LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -29.256443 0.0000000) to (14.628221 29.256443 2.8688302) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3757434 3.3757434 2.8688302 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -29.256443 0.0000000) to (14.628221 29.256443 2.8688302) create_atoms CPU = 0.002 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3757434 3.3757434 2.8688302 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -29.256443 0.0000000) to (14.628221 29.256443 2.8688302) create_atoms CPU = 0.001 seconds 106 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 12 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 210 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_984358344196_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -703.1944 0 -703.1944 144175.89 49 0 -860.45393 0 -860.45393 26330.825 Loop time of 0.972293 on 1 procs for 49 steps with 210 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -703.194397199934 -860.45314005152 -860.453933670497 Force two-norm initial, final = 288.15847 0.12182333 Force max component initial, final = 62.955890 0.018240204 Final line search alpha, max atom move = 1.0000000 0.018240204 Iterations, force evaluations = 49 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95586 | 0.95586 | 0.95586 | 0.0 | 98.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010936 | 0.010936 | 0.010936 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0055 | | | 0.57 Nlocal: 210.000 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5294.00 ave 5294 max 5294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82028.0 ave 82028 max 82028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82028 Ave neighs/atom = 390.60952 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -860.45393 0 -860.45393 26330.825 2455.5449 161 0 -862.63693 0 -862.63693 377.18818 2488.0321 Loop time of 1.53791 on 1 procs for 112 steps with 210 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -860.453933670497 -862.636280103464 -862.636926520629 Force two-norm initial, final = 79.615903 1.7582934 Force max component initial, final = 62.562102 1.0733049 Final line search alpha, max atom move = 0.00051251718 0.00055008717 Iterations, force evaluations = 112 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4552 | 1.4552 | 1.4552 | 0.0 | 94.62 Neigh | 0.021148 | 0.021148 | 0.021148 | 0.0 | 1.38 Comm | 0.016228 | 0.016228 | 0.016228 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04532 | | | 2.95 Nlocal: 210.000 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5397.00 ave 5397 max 5397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78488.0 ave 78488 max 78488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78488 Ave neighs/atom = 373.75238 Neighbor list builds = 2 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -862.63693 0 -862.63693 377.18818 Loop time of 6.836e-06 on 1 procs for 0 steps with 210 atoms 160.9% CPU use with 1 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 | | 6.836e-06 | | |100.00 Nlocal: 210.000 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5397.00 ave 5397 max 5397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78628.0 ave 78628 max 78628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78628 Ave neighs/atom = 374.41905 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.597 | 4.597 | 4.597 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -862.63693 -862.63693 15.07416 60.651261 2.7213413 377.18818 377.18818 -62.897297 716.41685 478.04499 2.3698097 226.96789 Loop time of 7.227e-06 on 1 procs for 0 steps with 210 atoms 249.1% CPU use with 1 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 | | 7.227e-06 | | |100.00 Nlocal: 210.000 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5397.00 ave 5397 max 5397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39314.0 ave 39314 max 39314 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78628.0 ave 78628 max 78628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78628 Ave neighs/atom = 374.41905 Neighbor list builds = 0 Dangerous builds = 0 210 -862.63692652063 eV 2.3698096795166 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02