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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -53.263995 0.0000000) to (26.631997 53.263995 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0731290 4.0731290 2.8886457 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -53.263995 0.0000000) to (26.631997 53.263995 2.8886457) create_atoms CPU = 0.002 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0731290 4.0731290 2.8886457 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -53.263995 0.0000000) to (26.631997 53.263995 2.8886457) create_atoms CPU = 0.001 seconds 341 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 681 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.271 | 5.271 | 5.271 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2742.4532 0 -2742.4532 37346.577 41 0 -2836.8115 0 -2836.8115 5854.1738 Loop time of 8.96664 on 1 procs for 41 steps with 681 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 = -2742.45316128934 -2836.80888383128 -2836.81146826047 Force two-norm initial, final = 228.21292 0.17830202 Force max component initial, final = 93.822969 0.031409478 Final line search alpha, max atom move = 1.0000000 0.031409478 Iterations, force evaluations = 41 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9527 | 8.9527 | 8.9527 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071189 | 0.0071189 | 0.0071189 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006872 | | | 0.08 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4559.00 ave 4559 max 4559 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: 39384.0 ave 39384 max 39384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39384 Ave neighs/atom = 57.832599 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.271 | 5.271 | 5.271 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -2836.8115 0 -2836.8115 5854.1738 8195.2412 49 0 -2837.0465 0 -2837.0465 198.21074 8217.9779 Loop time of 1.20579 on 1 procs for 8 steps with 681 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2836.81146826047 -2837.04623898834 -2837.04650864132 Force two-norm initial, final = 78.888669 2.2638623 Force max component initial, final = 78.478649 1.5753623 Final line search alpha, max atom move = 0.00040817089 0.00064301705 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2014 | 1.2014 | 1.2014 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092733 | 0.00092733 | 0.00092733 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003429 | | | 0.28 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 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: 39332.0 ave 39332 max 39332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39332 Ave neighs/atom = 57.756241 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.409 | 5.409 | 5.409 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2837.0465 0 -2837.0465 198.21074 Loop time of 6.104e-06 on 1 procs for 0 steps with 681 atoms 163.8% 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 | | 6.104e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 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: 39326.0 ave 39326 max 39326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39326 Ave neighs/atom = 57.747430 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.409 | 5.409 | 5.409 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 -2837.0465 -2837.0465 26.644297 107.17799 2.8777635 198.21074 198.21074 307.2744 297.99279 -10.634975 2.4063846 284.49543 Loop time of 6.816e-06 on 1 procs for 0 steps with 681 atoms 278.8% 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 | | 6.816e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4549.00 ave 4549 max 4549 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19663.0 ave 19663 max 19663 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39326.0 ave 39326 max 39326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39326 Ave neighs/atom = 57.747430 Neighbor list builds = 0 Dangerous builds = 0 681 -2837.04650864132 eV 2.40638457108928 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11