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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.583316 0.0000000) to (21.698737 37.583316 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7101941 5.2748513 6.0968189 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.583316 0.0000000) to (21.698737 37.583316 6.0968189) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7101941 5.2748513 6.0968189 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.583316 0.0000000) to (21.698737 37.583316 6.0968189) create_atoms CPU = 0.001 seconds 458 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3982.9455 0 -3982.9455 11556.961 63 0 -4044.5975 0 -4044.5975 13428.158 Loop time of 1.47399 on 1 procs for 63 steps with 914 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 = -3982.94551895607 -4044.59356313267 -4044.59747116835 Force two-norm initial, final = 32.559800 0.21404258 Force max component initial, final = 5.2183994 0.022881627 Final line search alpha, max atom move = 1.0000000 0.022881627 Iterations, force evaluations = 63 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4313 | 1.4313 | 1.4313 | 0.0 | 97.11 Neigh | 0.028629 | 0.028629 | 0.028629 | 0.0 | 1.94 Comm | 0.0080218 | 0.0080218 | 0.0080218 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00602 | | | 0.41 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7155.00 ave 7155 max 7155 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: 226836.0 ave 226836 max 226836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226836 Ave neighs/atom = 248.17943 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -4044.5975 0 -4044.5975 13428.158 9944.0396 69 0 -4044.9927 0 -4044.9927 -42.030638 10019.427 Loop time of 0.119261 on 1 procs for 6 steps with 914 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 = -4044.59747116835 -4044.99258470382 -4044.99270492154 Force two-norm initial, final = 152.60465 0.90209299 Force max component initial, final = 112.33760 0.82756616 Final line search alpha, max atom move = 0.00044101829 0.00036497181 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11673 | 0.11673 | 0.11673 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049202 | 0.00049202 | 0.00049202 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002036 | | | 1.71 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7133.00 ave 7133 max 7133 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: 227060.0 ave 227060 max 227060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227060 Ave neighs/atom = 248.42451 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.555 | 5.555 | 5.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4044.9927 0 -4044.9927 -42.030638 Loop time of 1.864e-06 on 1 procs for 0 steps with 914 atoms 160.9% 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 | | 1.864e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7121.00 ave 7121 max 7121 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: 226600.0 ave 226600 max 226600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226600 Ave neighs/atom = 247.92123 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.555 | 5.555 | 5.555 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 -4044.9927 -4044.9927 21.763828 75.515439 6.0963775 -42.030638 -42.030638 -132.73059 6.6287915 0.009881229 2.2297053 621.85836 Loop time of 2.111e-06 on 1 procs for 0 steps with 914 atoms 189.5% 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 | | 2.111e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7121.00 ave 7121 max 7121 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113300.0 ave 113300 max 113300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226600.0 ave 226600 max 226600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226600 Ave neighs/atom = 247.92123 Neighbor list builds = 0 Dangerous builds = 0 914 -4024.3823246807 eV 2.22970526812619 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02