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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -64.279100 0.0000000) to (37.111555 64.279100 6.3030843) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7094701 5.7686371 6.3030843 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -64.279100 0.0000000) to (37.111555 64.279100 6.3030843) create_atoms CPU = 0.009 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7094701 5.7686371 6.3030843 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -64.279100 0.0000000) to (37.111555 64.279100 6.3030843) create_atoms CPU = 0.009 seconds 1250 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2492 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7117.2847 0 -7117.2847 94103.296 84 0 -8152.3685 0 -8152.3685 3433.871 Loop time of 12.6769 on 1 procs for 84 steps with 2492 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 = -7117.2846584687 -8152.3605537296 -8152.36853179142 Force two-norm initial, final = 1985.8938 0.24273805 Force max component initial, final = 547.15764 0.011711252 Final line search alpha, max atom move = 1.0000000 0.011711252 Iterations, force evaluations = 84 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.304 | 12.304 | 12.304 | 0.0 | 97.06 Neigh | 0.28365 | 0.28365 | 0.28365 | 0.0 | 2.24 Comm | 0.050322 | 0.050322 | 0.050322 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03912 | | | 0.31 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14856.0 ave 14856 max 14856 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: 791362.0 ave 791362 max 791362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 791362 Ave neighs/atom = 317.56100 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -8152.3685 0 -8152.3685 3433.871 30071.982 88 0 -8152.5635 0 -8152.5635 -95.164393 30146.163 Loop time of 0.546686 on 1 procs for 4 steps with 2492 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8152.36853179143 -8152.56152928062 -8152.56351913435 Force two-norm initial, final = 134.84857 5.5228361 Force max component initial, final = 121.68471 4.9944698 Final line search alpha, max atom move = 6.9618086e-05 0.00034770543 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53851 | 0.53851 | 0.53851 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019742 | 0.0019742 | 0.0019742 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006204 | | | 1.13 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14836.0 ave 14836 max 14836 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: 791542.0 ave 791542 max 791542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 791542 Ave neighs/atom = 317.63323 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.52 | 11.52 | 11.52 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8152.5635 0 -8152.5635 -95.164393 Loop time of 6.485e-06 on 1 procs for 0 steps with 2492 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14848.0 ave 14848 max 14848 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: 791244.0 ave 791244 max 791244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 791244 Ave neighs/atom = 317.51364 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.52 | 11.52 | 11.52 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 -8152.5635 -8152.5635 37.070324 128.94944 6.3064683 -95.164393 -95.164393 -265.14591 77.188388 -97.53566 2.2713501 1102.6975 Loop time of 6.816e-06 on 1 procs for 0 steps with 2492 atoms 293.4% 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 | | 6.816e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14848.0 ave 14848 max 14848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 395622.0 ave 395622 max 395622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 791244.0 ave 791244 max 791244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 791244 Ave neighs/atom = 317.51364 Neighbor list builds = 0 Dangerous builds = 0 2492 -8152.56351913435 eV 2.2713501324946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15