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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -58.630032 0.0000000) to (20.728847 58.630032 5.1030893) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6533218 6.2183367 5.1030893 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.630032 0.0000000) to (20.728847 58.630032 5.1030893) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6533218 6.2183367 5.1030893 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.630032 0.0000000) to (20.728847 58.630032 5.1030893) create_atoms CPU = 0.001 seconds 530 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1050 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_549900287421_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4289.8855 0 -4289.8855 50088.408 122 0 -4463.3474 0 -4463.3474 -7826.6317 Loop time of 8.29019 on 1 procs for 122 steps with 1050 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4289.88549534104 -4463.34347982887 -4463.3473597436 Force two-norm initial, final = 613.48223 0.20751276 Force max component initial, final = 194.71389 0.050795915 Final line search alpha, max atom move = 1.0000000 0.050795915 Iterations, force evaluations = 122 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2511 | 8.2511 | 8.2511 | 0.0 | 99.53 Neigh | 0.012347 | 0.012347 | 0.012347 | 0.0 | 0.15 Comm | 0.014195 | 0.014195 | 0.014195 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01258 | | | 0.15 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5348.00 ave 5348 max 5348 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: 80424.0 ave 80424 max 80424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80424 Ave neighs/atom = 76.594286 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -4463.3474 0 -4463.3474 -7826.6317 12403.905 147 0 -4468.245 0 -4468.245 -1.4017892 12339.166 Loop time of 0.974813 on 1 procs for 25 steps with 1050 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 = -4463.3473597436 -4468.24480947236 -4468.24501803754 Force two-norm initial, final = 326.60191 1.1224599 Force max component initial, final = 280.62815 0.50891741 Final line search alpha, max atom move = 0.00091721916 0.00046678880 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95509 | 0.95509 | 0.95509 | 0.0 | 97.98 Neigh | 0.011883 | 0.011883 | 0.011883 | 0.0 | 1.22 Comm | 0.0015229 | 0.0015229 | 0.0015229 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006314 | | | 0.65 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5404.00 ave 5404 max 5404 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: 80192.0 ave 80192 max 80192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80192 Ave neighs/atom = 76.373333 Neighbor list builds = 2 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.762 | 4.762 | 4.762 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4468.245 0 -4468.245 -1.4017892 Loop time of 1.611e-06 on 1 procs for 0 steps with 1050 atoms 124.1% 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 | | 1.611e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5404.00 ave 5404 max 5404 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: 80176.0 ave 80176 max 80176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80176 Ave neighs/atom = 76.358095 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.762 | 4.762 | 4.762 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 -4468.245 -4468.245 20.228637 119.4112 5.1082732 -1.4017892 -1.4017892 42.48089 19.461149 -66.147406 2.367708 1434.964 Loop time of 1.5e-06 on 1 procs for 0 steps with 1050 atoms 200.0% 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 | | 1.5e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5404.00 ave 5404 max 5404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40088.0 ave 40088 max 40088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80176.0 ave 80176 max 80176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80176 Ave neighs/atom = 76.358095 Neighbor list builds = 0 Dangerous builds = 0 1050 -4468.24501803754 eV 2.36770797223723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09