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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -37.559021 0.0000000) to (26.558239 37.559021 4.0500934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9410676 4.8040608 4.0500934 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -37.559021 0.0000000) to (26.558239 37.559021 4.0500934) create_atoms CPU = 0.001 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9410676 4.8040608 4.0500934 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -37.559021 0.0000000) to (26.558239 37.559021 4.0500934) create_atoms CPU = 0.001 seconds 346 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 684 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.186 | 6.186 | 6.186 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2629.5229 0 -2629.5229 46284.055 83 0 -2844.1182 0 -2844.1182 -4310.9043 Loop time of 2.83113 on 1 procs for 83 steps with 684 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 = -2629.52285249289 -2844.11583934614 -2844.11822831962 Force two-norm initial, final = 362.14440 0.21085825 Force max component initial, final = 120.59246 0.026595884 Final line search alpha, max atom move = 1.0000000 0.026595884 Iterations, force evaluations = 83 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7676 | 2.7676 | 2.7676 | 0.0 | 97.75 Neigh | 0.041733 | 0.041733 | 0.041733 | 0.0 | 1.47 Comm | 0.014226 | 0.014226 | 0.014226 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007615 | | | 0.27 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10451.0 ave 10451 max 10451 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: 412856.0 ave 412856 max 412856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412856 Ave neighs/atom = 603.59064 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.188 | 6.188 | 6.188 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -2844.1182 0 -2844.1182 -4310.9043 8079.948 90 0 -2844.4558 0 -2844.4558 -54.521724 8059.2765 Loop time of 0.159583 on 1 procs for 7 steps with 684 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 = -2844.1182283196 -2844.45391823866 -2844.45575118619 Force two-norm initial, final = 97.125118 0.64813251 Force max component initial, final = 90.704662 0.36545372 Final line search alpha, max atom move = 0.00019766469 7.2237295e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15628 | 0.15628 | 0.15628 | 0.0 | 97.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071816 | 0.00071816 | 0.00071816 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002587 | | | 1.62 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10415.0 ave 10415 max 10415 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: 413288.0 ave 413288 max 413288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413288 Ave neighs/atom = 604.22222 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.326 | 6.326 | 6.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2844.4558 0 -2844.4558 -54.521724 Loop time of 1.873e-06 on 1 procs for 0 steps with 684 atoms 106.8% 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 | | 1.873e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10415.0 ave 10415 max 10415 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: 413392.0 ave 413392 max 413392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413392 Ave neighs/atom = 604.37427 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.326 | 6.326 | 6.326 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 -2844.4558 -2844.4558 26.636745 75.187928 4.0240816 -54.521724 -54.521724 -72.866613 -39.154842 -51.543717 2.323857 491.09596 Loop time of 2.164e-06 on 1 procs for 0 steps with 684 atoms 231.1% 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 | | 2.164e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10415.0 ave 10415 max 10415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206696.0 ave 206696 max 206696 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 413392.0 ave 413392 max 413392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413392 Ave neighs/atom = 604.37427 Neighbor list builds = 0 Dangerous builds = 0 684 -2844.45575118619 eV 2.32385697156597 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03