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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -37.554291 0.0000000) to (26.552339 37.554291 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9005197 4.8676804 5.1100000 Created 438 atoms using lattice units in orthogonal box = (0.0000000 -37.554291 0.0000000) to (26.552339 37.554291 5.1100000) create_atoms CPU = 0.003 seconds 438 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9005197 4.8676804 5.1100000 Created 438 atoms using lattice units in orthogonal box = (0.0000000 -37.554291 0.0000000) to (26.552339 37.554291 5.1100000) create_atoms CPU = 0.002 seconds 438 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 10 27 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 856 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2980.4455 0 -2980.4455 12839.36 45 0 -3016.1967 0 -3016.1967 -5143.8605 Loop time of 2.44244 on 1 procs for 45 steps with 856 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 = -2980.44549409659 -3016.19422927037 -3016.19673290316 Force two-norm initial, final = 40.520288 0.14711272 Force max component initial, final = 6.2593221 0.021349226 Final line search alpha, max atom move = 1.0000000 0.021349226 Iterations, force evaluations = 45 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4147 | 2.4147 | 2.4147 | 0.0 | 98.87 Neigh | 0.01006 | 0.01006 | 0.01006 | 0.0 | 0.41 Comm | 0.0083317 | 0.0083317 | 0.0083317 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009309 | | | 0.38 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3767.00 ave 3767 max 3767 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: 49784.0 ave 49784 max 49784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49784 Ave neighs/atom = 58.158879 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -3016.1967 0 -3016.1967 -5143.8605 10190.916 48 0 -3016.2366 0 -3016.2366 -1659.8973 10165.393 Loop time of 0.157898 on 1 procs for 3 steps with 856 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 = -3016.19673290315 -3016.23581046807 -3016.23656774516 Force two-norm initial, final = 37.059763 0.52631804 Force max component initial, final = 33.859358 0.43987321 Final line search alpha, max atom move = 0.00025763820 0.00011332814 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15576 | 0.15576 | 0.15576 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044225 | 0.00044225 | 0.00044225 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001696 | | | 1.07 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3753.00 ave 3753 max 3753 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: 49648.0 ave 49648 max 49648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49648 Ave neighs/atom = 58.000000 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.690 | 4.690 | 4.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3016.2366 0 -3016.2366 -1659.8973 Loop time of 6.755e-06 on 1 procs for 0 steps with 856 atoms 236.9% 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 | | 6.755e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3753.00 ave 3753 max 3753 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: 50720.0 ave 50720 max 50720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50720 Ave neighs/atom = 59.252336 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.690 | 4.690 | 4.690 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 -3016.2366 -3016.2366 26.543161 75.108582 5.0989646 -1659.8973 -1659.8973 -37.134088 -4873.3787 -69.179079 2.3926049 482.00502 Loop time of 7.608e-06 on 1 procs for 0 steps with 856 atoms 289.2% 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 | | 7.608e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3753.00 ave 3753 max 3753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25360.0 ave 25360 max 25360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50720.0 ave 50720 max 50720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50720 Ave neighs/atom = 59.252336 Neighbor list builds = 0 Dangerous builds = 0 856 -3016.23656774516 eV 2.39260485575334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03