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 = 3.6800447 3.6800447 3.6800447 Created orthogonal box = (0.0000000 -44.618171 0.0000000) to (36.430584 44.618171 9.0142317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2043691 5.1599245 6.0094878 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.618171 0.0000000) to (36.430584 44.618171 9.0142317) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2043691 5.1599245 6.0094878 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.618171 0.0000000) to (36.430584 44.618171 9.0142317) create_atoms CPU = 0.002 seconds 1184 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 13 32 4 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 13 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9542.8769 0 -9542.8769 21215.862 92 0 -9972.3154 0 -9972.3154 -4504.0707 Loop time of 1.20167 on 1 procs for 92 steps with 2352 atoms 86.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9542.87691970982 -9972.30573233536 -9972.31544447065 Force two-norm initial, final = 221.79459 0.47466415 Force max component initial, final = 29.405716 0.050884732 Final line search alpha, max atom move = 1.0000000 0.050884732 Iterations, force evaluations = 92 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1592 | 1.1592 | 1.1592 | 0.0 | 96.46 Neigh | 0.013374 | 0.013374 | 0.013374 | 0.0 | 1.11 Comm | 0.010365 | 0.010365 | 0.010365 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01876 | | | 1.56 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5507.00 ave 5507 max 5507 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: 130224.0 ave 130224 max 130224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130224 Ave neighs/atom = 55.367347 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 13 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -9972.3154 0 -9972.3154 -4504.0707 29304.655 98 0 -9972.9991 0 -9972.9991 166.31961 29208.354 Loop time of 0.0496019 on 1 procs for 6 steps with 2352 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 = -9972.31544447063 -9972.99806477446 -9972.99914952396 Force two-norm initial, final = 229.93841 5.7512008 Force max component initial, final = 187.93225 4.5195505 Final line search alpha, max atom move = 0.00015146022 0.00068453213 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046187 | 0.046187 | 0.046187 | 0.0 | 93.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038262 | 0.00038262 | 0.00038262 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003032 | | | 6.11 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5486.00 ave 5486 max 5486 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: 131872.0 ave 131872 max 131872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131872 Ave neighs/atom = 56.068027 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9972.9991 0 -9972.9991 166.31961 Loop time of 2.299e-06 on 1 procs for 0 steps with 2352 atoms 174.0% 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 | | 2.299e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 132240.0 ave 132240 max 132240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132240 Ave neighs/atom = 56.224490 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.226 | 5.226 | 5.226 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 -9972.9991 -9972.9991 36.242969 89.09085 9.0458674 166.31961 166.31961 74.953962 247.50835 176.4965 2.2578691 2032.3069 Loop time of 2.394e-06 on 1 procs for 0 steps with 2352 atoms 208.9% 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 | | 2.394e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66120.0 ave 66120 max 66120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132240.0 ave 132240 max 132240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132240 Ave neighs/atom = 56.224490 Neighbor list builds = 0 Dangerous builds = 0 2352 -9972.99914952396 eV 2.25786909177965 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01