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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -58.827942 0.0000000) to (20.797538 58.827942 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6720559 6.2389432 5.1200000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.827942 0.0000000) to (20.797538 58.827942 5.1200000) create_atoms CPU = 0.002 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6720559 6.2389432 5.1200000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.827942 0.0000000) to (20.797538 58.827942 5.1200000) create_atoms CPU = 0.001 seconds 530 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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_390178379548_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3679.6874 0 -3679.6874 3735.5797 67 0 -3702.2841 0 -3702.2841 -7281.6299 Loop time of 1.88426 on 1 procs for 67 steps with 1048 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 = -3679.68744097804 -3702.2807148727 -3702.28406642763 Force two-norm initial, final = 39.148320 0.16001385 Force max component initial, final = 11.074623 0.033339799 Final line search alpha, max atom move = 1.0000000 0.033339799 Iterations, force evaluations = 67 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8676 | 1.8676 | 1.8676 | 0.0 | 99.12 Neigh | 0.005708 | 0.005708 | 0.005708 | 0.0 | 0.30 Comm | 0.00537 | 0.00537 | 0.00537 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005569 | | | 0.30 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4874.00 ave 4874 max 4874 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: 81124.0 ave 81124 max 81124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81124 Ave neighs/atom = 77.408397 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -3702.2841 0 -3702.2841 -7281.6299 12528.398 71 0 -3702.4039 0 -3702.4039 -1706.3504 12478.974 Loop time of 0.0967479 on 1 procs for 4 steps with 1048 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 = -3702.28406642763 -3702.40076527996 -3702.40386887488 Force two-norm initial, final = 74.964975 0.34718954 Force max component initial, final = 63.541220 0.24572103 Final line search alpha, max atom move = 0.00012185170 2.9941526e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095472 | 0.095472 | 0.095472 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022892 | 0.00022892 | 0.00022892 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001047 | | | 1.08 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4878.00 ave 4878 max 4878 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: 81048.0 ave 81048 max 81048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81048 Ave neighs/atom = 77.335878 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.758 | 4.758 | 4.758 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3702.4039 0 -3702.4039 -1706.3504 Loop time of 1.637e-06 on 1 procs for 0 steps with 1048 atoms 122.2% 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 | | 1.637e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4891.00 ave 4891 max 4891 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: 81076.0 ave 81076 max 81076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81076 Ave neighs/atom = 77.362595 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 ghost atom cutoff = 6 binsize = 3, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.758 | 4.758 | 4.758 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 -3702.4039 -3702.4039 20.727003 117.65588 5.1171568 -1706.3504 -1706.3504 -31.441147 -5065.575 -22.035 2.398495 441.69501 Loop time of 1.616e-06 on 1 procs for 0 steps with 1048 atoms 185.6% 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 | | 1.616e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4891.00 ave 4891 max 4891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40538.0 ave 40538 max 40538 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81076.0 ave 81076 max 81076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81076 Ave neighs/atom = 77.362595 Neighbor list builds = 0 Dangerous builds = 0 1048 -3702.40386887488 eV 2.39849500837169 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02