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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -43.957882 0.0000000) to (21.978941 43.957882 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1581780 4.1581780 3.6133156 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -43.957882 0.0000000) to (21.978941 43.957882 3.6133156) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1581780 4.1581780 3.6133156 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.957882 0.0000000) to (21.978941 43.957882 3.6133156) create_atoms CPU = 0.000 seconds 298 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 592 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_122936827583_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1576.3537 0 -1576.3537 228973.22 52 0 -2086.8131 0 -2086.8131 6039.5952 Loop time of 3.75617 on 1 procs for 52 steps with 592 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1576.35372540025 -2086.81135316158 -2086.81311404121 Force two-norm initial, final = 1620.9761 0.11968054 Force max component initial, final = 480.53892 0.022063682 Final line search alpha, max atom move = 1.0000000 0.022063682 Iterations, force evaluations = 52 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7407 | 3.7407 | 3.7407 | 0.0 | 99.59 Neigh | 0.0044637 | 0.0044637 | 0.0044637 | 0.0 | 0.12 Comm | 0.0060814 | 0.0060814 | 0.0060814 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004935 | | | 0.13 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5023.00 ave 5023 max 5023 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: 78228.0 ave 78228 max 78228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78228 Ave neighs/atom = 132.14189 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -2086.8131 0 -2086.8131 6039.5952 6981.9931 55 0 -2086.8777 0 -2086.8777 -2.0265958 7015.9632 Loop time of 0.237441 on 1 procs for 3 steps with 592 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 = -2086.81311404121 -2086.87714912627 -2086.87767924014 Force two-norm initial, final = 45.629756 0.22836302 Force max component initial, final = 27.766737 0.15806991 Final line search alpha, max atom move = 0.00082045492 0.00012968924 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23598 | 0.23598 | 0.23598 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026285 | 0.00026285 | 0.00026285 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001201 | | | 0.51 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5028.00 ave 5028 max 5028 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: 78340.0 ave 78340 max 78340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78340 Ave neighs/atom = 132.33108 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.651 | 4.651 | 4.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2086.8777 0 -2086.8777 -2.0265958 Loop time of 2.14e-06 on 1 procs for 0 steps with 592 atoms 140.2% 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 | | 2.14e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5008.00 ave 5008 max 5008 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: 78296.0 ave 78296 max 78296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78296 Ave neighs/atom = 132.25676 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.651 | 4.651 | 4.651 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 -2086.8777 -2086.8777 22.002574 88.050298 3.6214541 -2.0265958 -2.0265958 20.492992 -36.152335 9.5795556 2.3453731 216.07564 Loop time of 2.278e-06 on 1 procs for 0 steps with 592 atoms 219.5% 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 | | 2.278e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5008.00 ave 5008 max 5008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39148.0 ave 39148 max 39148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78296.0 ave 78296 max 78296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78296 Ave neighs/atom = 132.25676 Neighbor list builds = 0 Dangerous builds = 0 592 -2086.87767924014 eV 2.34537305725301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04