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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -29.893602 0.0000000) to (36.612035 29.893602 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6597136 4.3481602 4.6544275 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -29.893602 0.0000000) to (36.612035 29.893602 6.9816412) create_atoms CPU = 0.001 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6597136 4.3481602 4.6544275 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -29.893602 0.0000000) to (36.612035 29.893602 6.9816412) create_atoms CPU = 0.001 seconds 662 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 20 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1310 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3924.6992 0 -3924.6992 236901.93 56 0 -5586.2425 0 -5586.2425 -2240.7088 Loop time of 6.59192 on 1 procs for 56 steps with 1310 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 = -3924.69922400159 -5586.23724839238 -5586.24252193339 Force two-norm initial, final = 2467.9847 0.22539184 Force max component initial, final = 413.79573 0.061613678 Final line search alpha, max atom move = 1.0000000 0.061613678 Iterations, force evaluations = 56 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5624 | 6.5624 | 6.5624 | 0.0 | 99.55 Neigh | 0.01723 | 0.01723 | 0.01723 | 0.0 | 0.26 Comm | 0.0047734 | 0.0047734 | 0.0047734 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007487 | | | 0.11 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4621.00 ave 4621 max 4621 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: 86296.0 ave 86296 max 86296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86296 Ave neighs/atom = 65.874809 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -5586.2425 0 -5586.2425 -2240.7088 15282.332 60 0 -5586.3259 0 -5586.3259 3.8199388 15261.419 Loop time of 0.577344 on 1 procs for 4 steps with 1310 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 = -5586.24252193343 -5586.32533126181 -5586.32586375904 Force two-norm initial, final = 60.255249 0.69460370 Force max component initial, final = 57.387560 0.48217537 Final line search alpha, max atom move = 0.00016557366 7.9835539e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5754 | 0.5754 | 0.5754 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027025 | 0.00027025 | 0.00027025 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001669 | | | 0.29 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4621.00 ave 4621 max 4621 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: 86316.0 ave 86316 max 86316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86316 Ave neighs/atom = 65.890076 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.784 | 4.784 | 4.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5586.3259 0 -5586.3259 3.8199388 Loop time of 1.981e-06 on 1 procs for 0 steps with 1310 atoms 201.9% 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 | | 1.981e-06 | | |100.00 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4621.00 ave 4621 max 4621 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: 86328.0 ave 86328 max 86328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86328 Ave neighs/atom = 65.899237 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.784 | 4.784 | 4.784 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 -5586.3259 -5586.3259 36.602567 59.875954 6.9635534 3.8199388 3.8199388 -50.606715 29.253706 32.812826 2.2115115 1898.3322 Loop time of 2.534e-06 on 1 procs for 0 steps with 1310 atoms 236.8% 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 | | 2.534e-06 | | |100.00 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4621.00 ave 4621 max 4621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43164.0 ave 43164 max 43164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86328.0 ave 86328 max 86328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86328 Ave neighs/atom = 65.899237 Neighbor list builds = 0 Dangerous builds = 0 1310 -5586.32586375904 eV 2.21151149867817 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07