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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -67.456914 0.0000000) to (33.728457 67.456914 3.6583648) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1584699 5.1584699 3.6583648 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -67.456914 0.0000000) to (33.728457 67.456914 3.6583648) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1584699 5.1584699 3.6583648 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -67.456914 0.0000000) to (33.728457 67.456914 3.6583648) create_atoms CPU = 0.002 seconds 682 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_769582363439_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5172.8315 0 -5172.8315 59434.604 297 0 -5457.217 0 -5457.217 -8862.0248 Loop time of 13.3295 on 1 procs for 297 steps with 1362 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 = -5172.83145663154 -5457.21155572952 -5457.21697347352 Force two-norm initial, final = 513.44539 0.20801995 Force max component initial, final = 110.27612 0.052985680 Final line search alpha, max atom move = 1.0000000 0.052985680 Iterations, force evaluations = 297 582 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.005 | 13.005 | 13.005 | 0.0 | 97.56 Neigh | 0.10214 | 0.10214 | 0.10214 | 0.0 | 0.77 Comm | 0.12698 | 0.12698 | 0.12698 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09572 | | | 0.72 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9493.00 ave 9493 max 9493 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: 190244.0 ave 190244 max 190244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190244 Ave neighs/atom = 139.67988 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 297 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press Volume 297 0 -5457.217 0 -5457.217 -8862.0248 16647.152 363 0 -5494.9909 0 -5494.9909 149.46259 16471.531 Loop time of 1.71643 on 1 procs for 66 steps with 1362 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5457.2169734735 -5494.98736240592 -5494.99091808007 Force two-norm initial, final = 881.09951 6.7538223 Force max component initial, final = 615.29690 4.1097897 Final line search alpha, max atom move = 0.00025984400 0.0010679042 Iterations, force evaluations = 66 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5131 | 1.5131 | 1.5131 | 0.0 | 88.16 Neigh | 0.13526 | 0.13526 | 0.13526 | 0.0 | 7.88 Comm | 0.015945 | 0.015945 | 0.015945 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05209 | | | 3.03 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9638.00 ave 9638 max 9638 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: 194440.0 ave 194440 max 194440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194440 Ave neighs/atom = 142.76065 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.234 | 5.234 | 5.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5494.9909 0 -5494.9909 149.46259 Loop time of 6.455e-06 on 1 procs for 0 steps with 1362 atoms 185.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9638.00 ave 9638 max 9638 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: 194440.0 ave 194440 max 194440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194440 Ave neighs/atom = 142.76065 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.234 | 5.234 | 5.234 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 -5494.9909 -5494.9909 32.591618 129.83615 3.892534 149.46259 149.46259 386.28287 -181.95802 244.06291 2.2419034 379.9467 Loop time of 7.267e-06 on 1 procs for 0 steps with 1362 atoms 261.5% 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 | | 7.267e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9638.00 ave 9638 max 9638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97220.0 ave 97220 max 97220 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 194440.0 ave 194440 max 194440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194440 Ave neighs/atom = 142.76065 Neighbor list builds = 0 Dangerous builds = 0 1362 -5494.99091808007 eV 2.2419034178033 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15