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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -42.136186 0.0000000) to (21.068093 42.136186 3.6131481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9571983 4.9571983 3.6131481 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.136186 0.0000000) to (21.068093 42.136186 3.6131481) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9571983 4.9571983 3.6131481 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.136186 0.0000000) to (21.068093 42.136186 3.6131481) create_atoms CPU = 0.000 seconds 274 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 17 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_173787283511_004#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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 5.347 | 5.347 | 5.347 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1715.7982 0 -1715.7982 51426.765 60 0 -1887.2924 0 -1887.2924 5827.7644 Loop time of 1.07043 on 1 procs for 60 steps with 544 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1715.79818450116 -1887.29119267261 -1887.29239750446 Force two-norm initial, final = 301.68626 0.13572541 Force max component initial, final = 84.598787 0.014132235 Final line search alpha, max atom move = 1.0000000 0.014132235 Iterations, force evaluations = 60 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0454 | 1.0454 | 1.0454 | 0.0 | 97.67 Neigh | 0.010506 | 0.010506 | 0.010506 | 0.0 | 0.98 Comm | 0.0094098 | 0.0094098 | 0.0094098 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005067 | | | 0.47 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8906.00 ave 8906 max 8906 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: 210536.0 ave 210536 max 210536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210536 Ave neighs/atom = 387.01471 Neighbor list builds = 1 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.347 | 5.347 | 5.347 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1887.2924 0 -1887.2924 5827.7644 6414.9933 68 0 -1887.4581 0 -1887.4581 100.18798 6442.601 Loop time of 0.103527 on 1 procs for 8 steps with 544 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 = -1887.29239750446 -1887.4579819702 -1887.45812197012 Force two-norm initial, final = 52.499051 1.1133947 Force max component initial, final = 38.805799 1.0415101 Final line search alpha, max atom move = 0.00075452566 0.00078584610 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099306 | 0.099306 | 0.099306 | 0.0 | 95.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007919 | 0.0007919 | 0.0007919 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00343 | | | 3.31 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8885.00 ave 8885 max 8885 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: 208800.0 ave 208800 max 208800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208800 Ave neighs/atom = 383.82353 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 5.485 | 5.485 | 5.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1887.4581 0 -1887.4581 100.18798 Loop time of 1.941e-06 on 1 procs for 0 steps with 544 atoms 206.1% 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 | | 1.941e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8920.00 ave 8920 max 8920 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: 208212.0 ave 208212 max 208212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208212 Ave neighs/atom = 382.74265 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 5.485 | 5.485 | 5.485 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 -1887.4581 -1887.4581 20.98101 84.42025 3.6373761 100.18798 100.18798 9.4589433 30.360561 260.74443 2.2794662 233.75935 Loop time of 2.434e-06 on 1 procs for 0 steps with 544 atoms 287.6% 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 | | 2.434e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8920.00 ave 8920 max 8920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104106.0 ave 104106 max 104106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208212.0 ave 208212 max 208212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208212 Ave neighs/atom = 382.74265 Neighbor list builds = 0 Dangerous builds = 0 544 -1887.45812197012 eV 2.27946621142016 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01