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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -51.513942 0.0000000) to (12.140999 51.513942 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7449993 5.7233217 5.7233217 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -51.513942 0.0000000) to (12.140999 51.513942 5.7233217) create_atoms CPU = 0.001 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7449993 5.7233217 5.7233217 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -51.513942 0.0000000) to (12.140999 51.513942 5.7233217) create_atoms CPU = 0.000 seconds 218 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 432 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_958395190627_001#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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1424.7447 0 -1424.7447 14095.469 47 0 -1448.0431 0 -1448.0431 2782.4491 Loop time of 1.66436 on 1 procs for 47 steps with 432 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1424.74467674042 -1448.04168326972 -1448.04308995666 Force two-norm initial, final = 30.448873 0.10836957 Force max component initial, final = 8.0127579 0.013837054 Final line search alpha, max atom move = 1.0000000 0.013837054 Iterations, force evaluations = 47 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.657 | 1.657 | 1.657 | 0.0 | 99.56 Neigh | 0.0026446 | 0.0026446 | 0.0026446 | 0.0 | 0.16 Comm | 0.0024733 | 0.0024733 | 0.0024733 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002216 | | | 0.13 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3038.00 ave 3038 max 3038 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: 37008.0 ave 37008 max 37008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37008 Ave neighs/atom = 85.666667 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1448.0431 0 -1448.0431 2782.4491 7159.0822 49 0 -1448.0517 0 -1448.0517 1097.7046 7174.3703 Loop time of 0.0782988 on 1 procs for 2 steps with 432 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 = -1448.04308995666 -1448.05127676941 -1448.05174736029 Force two-norm initial, final = 11.484832 1.1220861 Force max component initial, final = 9.4364214 1.1139913 Final line search alpha, max atom move = 0.00043710706 0.00048693345 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077833 | 0.077833 | 0.077833 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.3353e-05 | 9.3353e-05 | 9.3353e-05 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003729 | | | 0.48 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3040.00 ave 3040 max 3040 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: 37032.0 ave 37032 max 37032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37032 Ave neighs/atom = 85.722222 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1448.0517 0 -1448.0517 1097.7046 Loop time of 1.838e-06 on 1 procs for 0 steps with 432 atoms 163.2% 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 | | 1.838e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3027.00 ave 3027 max 3027 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: 37020.0 ave 37020 max 37020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37020 Ave neighs/atom = 85.694444 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.626 | 4.626 | 4.626 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 -1448.0517 -1448.0517 12.149802 103.02788 5.7313881 1097.7046 1097.7046 -248.95631 3525.5298 16.540266 2.5401588 316.17118 Loop time of 1.534e-06 on 1 procs for 0 steps with 432 atoms 195.6% 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 | | 1.534e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3027.00 ave 3027 max 3027 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18510.0 ave 18510 max 18510 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37020.0 ave 37020 max 37020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37020 Ave neighs/atom = 85.694444 Neighbor list builds = 0 Dangerous builds = 0 432 -1448.05174736029 eV 2.54015878160601 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02