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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -53.438673 0.0000000) to (43.632494 53.438673 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3793486 5.1242563 5.8968214 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -53.438673 0.0000000) to (43.632494 53.438673 8.8452321) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3793486 5.1242563 5.8968214 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.438673 0.0000000) to (43.632494 53.438673 8.8452321) create_atoms CPU = 0.002 seconds 1758 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 = 9 21 2 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 4 atoms, new total = 3504 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 = 9 21 2 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) = 14.20 | 14.20 | 14.20 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12902.362 0 -12902.362 68096.196 61 0 -14476.063 0 -14476.063 7553.5373 Loop time of 5.44223 on 1 procs for 61 steps with 3504 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 = -12902.3624849498 -14476.0492206509 -14476.0625857409 Force two-norm initial, final = 1218.8238 0.51340525 Force max component initial, final = 168.50014 0.068541035 Final line search alpha, max atom move = 1.0000000 0.068541035 Iterations, force evaluations = 61 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3162 | 5.3162 | 5.3162 | 0.0 | 97.68 Neigh | 0.077359 | 0.077359 | 0.077359 | 0.0 | 1.42 Comm | 0.026028 | 0.026028 | 0.026028 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02265 | | | 0.42 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17007.0 ave 17007 max 17007 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: 1.33223e+06 ave 1.33223e+06 max 1.33223e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1332228 Ave neighs/atom = 380.20205 Neighbor list builds = 1 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 = 9 21 2 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 14.20 | 14.20 | 14.20 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -14476.063 0 -14476.063 7553.5373 41248.194 66 0 -14476.778 0 -14476.778 226.19078 41423.466 Loop time of 0.358338 on 1 procs for 5 steps with 3504 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14476.0625857408 -14476.7743955336 -14476.7780566277 Force two-norm initial, final = 380.01088 10.725875 Force max component initial, final = 334.89826 8.1646846 Final line search alpha, max atom move = 5.6144547e-05 0.00045840252 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35177 | 0.35177 | 0.35177 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010105 | 0.0010105 | 0.0010105 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005562 | | | 1.55 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16996.0 ave 16996 max 16996 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: 1.32935e+06 ave 1.32935e+06 max 1.32935e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1329348 Ave neighs/atom = 379.38014 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 = 9 21 2 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) = 13.71 | 13.71 | 13.71 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14476.778 0 -14476.778 226.19078 Loop time of 2.298e-06 on 1 procs for 0 steps with 3504 atoms 174.1% 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 | | 2.298e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16957.0 ave 16957 max 16957 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: 1.32841e+06 ave 1.32841e+06 max 1.32841e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1328410 Ave neighs/atom = 379.11244 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 = 9 21 2 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) = 13.71 | 13.71 | 13.71 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 -14476.778 -14476.778 43.636938 107.32049 8.8452381 226.19078 226.19078 125.05073 317.10297 236.41865 2.2604897 1505.9663 Loop time of 2.739e-06 on 1 procs for 0 steps with 3504 atoms 328.6% 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 | | 2.739e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16957.0 ave 16957 max 16957 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 664205.0 ave 664205 max 664205 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.32841e+06 ave 1.32841e+06 max 1.32841e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1328410 Ave neighs/atom = 379.11244 Neighbor list builds = 0 Dangerous builds = 0 3504 -14476.7780566277 eV 2.26048968542706 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06