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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -72.580774 0.0000000) to (41.904529 72.580774 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6289666 5.7775740 6.2700239 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.580774 0.0000000) to (41.904529 72.580774 6.2700239) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6289666 5.7775740 6.2700239 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.580774 0.0000000) to (41.904529 72.580774 6.2700239) create_atoms CPU = 0.004 seconds 1610 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 = 14 49 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 = 3216 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_227887284491_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 ghost atom cutoff = 6 binsize = 3, bins = 14 49 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) = 5.759 | 5.759 | 5.759 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9229.8484 0 -9229.8484 134710.43 58 0 -11354.603 0 -11354.603 3822.4253 Loop time of 11.5584 on 1 procs for 58 steps with 3216 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9229.84837487266 -11354.5933347929 -11354.6034481965 Force two-norm initial, final = 3536.4318 0.29939978 Force max component initial, final = 821.43450 0.057771031 Final line search alpha, max atom move = 1.0000000 0.057771031 Iterations, force evaluations = 58 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.487 | 11.487 | 11.487 | 0.0 | 99.39 Neigh | 0.039825 | 0.039825 | 0.039825 | 0.0 | 0.34 Comm | 0.01197 | 0.01197 | 0.01197 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0192 | | | 0.17 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8704.00 ave 8704 max 8704 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: 249472.0 ave 249472 max 249472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249472 Ave neighs/atom = 77.572139 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.766 | 5.766 | 5.766 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -11354.603 0 -11354.603 3822.4253 38140.093 62 0 -11354.866 0 -11354.866 -20.461044 38242.065 Loop time of 0.767845 on 1 procs for 4 steps with 3216 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11354.6034481964 -11354.8642626439 -11354.8660220348 Force two-norm initial, final = 188.62493 3.2748769 Force max component initial, final = 160.12542 3.0519094 Final line search alpha, max atom move = 5.5881329e-05 0.00017054476 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76372 | 0.76372 | 0.76372 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053201 | 0.00053201 | 0.00053201 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003598 | | | 0.47 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8730.00 ave 8730 max 8730 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: 249324.0 ave 249324 max 249324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249324 Ave neighs/atom = 77.526119 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 = 14 49 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) = 5.904 | 5.904 | 5.904 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11354.866 0 -11354.866 -20.461044 Loop time of 2.29e-06 on 1 procs for 0 steps with 3216 atoms 174.7% 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 | | 2.29e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8729.00 ave 8729 max 8729 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: 249232.0 ave 249232 max 249232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249232 Ave neighs/atom = 77.497512 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 = 14 49 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) = 5.904 | 5.904 | 5.904 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 -11354.866 -11354.866 41.943863 145.57225 6.2631717 -20.461044 -20.461044 -127.98177 27.625478 38.973162 2.2976125 1119.4932 Loop time of 2.208e-06 on 1 procs for 0 steps with 3216 atoms 226.4% 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 | | 2.208e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8729.00 ave 8729 max 8729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124616.0 ave 124616 max 124616 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249232.0 ave 249232 max 249232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249232 Ave neighs/atom = 77.497512 Neighbor list builds = 0 Dangerous builds = 0 3216 -11354.8660220348 eV 2.29761250921856 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13