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 -46.158119 0.0000000) to (32.638719 46.158119 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5724642 6.1919427 5.0973115 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.158119 0.0000000) to (32.638719 46.158119 5.0973115) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5724642 6.1919427 5.0973115 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.158119 0.0000000) to (32.638719 46.158119 5.0973115) create_atoms CPU = 0.001 seconds 660 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 = 11 31 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, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1316 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 = 11 31 2 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) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4589.4749 0 -4589.4749 176260.47 378 0 -5624.0339 0 -5624.0339 -9187.4635 Loop time of 29.386 on 1 procs for 378 steps with 1316 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 = -4589.47491942622 -5624.02831800809 -5624.03385216041 Force two-norm initial, final = 2026.8802 0.19997888 Force max component initial, final = 499.06079 0.011602935 Final line search alpha, max atom move = 1.0000000 0.011602935 Iterations, force evaluations = 378 663 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.174 | 29.174 | 29.174 | 0.0 | 99.28 Neigh | 0.1291 | 0.1291 | 0.1291 | 0.0 | 0.44 Comm | 0.041216 | 0.041216 | 0.041216 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04124 | | | 0.14 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5589.00 ave 5589 max 5589 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: 84224.0 ave 84224 max 84224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84224 Ave neighs/atom = 64.000000 Neighbor list builds = 18 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 = 11 31 2 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 : 378 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press Volume 378 0 -5624.0339 0 -5624.0339 -9187.4635 15358.626 411 0 -5637.9659 0 -5637.9659 14.815952 15253.77 Loop time of 1.67393 on 1 procs for 33 steps with 1316 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 = -5624.03385216041 -5637.96544782455 -5637.96591590112 Force two-norm initial, final = 739.03699 0.31592505 Force max component initial, final = 677.70276 0.16728819 Final line search alpha, max atom move = 0.00027153645 4.5424841e-05 Iterations, force evaluations = 33 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6559 | 1.6559 | 1.6559 | 0.0 | 98.92 Neigh | 0.007098 | 0.007098 | 0.007098 | 0.0 | 0.42 Comm | 0.0018037 | 0.0018037 | 0.0018037 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009126 | | | 0.55 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5733.00 ave 5733 max 5733 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: 84224.0 ave 84224 max 84224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84224 Ave neighs/atom = 64.000000 Neighbor list builds = 1 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 = 11 32 2 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) = 4.795 | 4.795 | 4.795 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5637.9659 0 -5637.9659 14.815952 Loop time of 1.575e-06 on 1 procs for 0 steps with 1316 atoms 190.5% 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 | | 1.575e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5768.00 ave 5768 max 5768 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: 84224.0 ave 84224 max 84224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84224 Ave neighs/atom = 64.000000 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 = 11 32 2 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) = 4.795 | 4.795 | 4.795 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 -5637.9659 -5637.9659 32.907248 93.908588 4.9360588 14.815952 14.815952 13.249184 14.183451 17.015221 2.4522705 0.076188889 Loop time of 1.683e-06 on 1 procs for 0 steps with 1316 atoms 118.8% 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 | | 1.683e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5768.00 ave 5768 max 5768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42112.0 ave 42112 max 42112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84224.0 ave 84224 max 84224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84224 Ave neighs/atom = 64.000000 Neighbor list builds = 0 Dangerous builds = 0 1316 -5637.96591590112 eV 2.45227048671679 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31