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 -53.639763 0.0000000) to (26.818121 53.639763 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6238139 4.6238139 3.5213917 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -53.639763 0.0000000) to (26.818121 53.639763 3.5213917) create_atoms CPU = 0.002 seconds 466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6238139 4.6238139 3.5213917 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -53.639763 0.0000000) to (26.818121 53.639763 3.5213917) create_atoms CPU = 0.002 seconds 466 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 34 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 12 atoms, new total = 920 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 34 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4043.0946 0 -4043.0946 10478.259 46 0 -4075.4255 0 -4075.4255 -3924.698 Loop time of 10.0113 on 1 procs for 46 steps with 920 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 = -4043.09461271974 -4075.42192811835 -4075.42547347902 Force two-norm initial, final = 59.837963 0.23343353 Force max component initial, final = 13.566125 0.048097098 Final line search alpha, max atom move = 1.0000000 0.048097098 Iterations, force evaluations = 46 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9879 | 9.9879 | 9.9879 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012543 | 0.012543 | 0.012543 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01088 | | | 0.11 Nlocal: 920.000 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5947.00 ave 5947 max 5947 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: 79336.0 ave 79336 max 79336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79336 Ave neighs/atom = 86.234783 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 34 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -4075.4255 0 -4075.4255 -3924.698 10131.168 48 0 -4075.4591 0 -4075.4591 330.08494 10107.785 Loop time of 0.499269 on 1 procs for 2 steps with 920 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4075.42547347902 -4075.45772415928 -4075.45914960436 Force two-norm initial, final = 41.943199 3.3099358 Force max component initial, final = 31.757708 3.2055541 Final line search alpha, max atom move = 0.00013387573 0.00042914589 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49628 | 0.49628 | 0.49628 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069953 | 0.00069953 | 0.00069953 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002291 | | | 0.46 Nlocal: 920.000 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6715.00 ave 6715 max 6715 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: 80016.0 ave 80016 max 80016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80016 Ave neighs/atom = 86.973913 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 34 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) = 4.736 | 4.736 | 4.736 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4075.4591 0 -4075.4591 330.08494 Loop time of 8.309e-06 on 1 procs for 0 steps with 920 atoms 168.5% 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 | | 8.309e-06 | | |100.00 Nlocal: 920.000 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6715.00 ave 6715 max 6715 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: 80160.0 ave 80160 max 80160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80160 Ave neighs/atom = 87.130435 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 34 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) = 4.736 | 4.736 | 4.736 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 -4075.4591 -4075.4591 26.79264 107.27953 3.5166056 330.08494 330.08494 507.62689 607.19295 -124.56502 2.2219601 445.68908 Loop time of 8.73e-06 on 1 procs for 0 steps with 920 atoms 229.1% 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 | | 8.73e-06 | | |100.00 Nlocal: 920.000 ave 920 max 920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6715.00 ave 6715 max 6715 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40080.0 ave 40080 max 40080 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80160.0 ave 80160 max 80160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80160 Ave neighs/atom = 87.130435 Neighbor list builds = 0 Dangerous builds = 0 920 -4075.45914960436 eV 2.22196009129107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11