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 -41.193341 0.0000000) to (29.128091 41.193341 4.4419922) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4191797 5.2689157 4.4419922 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -41.193341 0.0000000) to (29.128091 41.193341 4.4419922) create_atoms CPU = 0.001 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4191797 5.2689157 4.4419922 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -41.193341 0.0000000) to (29.128091 41.193341 4.4419922) create_atoms CPU = 0.001 seconds 346 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 = 6 15 1 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 6 atoms, new total = 684 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 = 6 15 1 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) = 5.397 | 5.397 | 5.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3925.878 0 -3925.878 137179.04 94 0 -4593.3138 0 -4593.3138 -4959.4111 Loop time of 2.49619 on 1 procs for 94 steps with 684 atoms 95.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3925.87797187324 -4593.30987492223 -4593.31381952451 Force two-norm initial, final = 1250.3780 0.36399850 Force max component initial, final = 420.91112 0.060726175 Final line search alpha, max atom move = 1.0000000 0.060726175 Iterations, force evaluations = 94 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4233 | 2.4233 | 2.4233 | 0.0 | 97.08 Neigh | 0.047991 | 0.047991 | 0.047991 | 0.0 | 1.92 Comm | 0.015749 | 0.015749 | 0.015749 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009155 | | | 0.37 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9475.00 ave 9475 max 9475 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: 279132.0 ave 279132 max 279132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279132 Ave neighs/atom = 408.08772 Neighbor list builds = 3 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 = 6 15 1 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.399 | 5.399 | 5.399 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -4593.3138 0 -4593.3138 -4959.4111 10659.745 101 0 -4594.0682 0 -4594.0682 -61.590462 10640.792 Loop time of 0.138917 on 1 procs for 7 steps with 684 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 = -4593.31381952452 -4594.06589051117 -4594.06815841347 Force two-norm initial, final = 213.30799 1.1756282 Force max component initial, final = 193.10551 0.52287969 Final line search alpha, max atom move = 0.00012054207 6.3029001e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13535 | 0.13535 | 0.13535 | 0.0 | 97.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066289 | 0.00066289 | 0.00066289 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002906 | | | 2.09 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9526.00 ave 9526 max 9526 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: 279104.0 ave 279104 max 279104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279104 Ave neighs/atom = 408.04678 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 = 6 15 1 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) = 5.537 | 5.537 | 5.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4594.0682 0 -4594.0682 -61.590462 Loop time of 2.391e-06 on 1 procs for 0 steps with 684 atoms 167.3% 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 | | 2.391e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9490.00 ave 9490 max 9490 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: 278992.0 ave 278992 max 278992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278992 Ave neighs/atom = 407.88304 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 = 6 15 1 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) = 5.537 | 5.537 | 5.537 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 -4594.0682 -4594.0682 29.219827 82.502406 4.4139731 -61.590462 -61.590462 -45.172582 -78.840214 -60.75859 2.5654096 565.22798 Loop time of 2.585e-06 on 1 procs for 0 steps with 684 atoms 232.1% 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 | | 2.585e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9490.00 ave 9490 max 9490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 139496.0 ave 139496 max 139496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 278992.0 ave 278992 max 278992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278992 Ave neighs/atom = 407.88304 Neighbor list builds = 0 Dangerous builds = 0 684 -4594.06815841347 eV 2.565409575643 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03