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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -43.439990 0.0000000) to (21.719995 43.439990 4.0333018) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2427575 5.2427575 4.0333018 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -43.439990 0.0000000) to (21.719995 43.439990 4.0333018) create_atoms CPU = 0.001 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2427575 5.2427575 4.0333018 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.439990 0.0000000) to (21.719995 43.439990 4.0333018) create_atoms CPU = 0.000 seconds 233 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 463 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1447.4795 0 -1447.4795 36386.879 108 0 -1553.7876 0 -1553.7876 4845.2204 Loop time of 1.02394 on 1 procs for 108 steps with 463 atoms 95.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1447.47954818474 -1553.78656291748 -1553.78762128638 Force two-norm initial, final = 212.04972 0.084660616 Force max component initial, final = 59.218074 0.027694824 Final line search alpha, max atom move = 1.0000000 0.027694824 Iterations, force evaluations = 108 196 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99546 | 0.99546 | 0.99546 | 0.0 | 97.22 Neigh | 0.0093312 | 0.0093312 | 0.0093312 | 0.0 | 0.91 Comm | 0.011821 | 0.011821 | 0.011821 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007324 | | | 0.72 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4959.00 ave 4959 max 4959 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: 67738.0 ave 67738 max 67738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67738 Ave neighs/atom = 146.30238 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -1553.7876 0 -1553.7876 4845.2204 7610.9727 117 0 -1553.9407 0 -1553.9407 85.19747 7654.5918 Loop time of 0.0525078 on 1 procs for 9 steps with 463 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 = -1553.78762128636 -1553.94053888544 -1553.9406755438 Force two-norm initial, final = 46.068685 0.75992206 Force max component initial, final = 41.843273 0.54403233 Final line search alpha, max atom move = 0.0013988005 0.00076099273 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.050142 | 0.050142 | 0.050142 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049529 | 0.00049529 | 0.00049529 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001871 | | | 3.56 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4971.00 ave 4971 max 4971 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: 66802.0 ave 66802 max 66802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66802 Ave neighs/atom = 144.28078 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1553.9407 0 -1553.9407 85.19747 Loop time of 2.071e-06 on 1 procs for 0 steps with 463 atoms 144.9% 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 | | 2.071e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4977.00 ave 4977 max 4977 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: 65734.0 ave 65734 max 65734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65734 Ave neighs/atom = 141.97408 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.633 | 4.633 | 4.633 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 -1553.9407 -1553.9407 21.705269 87.588223 4.0263464 85.19747 85.19747 81.535828 114.79925 59.257337 2.5720983 371.9396 Loop time of 1.914e-06 on 1 procs for 0 steps with 463 atoms 209.0% 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 | | 1.914e-06 | | |100.00 Nlocal: 463.000 ave 463 max 463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4977.00 ave 4977 max 4977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32867.0 ave 32867 max 32867 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65734.0 ave 65734 max 65734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65734 Ave neighs/atom = 141.97408 Neighbor list builds = 0 Dangerous builds = 0 463 -1553.9406755438 eV 2.57209833386597 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01