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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -34.407524 0.0000000) to (7.0234064 34.407524 7.6937562) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2140438 4.5876698 5.1291708 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -34.407524 0.0000000) to (7.0234064 34.407524 7.6937562) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2140438 4.5876698 5.1291708 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -34.407524 0.0000000) to (7.0234064 34.407524 7.6937562) create_atoms CPU = 0.000 seconds 122 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 12 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_666830945336_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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 12 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.928 | 4.928 | 4.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1186.5646 0 -1186.5646 261917.67 77 0 -1608.8585 0 -1608.8585 17870.507 Loop time of 0.817094 on 1 procs for 77 steps with 240 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1186.56461502776 -1608.85708776357 -1608.85853875868 Force two-norm initial, final = 954.03290 0.21442593 Force max component initial, final = 300.80602 0.025099569 Final line search alpha, max atom move = 1.0000000 0.025099569 Iterations, force evaluations = 77 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79426 | 0.79426 | 0.79426 | 0.0 | 97.21 Neigh | 0.012205 | 0.012205 | 0.012205 | 0.0 | 1.49 Comm | 0.0074435 | 0.0074435 | 0.0074435 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003184 | | | 0.39 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5232.00 ave 5232 max 5232 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: 98532.0 ave 98532 max 98532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98532 Ave neighs/atom = 410.55000 Neighbor list builds = 2 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 12 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -1608.8585 0 -1608.8585 17870.507 3718.5158 117 0 -1610.657 0 -1610.657 542.58492 3739.4844 Loop time of 0.320906 on 1 procs for 40 steps with 240 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1608.85853875868 -1610.65567068667 -1610.65695682695 Force two-norm initial, final = 160.56464 2.9140387 Force max component initial, final = 139.23990 2.3090294 Final line search alpha, max atom move = 0.00021053921 0.00048614123 Iterations, force evaluations = 40 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30086 | 0.30086 | 0.30086 | 0.0 | 93.75 Neigh | 0.005597 | 0.005597 | 0.005597 | 0.0 | 1.74 Comm | 0.0028472 | 0.0028472 | 0.0028472 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0116 | | | 3.61 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5216.00 ave 5216 max 5216 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: 97336.0 ave 97336 max 97336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97336 Ave neighs/atom = 405.56667 Neighbor list builds = 1 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.685 | 4.685 | 4.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1610.657 0 -1610.657 542.58492 Loop time of 1.867e-06 on 1 procs for 0 steps with 240 atoms 107.1% 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 | | 1.867e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5228.00 ave 5228 max 5228 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: 97580.0 ave 97580 max 97580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97580 Ave neighs/atom = 406.58333 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 2 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.685 | 4.685 | 4.685 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 -1610.657 -1610.657 7.0195 70.164265 7.5925833 542.58492 542.58492 988.74998 298.7262 340.27857 2.5967313 549.45948 Loop time of 1.806e-06 on 1 procs for 0 steps with 240 atoms 166.1% 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 | | 1.806e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5228.00 ave 5228 max 5228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48790.0 ave 48790 max 48790 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97580.0 ave 97580 max 97580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97580 Ave neighs/atom = 406.58333 Neighbor list builds = 0 Dangerous builds = 0 240 -1610.65695682694 eV 2.59673133360165 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01