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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -46.698090 0.0000000) to (28.596623 46.698090 8.6222063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1993860 5.3066012 5.7481376 Created 1045 atoms using lattice units in orthogonal box = (0.0000000 -46.698090 0.0000000) to (28.596623 46.698090 8.6222063) create_atoms CPU = 0.002 seconds 1045 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1993860 5.3066012 5.7481376 Created 1069 atoms using lattice units in orthogonal box = (0.0000000 -46.698090 0.0000000) to (28.596623 46.698090 8.6222063) create_atoms CPU = 0.002 seconds 1069 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 25 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2110 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.037 | 6.037 | 6.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9254.9766 0 -9254.9766 27106.892 41 0 -9374.0468 0 -9374.0468 4449.0322 Loop time of 1.39284 on 1 procs for 41 steps with 2110 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 = -9254.97659579762 -9374.0385950466 -9374.0468217287 Force two-norm initial, final = 124.86263 0.26459062 Force max component initial, final = 10.905824 0.024016660 Final line search alpha, max atom move = 1.0000000 0.024016660 Iterations, force evaluations = 41 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3795 | 1.3795 | 1.3795 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058562 | 0.0058562 | 0.0058562 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007534 | | | 0.54 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8599.00 ave 8599 max 8599 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: 369568.0 ave 369568 max 369568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369568 Ave neighs/atom = 175.15071 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.035 | 6.035 | 6.035 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -9374.0468 0 -9374.0468 4449.0322 23028.321 46 0 -9374.3287 0 -9374.3287 -36.003252 23085.385 Loop time of 0.123057 on 1 procs for 5 steps with 2110 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 = -9374.0468217287 -9374.32818641287 -9374.32870455074 Force two-norm initial, final = 149.68740 2.2149718 Force max component initial, final = 146.15711 1.9954121 Final line search alpha, max atom move = 0.00014855616 0.00029643076 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12017 | 0.12017 | 0.12017 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044456 | 0.00044456 | 0.00044456 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002443 | | | 1.99 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8332.00 ave 8332 max 8332 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: 368416.0 ave 368416 max 368416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368416 Ave neighs/atom = 174.60474 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.173 | 6.173 | 6.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9374.3287 0 -9374.3287 -36.003252 Loop time of 2.076e-06 on 1 procs for 0 steps with 2110 atoms 144.5% 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 | | 2.076e-06 | | |100.00 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8332.00 ave 8332 max 8332 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: 368416.0 ave 368416 max 368416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368416 Ave neighs/atom = 174.60474 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.173 | 6.173 | 6.173 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 -9374.3287 -9374.3287 28.569821 93.778864 8.6163757 -36.003252 -36.003252 -138.3562 56.391617 -26.045178 2.3570369 694.10165 Loop time of 1.956e-06 on 1 procs for 0 steps with 2110 atoms 255.6% 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 | | 1.956e-06 | | |100.00 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8332.00 ave 8332 max 8332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184208.0 ave 184208 max 184208 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368416.0 ave 368416 max 368416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368416 Ave neighs/atom = 174.60474 Neighbor list builds = 0 Dangerous builds = 0 2110 -9297.41452762539 eV 2.3570368821547 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02