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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -39.557603 0.0000000) to (8.0746619 39.557603 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8447971 5.2743471 5.8968993 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.557603 0.0000000) to (8.0746619 39.557603 8.8453489) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8447971 5.2743471 5.8968993 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.557603 0.0000000) to (8.0746619 39.557603 8.8453489) create_atoms CPU = 0.001 seconds 242 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 = 3 27 3 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 2 atoms, new total = 480 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_150993986463_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1852.6132 0 -1852.6132 77393.233 76 0 -2028.7471 0 -2028.7471 9217.4007 Loop time of 4.8932 on 1 procs for 76 steps with 480 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 = -1852.6132027538 -2028.74544210217 -2028.74708026803 Force two-norm initial, final = 338.42358 0.19242872 Force max component initial, final = 97.365171 0.059455541 Final line search alpha, max atom move = 1.0000000 0.059455541 Iterations, force evaluations = 76 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8712 | 4.8712 | 4.8712 | 0.0 | 99.55 Neigh | 0.0068202 | 0.0068202 | 0.0068202 | 0.0 | 0.14 Comm | 0.0074032 | 0.0074032 | 0.0074032 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007822 | | | 0.16 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772.00 ave 2772 max 2772 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: 37132.0 ave 37132 max 37132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37132 Ave neighs/atom = 77.358333 Neighbor list builds = 1 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 = 3 27 3 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -2028.7471 0 -2028.7471 9217.4007 5650.6613 92 0 -2029.4739 0 -2029.4739 -1.7183119 5679.7062 Loop time of 0.350455 on 1 procs for 16 steps with 480 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 = -2028.74708026802 -2029.47278324465 -2029.47393632303 Force two-norm initial, final = 86.430962 0.83484621 Force max component initial, final = 59.305687 0.18719686 Final line search alpha, max atom move = 0.00059700402 0.00011175728 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34415 | 0.34415 | 0.34415 | 0.0 | 98.20 Neigh | 0.0033277 | 0.0033277 | 0.0033277 | 0.0 | 0.95 Comm | 0.000521 | 0.000521 | 0.000521 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002461 | | | 0.70 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2829.00 ave 2829 max 2829 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: 36900.0 ave 36900 max 36900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36900 Ave neighs/atom = 76.875000 Neighbor list builds = 1 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 = 3 26 3 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2029.4739 0 -2029.4739 -1.7183119 Loop time of 1.798e-06 on 1 procs for 0 steps with 480 atoms 166.9% 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 | | 1.798e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2829.00 ave 2829 max 2829 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: 36884.0 ave 36884 max 36884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36884 Ave neighs/atom = 76.841667 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 = 3 26 3 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) = 4.598 | 4.598 | 4.598 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 -2029.4739 -2029.4739 8.1719243 77.973188 8.9136638 -1.7183119 -1.7183119 -50.796128 52.043724 -6.4025317 2.2174279 350.06076 Loop time of 2.193e-06 on 1 procs for 0 steps with 480 atoms 182.4% 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 | | 2.193e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2829.00 ave 2829 max 2829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18442.0 ave 18442 max 18442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36884.0 ave 36884 max 36884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36884 Ave neighs/atom = 76.841667 Neighbor list builds = 0 Dangerous builds = 0 480 -2029.47393632303 eV 2.21742789305533 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05