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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -43.723196 0.0000000) to (21.859801 43.723196 3.5937292) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1356381 4.1356381 3.5937292 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.723196 0.0000000) to (21.859801 43.723196 3.5937292) create_atoms CPU = 0.002 seconds 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1356381 4.1356381 3.5937292 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.723196 0.0000000) to (21.859801 43.723196 3.5937292) create_atoms CPU = 0.001 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 25 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 8 atoms, new total = 588 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_262519520678_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 25 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 -2472.106 0 -2472.106 27848.329 25 0 -2501.9232 0 -2501.9232 -3988.5321 Loop time of 4.29404 on 1 procs for 25 steps with 588 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 = -2472.10600731353 -2501.92095301622 -2501.92322048154 Force two-norm initial, final = 70.739615 0.16685831 Force max component initial, final = 22.551867 0.035284882 Final line search alpha, max atom move = 1.0000000 0.035284882 Iterations, force evaluations = 25 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2839 | 4.2839 | 4.2839 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0056122 | 0.0056122 | 0.0056122 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0045 | | | 0.10 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4957.00 ave 4957 max 4957 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: 77760.0 ave 77760 max 77760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77760 Ave neighs/atom = 132.24490 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 25 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -2501.9232 0 -2501.9232 -3988.5321 6869.6317 29 0 -2501.9454 0 -2501.9454 -2703.3374 6864.2115 Loop time of 0.60464 on 1 procs for 4 steps with 588 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2501.92322048154 -2501.94500999832 -2501.94535810333 Force two-norm initial, final = 14.162232 0.78452576 Force max component initial, final = 14.118938 0.74271326 Final line search alpha, max atom move = 0.00032257234 0.00023957875 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60152 | 0.60152 | 0.60152 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076721 | 0.00076721 | 0.00076721 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002355 | | | 0.39 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4957.00 ave 4957 max 4957 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: 78000.0 ave 78000 max 78000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78000 Ave neighs/atom = 132.65306 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 25 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 -2501.9454 0 -2501.9454 -2703.3374 Loop time of 6.525e-06 on 1 procs for 0 steps with 588 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4957.00 ave 4957 max 4957 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: 78004.0 ave 78004 max 78004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78004 Ave neighs/atom = 132.65986 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 25 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 -2501.9454 -2501.9454 21.798111 87.446392 3.6010562 -2703.3374 -2703.3374 -172.86757 -7943.549 6.404446 2.3334448 210.6022 Loop time of 7.357e-06 on 1 procs for 0 steps with 588 atoms 271.8% 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 | | 7.357e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4957.00 ave 4957 max 4957 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39002.0 ave 39002 max 39002 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78004.0 ave 78004 max 78004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78004 Ave neighs/atom = 132.65986 Neighbor list builds = 0 Dangerous builds = 0 588 -2501.94535810333 eV 2.33344483930871 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05