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 = 3.6135806 3.6135806 3.6135806 Created orthogonal box = (0.0000000 -43.812336 0.0000000) to (35.772623 43.812336 8.8514286) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1103747 5.0667328 5.9009524 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.812336 0.0000000) to (35.772623 43.812336 8.8514286) create_atoms CPU = 0.004 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1103747 5.0667328 5.9009524 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.812336 0.0000000) to (35.772623 43.812336 8.8514286) create_atoms CPU = 0.004 seconds 1184 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 24 3 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_426403318662_000#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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.021 | 6.021 | 6.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7789.1247 0 -7789.1247 48971.229 80 0 -8233.0623 0 -8233.0623 -1526.9311 Loop time of 5.02516 on 1 procs for 80 steps with 2336 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 = -7789.1247339593 -8233.05480511809 -8233.06233283677 Force two-norm initial, final = 656.39486 0.27208470 Force max component initial, final = 106.29313 0.042473520 Final line search alpha, max atom move = 1.0000000 0.042473520 Iterations, force evaluations = 80 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8494 | 4.8494 | 4.8494 | 0.0 | 96.50 Neigh | 0.10699 | 0.10699 | 0.10699 | 0.0 | 2.13 Comm | 0.03062 | 0.03062 | 0.03062 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03814 | | | 0.76 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8282.00 ave 8282 max 8282 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: 327792.0 ave 327792 max 327792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327792 Ave neighs/atom = 140.32192 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.019 | 6.019 | 6.019 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -8233.0623 0 -8233.0623 -1526.9311 27745.373 83 0 -8233.1408 0 -8233.1408 298.0713 27708.445 Loop time of 0.156327 on 1 procs for 3 steps with 2336 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 = -8233.06233283678 -8233.13694413723 -8233.14077806118 Force two-norm initial, final = 67.884660 11.810191 Force max component initial, final = 60.284286 11.453830 Final line search alpha, max atom move = 7.7841563e-05 0.00089158404 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15201 | 0.15201 | 0.15201 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090441 | 0.00090441 | 0.00090441 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003416 | | | 2.19 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8045.00 ave 8045 max 8045 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: 327504.0 ave 327504 max 327504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327504 Ave neighs/atom = 140.19863 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.157 | 6.157 | 6.157 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8233.1408 0 -8233.1408 298.0713 Loop time of 6.495e-06 on 1 procs for 0 steps with 2336 atoms 200.2% 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 | | 6.495e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8045.00 ave 8045 max 8045 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: 327552.0 ave 327552 max 327552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327552 Ave neighs/atom = 140.21918 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.157 | 6.157 | 6.157 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 -8233.1408 -8233.1408 35.746105 87.736733 8.8349068 298.0713 298.0713 97.878549 663.13811 133.19723 2.2974448 1334.1488 Loop time of 7.347e-06 on 1 procs for 0 steps with 2336 atoms 285.8% 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 | | 7.347e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8045.00 ave 8045 max 8045 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163776.0 ave 163776 max 163776 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 327552.0 ave 327552 max 327552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327552 Ave neighs/atom = 140.21918 Neighbor list builds = 0 Dangerous builds = 0 2336 -8233.15245806118 eV 2.29744477912812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06