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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -40.075379 0.0000000) to (8.1803525 40.075379 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9082115 5.3433839 5.9740848 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -40.075379 0.0000000) to (8.1803525 40.075379 8.9611272) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9082115 5.3433839 5.9740848 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -40.075379 0.0000000) to (8.1803525 40.075379 8.9611272) create_atoms CPU = 0.001 seconds 242 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 = 3 22 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 0 atoms, new total = 482 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 = 3 22 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1780.672 0 -1780.672 96836.255 224 0 -1932.6261 0 -1932.6261 -76192.957 Loop time of 1.63227 on 1 procs for 224 steps with 482 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1780.67195962746 -1932.6246169571 -1932.62610209939 Force two-norm initial, final = 328.49942 0.099333071 Force max component initial, final = 100.93621 0.012459767 Final line search alpha, max atom move = 1.0000000 0.012459767 Iterations, force evaluations = 224 438 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5985 | 1.5985 | 1.5985 | 0.0 | 97.93 Neigh | 0.0099358 | 0.0099358 | 0.0099358 | 0.0 | 0.61 Comm | 0.01363 | 0.01363 | 0.01363 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01017 | | | 0.62 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3987.00 ave 3987 max 3987 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: 71472.0 ave 71472 max 71472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71472 Ave neighs/atom = 148.28216 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 22 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 : 224 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press Volume 224 0 -1932.6261 0 -1932.6261 -76192.957 5875.4657 267 0 -1941.608 0 -1941.608 4.6703343 5561.3809 Loop time of 0.195842 on 1 procs for 43 steps with 482 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 = -1932.62610209939 -1941.60728838486 -1941.60803920981 Force two-norm initial, final = 490.63737 2.0329401 Force max component initial, final = 312.95542 0.96396911 Final line search alpha, max atom move = 0.00039603672 0.00038176717 Iterations, force evaluations = 43 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18771 | 0.18771 | 0.18771 | 0.0 | 95.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014342 | 0.0014342 | 0.0014342 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006696 | | | 3.42 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3993.00 ave 3993 max 3993 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: 71452.0 ave 71452 max 71452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71452 Ave neighs/atom = 148.24066 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 = 3 22 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) = 4.657 | 4.657 | 4.657 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1941.608 0 -1941.608 4.6703343 Loop time of 1.503e-06 on 1 procs for 0 steps with 482 atoms 133.1% 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 | | 1.503e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4061.00 ave 4061 max 4061 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: 77192.0 ave 77192 max 77192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77192 Ave neighs/atom = 160.14938 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 = 3 22 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) = 4.657 | 4.657 | 4.657 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 -1941.608 -1941.608 7.9958263 79.943257 8.7003647 4.6703343 4.6703343 -13.566618 -242.05079 269.62841 2.2900463 2073.6382 Loop time of 1.486e-06 on 1 procs for 0 steps with 482 atoms 134.6% 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 | | 1.486e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4061.00 ave 4061 max 4061 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38596.0 ave 38596 max 38596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77192.0 ave 77192 max 77192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77192 Ave neighs/atom = 160.14938 Neighbor list builds = 0 Dangerous builds = 0 482 -1941.60803920981 eV 2.29004627951126 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02