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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -58.370746 0.0000000) to (29.185373 58.370746 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9390632 4.9390632 3.6200000 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.370746 0.0000000) to (29.185373 58.370746 3.6200000) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9390632 4.9390632 3.6200000 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.370746 0.0000000) to (29.185373 58.370746 3.6200000) create_atoms CPU = 0.002 seconds 522 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 34 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1042 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_262519520678_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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.018 | 5.018 | 5.018 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3522.6911 0 -3522.6911 58035.892 33 0 -3677.1217 0 -3677.1217 8609.69 Loop time of 8.84877 on 1 procs for 33 steps with 1042 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 = -3522.69111123547 -3677.11856650299 -3677.12167706643 Force two-norm initial, final = 474.10867 0.17740617 Force max component initial, final = 153.86911 0.042850240 Final line search alpha, max atom move = 1.0000000 0.042850240 Iterations, force evaluations = 33 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8134 | 8.8134 | 8.8134 | 0.0 | 99.60 Neigh | 0.017368 | 0.017368 | 0.017368 | 0.0 | 0.20 Comm | 0.0098406 | 0.0098406 | 0.0098406 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008197 | | | 0.09 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7593.00 ave 7593 max 7593 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: 138280.0 ave 138280 max 138280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138280 Ave neighs/atom = 132.70633 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.018 | 5.018 | 5.018 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -3677.1217 0 -3677.1217 8609.69 12333.861 43 0 -3677.6188 0 -3677.6188 162.99283 12408.219 Loop time of 1.94593 on 1 procs for 10 steps with 1042 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 = -3677.12167706643 -3677.61669437374 -3677.61879323006 Force two-norm initial, final = 135.54307 2.6660756 Force max component initial, final = 124.21968 2.4335510 Final line search alpha, max atom move = 0.00027711347 0.00067436976 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9188 | 1.9188 | 1.9188 | 0.0 | 98.61 Neigh | 0.017835 | 0.017835 | 0.017835 | 0.0 | 0.92 Comm | 0.0023543 | 0.0023543 | 0.0023543 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006912 | | | 0.36 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7588.00 ave 7588 max 7588 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: 138068.0 ave 138068 max 138068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138068 Ave neighs/atom = 132.50288 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.156 | 5.156 | 5.156 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3677.6188 0 -3677.6188 162.99283 Loop time of 6.395e-06 on 1 procs for 0 steps with 1042 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7583.00 ave 7583 max 7583 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: 138084.0 ave 138084 max 138084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138084 Ave neighs/atom = 132.51823 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.156 | 5.156 | 5.156 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 -3677.6188 -3677.6188 29.175699 117.797 3.6103886 162.99283 162.99283 65.510165 317.06649 106.40184 2.2887356 407.42557 Loop time of 7.076e-06 on 1 procs for 0 steps with 1042 atoms 254.4% 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 | | 7.076e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7583.00 ave 7583 max 7583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69042.0 ave 69042 max 69042 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138084.0 ave 138084 max 138084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138084 Ave neighs/atom = 132.51823 Neighbor list builds = 0 Dangerous builds = 0 1042 -3677.61879323006 eV 2.28873558631772 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12