LAMMPS (29 Sep 2021 - Update 3) atom_style atomic atom_modify map yes region box block 0 100 0 100 0 100 create_box 1 box Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) 1 by 2 by 7 MPI processor grid create_atoms 1 single 10 10 10 Created 1 atoms using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) create_atoms CPU = 0.000 seconds create_atoms 1 single 10 10 10.5 Created 1 atoms using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) create_atoms CPU = 0.001 seconds create_atoms 1 single 20 20 20 Created 1 atoms using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) create_atoms CPU = 0.000 seconds create_atoms 1 single 25 25 25 Created 1 atoms using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) create_atoms CPU = 0.000 seconds mass 1 1.0 pair_style lj/cut 3 pair_coeff * * 1 1 write_data system.data System init for write_data ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 61 61 61 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard compute cluster all cluster/atom 2.5 # clusters are (1 2), 3, 4 compute clchunk all chunk/atom c_cluster compress yes nchunk once ids once variable clust1 equal c_cluster[1] variable clust2 equal c_cluster[2] variable clust3 equal c_cluster[3] variable clust4 equal c_cluster[4] variable chunk1 equal c_clchunk[1] variable chunk2 equal c_clchunk[2] variable chunk3 equal c_clchunk[3] variable chunk4 equal c_clchunk[4] thermo_style custom v_clust1 v_clust2 v_clust3 v_clust4 v_chunk1 v_chunk2 v_chunk3 v_chunk4 thermo 1 run 0 post no WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.3 ghost atom cutoff = 3.3 binsize = 1.65, bins = 61 61 61 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard (2) compute cluster/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 0.9518 | 1.420 | 4.214 Mbytes v_clust1 v_clust2 v_clust3 v_clust4 v_chunk1 v_chunk2 v_chunk3 v_chunk4 1 1 3 4 1 1 2 3 Loop time of 6.86305e-06 on 14 procs for 0 steps with 4 atoms group a2 id 2 1 atoms in group a2 displace_atoms a2 move 0 0 4 Displacing atoms ... # now clusters are 1, 2, 3, 4 run 0 post no Per MPI rank memory allocation (min/avg/max) = 0.9518 | 1.438 | 4.339 Mbytes v_clust1 v_clust2 v_clust3 v_clust4 v_chunk1 v_chunk2 v_chunk3 v_chunk4 1 2 3 4 1 2 3 135169 Loop time of 6.35215e-06 on 14 procs for 0 steps with 4 atoms group a3 id 3 1 atoms in group a3 displace_atoms a3 move 4.5 4.5 4.5 Displacing atoms ... # now clusters are 1, 2, (3 4) run 0 post no Per MPI rank memory allocation (min/avg/max) = 0.9518 | 1.438 | 4.339 Mbytes v_clust1 v_clust2 v_clust3 v_clust4 v_chunk1 v_chunk2 v_chunk3 v_chunk4 1 2 3 3 1 2 3 135169 Loop time of 6.52245e-06 on 14 procs for 0 steps with 4 atoms Total wall time: 0:00:00