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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -44.780549 0.0000000) to (14.925643 44.780549 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3898950 4.3898950 3.6200001 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.780549 0.0000000) to (14.925643 44.780549 3.6200001) create_atoms CPU = 0.001 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3898950 4.3898950 3.6200001 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.780549 0.0000000) to (14.925643 44.780549 3.6200001) create_atoms CPU = 0.000 seconds 206 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 402 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1406.6519 0 -1406.6519 195.1469 124 0 -1417.7492 0 -1417.7492 -11965.569 Loop time of 0.90999 on 1 procs for 124 steps with 402 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1406.65190491945 -1417.74806562892 -1417.74915164135 Force two-norm initial, final = 17.381754 0.11459093 Force max component initial, final = 5.5597727 0.017274261 Final line search alpha, max atom move = 1.0000000 0.017274261 Iterations, force evaluations = 124 238 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89239 | 0.89239 | 0.89239 | 0.0 | 98.07 Neigh | 0.0041462 | 0.0041462 | 0.0041462 | 0.0 | 0.46 Comm | 0.0083962 | 0.0083962 | 0.0083962 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005058 | | | 0.56 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4857.00 ave 4857 max 4857 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: 69500.0 ave 69500 max 69500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69500 Ave neighs/atom = 172.88557 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 124 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 124 0 -1417.7492 0 -1417.7492 -11965.569 4839.0603 130 0 -1417.9158 0 -1417.9158 -396.88974 4796.4839 Loop time of 0.0351367 on 1 procs for 6 steps with 402 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 = -1417.74915164135 -1417.91491273026 -1417.91579907295 Force two-norm initial, final = 53.143474 0.15347087 Force max component initial, final = 38.416857 0.031580504 Final line search alpha, max atom move = 0.00081809249 2.5835774e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033652 | 0.033652 | 0.033652 | 0.0 | 95.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030715 | 0.00030715 | 0.00030715 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001177 | | | 3.35 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4878.00 ave 4878 max 4878 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: 69728.0 ave 69728 max 69728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69728 Ave neighs/atom = 173.45274 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1417.9158 0 -1417.9158 -396.88974 Loop time of 1.699e-06 on 1 procs for 0 steps with 402 atoms 117.7% 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 | | 1.699e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4906.00 ave 4906 max 4906 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: 69740.0 ave 69740 max 69740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69740 Ave neighs/atom = 173.48259 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.629 | 4.629 | 4.629 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 -1417.9158 -1417.9158 14.876522 89.561097 3.5999973 -396.88974 -396.88974 -3.8930383 -1189.6588 2.8825958 2.3796524 208.74473 Loop time of 1.39e-06 on 1 procs for 0 steps with 402 atoms 215.8% 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 | | 1.39e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4906.00 ave 4906 max 4906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34870.0 ave 34870 max 34870 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69740.0 ave 69740 max 69740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69740 Ave neighs/atom = 173.48259 Neighbor list builds = 0 Dangerous builds = 0 402 -1417.91579907295 eV 2.37965238803285 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01