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 -38.018842 0.0000000) to (8.9611271 38.018842 5.1737091) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9740847 6.3364737 5.1737091 Created 143 atoms using lattice units in orthogonal box = (0.0000000 -38.018842 0.0000000) to (8.9611271 38.018842 5.1737091) create_atoms CPU = 0.001 seconds 143 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9740847 6.3364737 5.1737091 Created 151 atoms using lattice units in orthogonal box = (0.0000000 -38.018842 0.0000000) to (8.9611271 38.018842 5.1737091) create_atoms CPU = 0.001 seconds 151 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 = 3 21 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 = 294 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 = 3 21 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) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -53.3189 0 -53.3189 691770.66 405 0 -1181.3055 0 -1181.3055 -29259.802 Loop time of 1.9741 on 1 procs for 405 steps with 294 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 = -53.3188996375824 -1181.30436034396 -1181.30552983782 Force two-norm initial, final = 2534.1509 0.13550921 Force max component initial, final = 681.68272 0.045370511 Final line search alpha, max atom move = 1.0000000 0.045370511 Iterations, force evaluations = 405 779 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9083 | 1.9083 | 1.9083 | 0.0 | 96.67 Neigh | 0.026893 | 0.026893 | 0.026893 | 0.0 | 1.36 Comm | 0.02381 | 0.02381 | 0.02381 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01513 | | | 0.77 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3173.00 ave 3173 max 3173 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: 40498.0 ave 40498 max 40498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40498 Ave neighs/atom = 137.74830 Neighbor list builds = 9 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 = 3 21 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 : 405 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press Volume 405 0 -1181.3055 0 -1181.3055 -29259.802 3525.2793 794 0 -1199.5545 0 -1199.5545 -565.71768 3447.4221 Loop time of 1.1967 on 1 procs for 389 steps with 294 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 = -1181.30552983783 -1199.55336003117 -1199.5545347201 Force two-norm initial, final = 299.36462 3.0748703 Force max component initial, final = 290.08474 1.8224330 Final line search alpha, max atom move = 0.00039829140 0.00072585940 Iterations, force evaluations = 389 455 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1224 | 1.1224 | 1.1224 | 0.0 | 93.79 Neigh | 0.0031388 | 0.0031388 | 0.0031388 | 0.0 | 0.26 Comm | 0.012815 | 0.012815 | 0.012815 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05832 | | | 4.87 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3372.00 ave 3372 max 3372 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: 41938.0 ave 41938 max 41938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41938 Ave neighs/atom = 142.64626 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 21 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1199.5545 0 -1199.5545 -565.71768 Loop time of 1.992e-06 on 1 procs for 0 steps with 294 atoms 150.6% 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 | | 1.992e-06 | | |100.00 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3404.00 ave 3404 max 3404 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: 40916.0 ave 40916 max 40916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40916 Ave neighs/atom = 139.17007 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 = 3 21 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) = 4.598 | 4.598 | 4.598 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 -1199.5545 -1199.5545 8.1144581 74.742475 5.6841753 -565.71768 -565.71768 -397.34325 -369.27432 -930.53546 2.3884732 298.98565 Loop time of 2.238e-06 on 1 procs for 0 steps with 294 atoms 178.7% 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 | | 2.238e-06 | | |100.00 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3404.00 ave 3404 max 3404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20458.0 ave 20458 max 20458 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40916.0 ave 40916 max 40916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40916 Ave neighs/atom = 139.17007 Neighbor list builds = 0 Dangerous builds = 0 294 -1199.5545347201 eV 2.38847322518509 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03