Atom styles:
atomic body charge ellipsoid hybrid
line sphere tri
===== END of information =====
I attempted to write out the diameter (radius) of spherical atoms, but the values do not appear in the generated VTK file. However, when using dump custom, the diameter is indeed present in the output (e.g., check.txt).
Below is a minimal example script (dumTest.in). In the resulting file (test_0.vtk), there is no diameter or radius information, yet check.txt shows the diameter is stored correctly.
Could you please advise if I am missing any steps or settings to ensure the diameter appears in the VTK output?
Thank you!
===== minimal example script (dumTest.in) =====
atom_style sphere
region box block 0 1 0 1 0 1
create_box 1 box
create_atoms 1 single 0.5 0.5 0.5
set atom 1 diameter 0.001
dump d all vtk 1 test_*.vtk id type radius diameter x y z vx vy vz
dump check all custom 100 check.txt id type radius diameter x y z vx vy vz
dump_modify check sort id
run 0
===== End of minimal example script (dumTest.in) =====
===== LAMMPS results =====
$ mpirun -np 4 ./lmp_OIGG -in dumTest.in
LAMMPS (29 Aug 2024 - Maintenance - stable_29Aug2024_update1-26-g89e442dac1-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Created orthogonal box = (0 0 0) to (1 1 1)
1 by 2 by 2 MPI processor grid
Created 1 atoms
using lattice units in orthogonal box = (0 0 0) to (1 1 1)
create_atoms CPU = 0.000 seconds
Setting atom values ...
1 settings made for diameter
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 0.06276 | 0.06276 | 0.06276 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
Loop time of 6.07325e-06 on 4 procs for 0 steps with 1 atoms
111.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.073e-06 | | |100.00
Nlocal: 0.25 ave 1 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 0.75 ave 1 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
===== End of LAMMPS results =====
===== VTK output file =====
$ cat test_0.vtk
# vtk DataFile Version 5.1
Generated by LAMMPS
ASCII
DATASET POLYDATA
POINTS 1 float
0.5 0.5 0.5
VERTICES 2 1
OFFSETS vtktypeint64
0 1
CONNECTIVITY vtktypeint64
0
POINT_DATA 1
FIELD FieldData 1
v 3 1 double
0 0 0
===== End of VTK output file =====
===== dump custom output file =====
$ cat check.txt
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
1
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 1.0000000000000000e+00
0.0000000000000000e+00 1.0000000000000000e+00
0.0000000000000000e+00 1.0000000000000000e+00
ITEM: ATOMS id type radius diameter x y z vx vy vz
1 1 0.0005 0.001 0.5 0.5 0.5 0 0 0
===== End of dump custom output file =====