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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -54.335845 0.0000000) to (27.167922 54.335845 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6841245 4.6841245 3.5673230 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -54.335845 0.0000000) to (27.167922 54.335845 3.5673230) create_atoms CPU = 0.002 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6841245 4.6841245 3.5673230 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -54.335845 0.0000000) to (27.167922 54.335845 3.5673230) create_atoms CPU = 0.002 seconds 466 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 39 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 928 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3605.545 0 -3605.545 64800.088 82 0 -3906.7755 0 -3906.7755 34816.716 Loop time of 10.3176 on 1 procs for 82 steps with 928 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 = -3605.54497340306 -3906.77159206067 -3906.77548758549 Force two-norm initial, final = 522.78708 0.24753374 Force max component initial, final = 150.14416 0.022026572 Final line search alpha, max atom move = 1.0000000 0.022026572 Iterations, force evaluations = 82 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.281 | 10.281 | 10.281 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018198 | 0.018198 | 0.018198 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01882 | | | 0.18 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4812.00 ave 4812 max 4812 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: 50528.0 ave 50528 max 50528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50528 Ave neighs/atom = 54.448276 Neighbor list builds = 0 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -3906.7755 0 -3906.7755 34816.716 10532.107 118 0 -3910.4971 0 -3910.4971 -81.685282 10798.716 Loop time of 2.46581 on 1 procs for 36 steps with 928 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 = -3906.7754875855 -3910.49655352843 -3910.49710844497 Force two-norm initial, final = 427.64963 2.9474271 Force max component initial, final = 318.02317 1.0105579 Final line search alpha, max atom move = 0.00012555928 0.00012688492 Iterations, force evaluations = 36 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4136 | 2.4136 | 2.4136 | 0.0 | 97.88 Neigh | 0.029319 | 0.029319 | 0.029319 | 0.0 | 1.19 Comm | 0.0050086 | 0.0050086 | 0.0050086 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01785 | | | 0.72 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4828.00 ave 4828 max 4828 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: 51832.0 ave 51832 max 51832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51832 Ave neighs/atom = 55.853448 Neighbor list builds = 3 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.700 | 4.700 | 4.700 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3910.4971 0 -3910.4971 -81.685282 Loop time of 6.806e-06 on 1 procs for 0 steps with 928 atoms 176.3% 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 | | 6.806e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4828.00 ave 4828 max 4828 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: 51984.0 ave 51984 max 51984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51984 Ave neighs/atom = 56.017241 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.700 | 4.700 | 4.700 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 -3910.4971 -3910.4971 27.097722 112.47716 3.5430313 -81.685282 -81.685282 42.16178 -138.30484 -148.91279 2.3327839 389.36988 Loop time of 7.537e-06 on 1 procs for 0 steps with 928 atoms 238.8% 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 | | 7.537e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4828.00 ave 4828 max 4828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25992.0 ave 25992 max 25992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51984.0 ave 51984 max 51984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51984 Ave neighs/atom = 56.017241 Neighbor list builds = 0 Dangerous builds = 0 928 -3910.49710844497 eV 2.33278387092208 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13