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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -37.598175 0.0000000) to (26.585925 37.598175 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1306170 5.9365540 4.9800000 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.598175 0.0000000) to (26.585925 37.598175 4.9800000) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1306170 5.9365540 4.9800000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.598175 0.0000000) to (26.585925 37.598175 4.9800000) create_atoms CPU = 0.001 seconds 458 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_008996216289_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3737.9323 0 -3737.9323 88591.14 59 0 -4042.9202 0 -4042.9202 19800.997 Loop time of 5.24002 on 1 procs for 59 steps with 914 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 = -3737.93232228466 -4042.91619240591 -4042.92016618954 Force two-norm initial, final = 432.22826 0.22825840 Force max component initial, final = 89.669512 0.053282346 Final line search alpha, max atom move = 1.0000000 0.053282346 Iterations, force evaluations = 59 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2257 | 5.2257 | 5.2257 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0073332 | 0.0073332 | 0.0073332 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006967 | | | 0.13 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4665.00 ave 4665 max 4665 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: 80240.0 ave 80240 max 80240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80240 Ave neighs/atom = 87.789934 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4042.9202 0 -4042.9202 19800.997 9955.8392 70 0 -4044.047 0 -4044.047 -138.38294 10060.713 Loop time of 0.61905 on 1 procs for 11 steps with 914 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 = -4042.92016618953 -4044.04679941978 -4044.04701450363 Force two-norm initial, final = 248.08699 1.7643869 Force max component initial, final = 224.07887 1.2671234 Final line search alpha, max atom move = 0.00049328800 0.00062505674 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61546 | 0.61546 | 0.61546 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057646 | 0.00057646 | 0.00057646 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003018 | | | 0.49 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4665.00 ave 4665 max 4665 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: 81368.0 ave 81368 max 81368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81368 Ave neighs/atom = 89.024070 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4044.047 0 -4044.047 -138.38294 Loop time of 2.09e-06 on 1 procs for 0 steps with 914 atoms 191.4% 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 | | 2.09e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4651.00 ave 4651 max 4651 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: 80140.0 ave 80140 max 80140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80140 Ave neighs/atom = 87.680525 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.718 | 4.718 | 4.718 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 -4044.047 -4044.047 26.615623 75.940007 4.9776172 -138.38294 -138.38294 -202.01581 -150.30342 -62.829598 2.3028096 642.73508 Loop time of 2.11e-06 on 1 procs for 0 steps with 914 atoms 189.6% 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 | | 2.11e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4651.00 ave 4651 max 4651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40070.0 ave 40070 max 40070 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80140.0 ave 80140 max 80140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80140 Ave neighs/atom = 87.680525 Neighbor list builds = 0 Dangerous builds = 0 914 -4044.04701450363 eV 2.30280961196043 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06