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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -65.015230 0.0000000) to (32.507615 65.015230 4.0320734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5012887 5.5012887 4.0320734 Created 519 atoms using lattice units in orthogonal box = (0.0000000 -65.015230 0.0000000) to (32.507615 65.015230 4.0320734) create_atoms CPU = 0.003 seconds 519 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5012887 5.5012887 4.0320734 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -65.015230 0.0000000) to (32.507615 65.015230 4.0320734) create_atoms CPU = 0.002 seconds 521 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 34 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1040 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3421.1492 0 -3421.1492 9907.2605 67 0 -3486.398 0 -3486.398 3958.7971 Loop time of 1.85341 on 1 procs for 67 steps with 1040 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 = -3421.14919503272 -3486.39523991091 -3486.3980112271 Force two-norm initial, final = 44.026832 0.14725616 Force max component initial, final = 7.7032251 0.049937772 Final line search alpha, max atom move = 1.0000000 0.049937772 Iterations, force evaluations = 67 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7768 | 1.7768 | 1.7768 | 0.0 | 95.87 Neigh | 0.037114 | 0.037114 | 0.037114 | 0.0 | 2.00 Comm | 0.022132 | 0.022132 | 0.022132 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01735 | | | 0.94 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7112.00 ave 7112 max 7112 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: 136954.0 ave 136954 max 136954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136954 Ave neighs/atom = 131.68654 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -3486.398 0 -3486.398 3958.7971 17043.494 76 0 -3486.7262 0 -3486.7262 34.414045 17124.798 Loop time of 0.187257 on 1 procs for 9 steps with 1040 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 = -3486.3980112271 -3486.72616970626 -3486.72620926767 Force two-norm initial, final = 93.419270 0.81672848 Force max component initial, final = 88.007826 0.62931113 Final line search alpha, max atom move = 0.0010938349 0.00068836249 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16265 | 0.16265 | 0.16265 | 0.0 | 86.86 Neigh | 0.016461 | 0.016461 | 0.016461 | 0.0 | 8.79 Comm | 0.0020678 | 0.0020678 | 0.0020678 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006077 | | | 3.25 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6654.00 ave 6654 max 6654 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: 137032.0 ave 137032 max 137032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137032 Ave neighs/atom = 131.76154 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.146 | 5.146 | 5.146 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3486.7262 0 -3486.7262 34.414045 Loop time of 6.856e-06 on 1 procs for 0 steps with 1040 atoms 160.4% 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 | | 6.856e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6654.00 ave 6654 max 6654 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: 137034.0 ave 137034 max 137034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137034 Ave neighs/atom = 131.76346 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.146 | 5.146 | 5.146 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 -3486.7262 -3486.7262 32.418364 131.06051 4.0305331 34.414045 34.414045 58.71598 34.514108 10.012047 2.5937309 590.18107 Loop time of 7.297e-06 on 1 procs for 0 steps with 1040 atoms 191.9% 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 | | 7.297e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6654.00 ave 6654 max 6654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68517.0 ave 68517 max 68517 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137034.0 ave 137034 max 137034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137034 Ave neighs/atom = 131.76346 Neighbor list builds = 0 Dangerous builds = 0 1040 -3486.72620926767 eV 2.59373085011153 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02