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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -70.629392 0.0000000) to (43.251493 70.629392 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0018733 5.0449566 5.8254141 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -70.629392 0.0000000) to (43.251493 70.629392 8.7381211) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0018733 5.0449566 5.8254141 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -70.629392 0.0000000) to (43.251493 70.629392 8.7381211) create_atoms CPU = 0.003 seconds 2358 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 4680 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.784 | 5.784 | 5.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19128.887 0 -19128.887 22049.106 116 0 -19733.197 0 -19733.197 31320.935 Loop time of 24.4785 on 1 procs for 116 steps with 4680 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19128.8866497178 -19733.1817044515 -19733.1972111768 Force two-norm initial, final = 646.24790 0.53459485 Force max component initial, final = 123.88977 0.034715758 Final line search alpha, max atom move = 1.0000000 0.034715758 Iterations, force evaluations = 116 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.383 | 24.383 | 24.383 | 0.0 | 99.61 Neigh | 0.023586 | 0.023586 | 0.023586 | 0.0 | 0.10 Comm | 0.024657 | 0.024657 | 0.024657 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0475 | | | 0.19 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9608.00 ave 9608 max 9608 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: 259788.0 ave 259788 max 259788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259788 Ave neighs/atom = 55.510256 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.785 | 5.785 | 5.785 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -19733.197 0 -19733.197 31320.935 53386.89 122 0 -19738.078 0 -19738.078 -39.141284 53853.359 Loop time of 1.00686 on 1 procs for 6 steps with 4680 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 = -19733.1972111767 -19738.0739599842 -19738.0784278011 Force two-norm initial, final = 1829.4299 3.9607926 Force max component initial, final = 1253.6898 2.7158047 Final line search alpha, max atom move = 1.8942891e-05 5.1445193e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0009 | 1.0009 | 1.0009 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067787 | 0.00067787 | 0.00067787 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005291 | | | 0.53 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9724.00 ave 9724 max 9724 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: 267552.0 ave 267552 max 267552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267552 Ave neighs/atom = 57.169231 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.923 | 5.923 | 5.923 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19738.078 0 -19738.078 -39.141284 Loop time of 1.888e-06 on 1 procs for 0 steps with 4680 atoms 158.9% 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 | | 1.888e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9694.00 ave 9694 max 9694 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: 262068.0 ave 262068 max 262068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262068 Ave neighs/atom = 55.997436 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 51 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.923 | 5.923 | 5.923 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 -19738.078 -19738.078 43.298477 141.98264 8.7600168 -39.141284 -39.141284 -26.148847 -10.275384 -80.99962 2.2929407 2048.4528 Loop time of 1.922e-06 on 1 procs for 0 steps with 4680 atoms 260.1% 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 | | 1.922e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9694.00 ave 9694 max 9694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131034.0 ave 131034 max 131034 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 262068.0 ave 262068 max 262068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262068 Ave neighs/atom = 55.997436 Neighbor list builds = 0 Dangerous builds = 0 4680 -19738.0784278011 eV 2.29294066438203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26