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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1194 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) create_atoms CPU = 0.002 seconds 1194 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1202 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) create_atoms CPU = 0.002 seconds 1202 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 = 8 36 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2386 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_122936827583_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 = 8 36 3 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) = 5.999 | 5.999 | 5.999 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8094.647 0 -8094.647 44449.083 115 0 -8425.621 0 -8425.621 -4226.9342 Loop time of 28.4933 on 1 procs for 115 steps with 2386 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 = -8094.64701301181 -8425.61275842236 -8425.62102980531 Force two-norm initial, final = 435.73729 0.28173466 Force max component initial, final = 73.461362 0.027189315 Final line search alpha, max atom move = 1.0000000 0.027189315 Iterations, force evaluations = 115 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.4 | 28.4 | 28.4 | 0.0 | 99.67 Neigh | 0.04306 | 0.04306 | 0.04306 | 0.0 | 0.15 Comm | 0.022004 | 0.022004 | 0.022004 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02816 | | | 0.10 Nlocal: 2386.00 ave 2386 max 2386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8140.00 ave 8140 max 8140 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: 315976.0 ave 315976 max 315976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315976 Ave neighs/atom = 132.42917 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 ghost atom cutoff = 7 binsize = 3.5, bins = 8 36 3 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 : 115 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.999 | 5.999 | 5.999 Mbytes Step Temp E_pair E_mol TotEng Press Volume 115 0 -8425.621 0 -8425.621 -4226.9342 28305.377 118 0 -8425.763 0 -8425.763 -5.6314282 28208.379 Loop time of 0.842902 on 1 procs for 3 steps with 2386 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 = -8425.62102980532 -8425.76147970888 -8425.76303030301 Force two-norm initial, final = 132.51634 1.5313063 Force max component initial, final = 92.595687 1.2317758 Final line search alpha, max atom move = 0.00010428870 0.00012846030 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84 | 0.84 | 0.84 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042934 | 0.00042934 | 0.00042934 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002473 | | | 0.29 Nlocal: 2386.00 ave 2386 max 2386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8249.00 ave 8249 max 8249 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: 315676.0 ave 315676 max 315676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315676 Ave neighs/atom = 132.30344 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 = 8 36 3 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) = 6.138 | 6.138 | 6.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8425.763 0 -8425.763 -5.6314282 Loop time of 2.239e-06 on 1 procs for 0 steps with 2386 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 | | 2.239e-06 | | |100.00 Nlocal: 2386.00 ave 2386 max 2386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8264.00 ave 8264 max 8264 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: 315920.0 ave 315920 max 315920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315920 Ave neighs/atom = 132.40570 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 = 8 36 3 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) = 6.138 | 6.138 | 6.138 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 -8425.763 -8425.763 25.50705 125.00003 8.8472388 -5.6314282 -5.6314282 48.756141 -69.867872 4.217446 2.3770123 1175.3469 Loop time of 2.921e-06 on 1 procs for 0 steps with 2386 atoms 239.6% 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 | | 2.921e-06 | | |100.00 Nlocal: 2386.00 ave 2386 max 2386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8264.00 ave 8264 max 8264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157960.0 ave 157960 max 157960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 315920.0 ave 315920 max 315920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315920 Ave neighs/atom = 132.40570 Neighbor list builds = 0 Dangerous builds = 0 2386 -8425.76303030301 eV 2.37701230093478 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30