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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -37.815598 0.0000000) to (23.155484 37.815598 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2100880 4.2969031 4.6544275 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -37.815598 0.0000000) to (23.155484 37.815598 6.9816412) create_atoms CPU = 0.001 seconds 531 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2100880 4.2969031 4.6544275 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -37.815598 0.0000000) to (23.155484 37.815598 6.9816412) create_atoms CPU = 0.001 seconds 531 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1050 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4367.9936 0 -4367.9936 35614.362 58 0 -4482.7443 0 -4482.7443 -1568.7572 Loop time of 5.93046 on 1 procs for 58 steps with 1050 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 = -4367.9935630185 -4482.7398578231 -4482.74432634151 Force two-norm initial, final = 226.21334 0.21208882 Force max component initial, final = 43.913757 0.042182847 Final line search alpha, max atom move = 1.0000000 0.042182847 Iterations, force evaluations = 58 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9026 | 5.9026 | 5.9026 | 0.0 | 99.53 Neigh | 0.018354 | 0.018354 | 0.018354 | 0.0 | 0.31 Comm | 0.004187 | 0.004187 | 0.004187 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005336 | | | 0.09 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3928.00 ave 3928 max 3928 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: 68278.0 ave 68278 max 68278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68278 Ave neighs/atom = 65.026667 Neighbor list builds = 3 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -4482.7443 0 -4482.7443 -1568.7572 12226.787 60 0 -4482.7858 0 -4482.7858 2385.4473 12197.555 Loop time of 0.23975 on 1 procs for 2 steps with 1050 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 = -4482.74432634151 -4482.78457891154 -4482.785849249 Force two-norm initial, final = 49.024743 0.69134098 Force max component initial, final = 35.069953 0.50193864 Final line search alpha, max atom move = 0.00014884833 7.4712730e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23906 | 0.23906 | 0.23906 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011886 | 0.00011886 | 0.00011886 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005697 | | | 0.24 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3898.00 ave 3898 max 3898 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: 68120.0 ave 68120 max 68120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68120 Ave neighs/atom = 64.876190 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.706 | 4.706 | 4.706 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4482.7858 0 -4482.7858 2385.4473 Loop time of 1.481e-06 on 1 procs for 0 steps with 1050 atoms 202.6% 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 | | 1.481e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3904.00 ave 3904 max 3904 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: 68176.0 ave 68176 max 68176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68176 Ave neighs/atom = 64.929524 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.706 | 4.706 | 4.706 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 -4482.7858 -4482.7858 23.126947 75.631195 6.9735433 2385.4473 2385.4473 -55.347794 7145.8354 65.854309 2.2554 818.79633 Loop time of 1.614e-06 on 1 procs for 0 steps with 1050 atoms 123.9% 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 | | 1.614e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3904.00 ave 3904 max 3904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34088.0 ave 34088 max 34088 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68176.0 ave 68176 max 68176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68176 Ave neighs/atom = 64.929524 Neighbor list builds = 0 Dangerous builds = 0 1050 -4482.785849249 eV 2.25539996958599 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06