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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -47.817020 0.0000000) to (29.281825 47.817020 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3239682 5.4337523 5.8858683 Created 1048 atoms using lattice units in orthogonal box = (0.0000000 -47.817020 0.0000000) to (29.281825 47.817020 8.8288024) create_atoms CPU = 0.002 seconds 1048 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3239682 5.4337523 5.8858683 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -47.817020 0.0000000) to (29.281825 47.817020 8.8288024) create_atoms CPU = 0.002 seconds 1072 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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2112 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_492310898779_001#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 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.102 | 5.102 | 5.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8948.2595 0 -8948.2595 2776.4034 33 0 -8958.9113 0 -8958.9113 1155.2583 Loop time of 4.88238 on 1 procs for 33 steps with 2112 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8948.25948166062 -8958.90471433404 -8958.91129054277 Force two-norm initial, final = 14.492424 0.18949992 Force max component initial, final = 1.5477446 0.023262134 Final line search alpha, max atom move = 1.0000000 0.023262134 Iterations, force evaluations = 33 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8681 | 4.8681 | 4.8681 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057294 | 0.0057294 | 0.0057294 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008547 | | | 0.18 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5979.00 ave 5979 max 5979 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: 164544.0 ave 164544 max 164544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164544 Ave neighs/atom = 77.909091 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -8958.9113 0 -8958.9113 1155.2583 24723.642 39 0 -8959.1737 0 -8959.1737 -1.3732095 24740.638 Loop time of 0.595958 on 1 procs for 6 steps with 2112 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 = -8958.91129054279 -8959.17347762534 -8959.17371464392 Force two-norm initial, final = 91.420284 0.28116570 Force max component initial, final = 85.929568 0.035608053 Final line search alpha, max atom move = 0.00019233808 6.8487844e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59235 | 0.59235 | 0.59235 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051182 | 0.00051182 | 0.00051182 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003101 | | | 0.52 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5956.00 ave 5956 max 5956 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: 164080.0 ave 164080 max 164080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164080 Ave neighs/atom = 77.689394 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 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8959.1737 0 -8959.1737 -1.3732095 Loop time of 2.159e-06 on 1 procs for 0 steps with 2112 atoms 185.3% 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 | | 2.159e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5966.00 ave 5966 max 5966 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: 164016.0 ave 164016 max 164016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164016 Ave neighs/atom = 77.659091 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 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.245 | 5.245 | 5.245 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 -8959.1737 -8959.1737 29.187723 96.104178 8.8199963 -1.3732095 -1.3732095 -1.7307516 -1.1422049 -1.2466719 2.4352279 474.39894 Loop time of 2.588e-06 on 1 procs for 0 steps with 2112 atoms 231.8% 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 | | 2.588e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5966.00 ave 5966 max 5966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82008.0 ave 82008 max 82008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164016.0 ave 164016 max 164016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164016 Ave neighs/atom = 77.659091 Neighbor list builds = 0 Dangerous builds = 0 2112 -8959.17371464392 eV 2.43522785534288 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06