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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -59.977214 0.0000000) to (21.205148 59.977214 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6891859 5.1200061 4.6834336 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -59.977214 0.0000000) to (21.205148 59.977214 4.6834336) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6891859 5.1200061 4.6834336 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -59.977214 0.0000000) to (21.205148 59.977214 4.6834336) create_atoms CPU = 0.002 seconds 658 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 32 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1308 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.529 | 5.529 | 5.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4677.9231 0 -4677.9231 94535.278 157 0 -5098.6723 0 -5098.6723 194866.2 Loop time of 4.15904 on 1 procs for 157 steps with 1308 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4677.92311082018 -5098.66764222801 -5098.67234440482 Force two-norm initial, final = 821.22620 0.37639409 Force max component initial, final = 272.28133 0.043437415 Final line search alpha, max atom move = 0.36320881 0.015776852 Iterations, force evaluations = 157 306 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0612 | 4.0612 | 4.0612 | 0.0 | 97.65 Neigh | 0.030904 | 0.030904 | 0.030904 | 0.0 | 0.74 Comm | 0.045428 | 0.045428 | 0.045428 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02149 | | | 0.52 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9212.00 ave 9212 max 9212 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: 251268.0 ave 251268 max 251268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251268 Ave neighs/atom = 192.10092 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 157 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.527 | 5.527 | 5.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 157 0 -5098.6723 0 -5098.6723 194866.2 11913.022 1069 0 -5211.2103 0 -5211.2103 753.42457 13675.379 Loop time of 14.6277 on 1 procs for 912 steps with 1308 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5098.6723444049 -5211.20546859075 -5211.21026669233 Force two-norm initial, final = 2599.8570 14.481299 Force max component initial, final = 1942.5655 9.7617346 Final line search alpha, max atom move = 0.00018429197 0.0017990093 Iterations, force evaluations = 912 1021 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.065 | 14.065 | 14.065 | 0.0 | 96.15 Neigh | 0.060814 | 0.060814 | 0.060814 | 0.0 | 0.42 Comm | 0.081052 | 0.081052 | 0.081052 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4211 | | | 2.88 Nlocal: 1308.00 ave 1308 max 1308 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: 222452.0 ave 222452 max 222452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222452 Ave neighs/atom = 170.07034 Neighbor list builds = 4 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.663 | 5.663 | 5.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5211.2103 0 -5211.2103 753.42457 Loop time of 3.446e-06 on 1 procs for 0 steps with 1308 atoms 203.1% 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 | | 3.446e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8711.00 ave 8711 max 8711 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: 220500.0 ave 220500 max 220500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 220500 Ave neighs/atom = 168.57798 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.663 | 5.663 | 5.663 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 -5211.2103 -5211.2103 23.426412 123.37152 4.7317162 753.42457 753.42457 860.46107 1176.2418 223.57086 2.2943925 3504.1322 Loop time of 2.298e-06 on 1 procs for 0 steps with 1308 atoms 217.6% 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 | | 2.298e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8711.00 ave 8711 max 8711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 110250.0 ave 110250 max 110250 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 220500.0 ave 220500 max 220500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 220500 Ave neighs/atom = 168.57798 Neighbor list builds = 0 Dangerous builds = 0 1308 -5211.21026669233 eV 2.29439254125199 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19