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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -44.620489 0.0000000) to (14.873496 44.620489 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3745577 4.3745577 3.6073527 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.620489 0.0000000) to (14.873496 44.620489 3.6073527) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3745577 4.3745577 3.6073527 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.620489 0.0000000) to (14.873496 44.620489 3.6073527) create_atoms CPU = 0.000 seconds 206 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.362 | 5.362 | 5.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1384.0102 0 -1384.0102 26971.633 49 0 -1431.2731 0 -1431.2731 7637.7337 Loop time of 1.27577 on 1 procs for 49 steps with 408 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1384.01019555494 -1431.2719345563 -1431.27307635359 Force two-norm initial, final = 101.92541 0.12099705 Force max component initial, final = 32.305149 0.017745081 Final line search alpha, max atom move = 1.0000000 0.017745081 Iterations, force evaluations = 49 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.248 | 1.248 | 1.248 | 0.0 | 97.82 Neigh | 0.013187 | 0.013187 | 0.013187 | 0.0 | 1.03 Comm | 0.010351 | 0.010351 | 0.010351 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004248 | | | 0.33 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9845.00 ave 9845 max 9845 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: 256676.0 ave 256676 max 256676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256676 Ave neighs/atom = 629.10784 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.362 | 5.362 | 5.362 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1431.2731 0 -1431.2731 7637.7337 4788.1307 55 0 -1431.3676 0 -1431.3676 -209.22359 4815.0894 Loop time of 0.104385 on 1 procs for 6 steps with 408 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1431.2730763536 -1431.36710352027 -1431.36761929602 Force two-norm initial, final = 41.807270 1.6407644 Force max component initial, final = 32.964624 1.1892702 Final line search alpha, max atom move = 0.00035308468 0.00041991309 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10135 | 0.10135 | 0.10135 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059394 | 0.00059394 | 0.00059394 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002444 | | | 2.34 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9762.00 ave 9762 max 9762 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: 256032.0 ave 256032 max 256032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256032 Ave neighs/atom = 627.52941 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.500 | 5.500 | 5.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1431.3676 0 -1431.3676 -209.22359 Loop time of 2.113e-06 on 1 procs for 0 steps with 408 atoms 189.3% 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 | | 2.113e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9762.00 ave 9762 max 9762 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: 255184.0 ave 255184 max 255184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255184 Ave neighs/atom = 625.45098 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.500 | 5.500 | 5.500 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 -1431.3676 -1431.3676 14.859512 89.708061 3.6121714 -209.22359 -209.22359 -395.3466 118.08325 -350.40742 2.2907631 199.51057 Loop time of 2.541e-06 on 1 procs for 0 steps with 408 atoms 196.8% 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 | | 2.541e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9762.00 ave 9762 max 9762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127592.0 ave 127592 max 127592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255184.0 ave 255184 max 255184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255184 Ave neighs/atom = 625.45098 Neighbor list builds = 0 Dangerous builds = 0 408 -1431.36761929602 eV 2.29076305063844 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01