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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -58.187778 0.0000000) to (29.092085 58.187778 3.6084290) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9232759 4.9232759 3.6084290 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.187778 0.0000000) to (29.092085 58.187778 3.6084290) create_atoms CPU = 0.003 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9232759 4.9232759 3.6084290 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.187778 0.0000000) to (29.092085 58.187778 3.6084290) 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 39 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 8 atoms, new total = 1036 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_549900287421_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 = 10 39 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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4362.0572 0 -4362.0572 7933.4902 63 0 -4393.5808 0 -4393.5808 -1591.4653 Loop time of 9.72892 on 1 procs for 63 steps with 1036 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 = -4362.05724053096 -4393.57778301877 -4393.58079415104 Force two-norm initial, final = 31.344289 0.16155054 Force max component initial, final = 8.7423266 0.030619714 Final line search alpha, max atom move = 1.0000000 0.030619714 Iterations, force evaluations = 63 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6842 | 9.6842 | 9.6842 | 0.0 | 99.54 Neigh | 0.013279 | 0.013279 | 0.013279 | 0.0 | 0.14 Comm | 0.0163 | 0.0163 | 0.0163 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01515 | | | 0.16 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219.00 ave 6219 max 6219 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: 80336.0 ave 80336 max 80336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80336 Ave neighs/atom = 77.544402 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 = 10 39 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -4393.5808 0 -4393.5808 -1591.4653 12216.725 67 0 -4393.6369 0 -4393.6369 -1848.7295 12218.554 Loop time of 0.541472 on 1 procs for 4 steps with 1036 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4393.58079415104 -4393.63599392861 -4393.63686060296 Force two-norm initial, final = 26.529943 3.6296232 Force max component initial, final = 22.003743 3.6190229 Final line search alpha, max atom move = 0.00018467130 0.00066832967 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53792 | 0.53792 | 0.53792 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079237 | 0.00079237 | 0.00079237 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002758 | | | 0.51 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6213.00 ave 6213 max 6213 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: 80320.0 ave 80320 max 80320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80320 Ave neighs/atom = 77.528958 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 = 10 39 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) = 4.750 | 4.750 | 4.750 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4393.6369 0 -4393.6369 -1848.7295 Loop time of 6.656e-06 on 1 procs for 0 steps with 1036 atoms 165.3% 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 | | 6.656e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6226.00 ave 6226 max 6226 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: 80320.0 ave 80320 max 80320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80320 Ave neighs/atom = 77.528958 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 = 10 39 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) = 4.750 | 4.750 | 4.750 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 -4393.6369 -4393.6369 29.013876 116.37556 3.6186976 -1848.7295 -1848.7295 -473.27413 -5096.3488 23.434464 2.2857916 397.17893 Loop time of 7.197e-06 on 1 procs for 0 steps with 1036 atoms 291.8% 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 | | 7.197e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6226.00 ave 6226 max 6226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40160.0 ave 40160 max 40160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80320.0 ave 80320 max 80320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80320 Ave neighs/atom = 77.528958 Neighbor list builds = 0 Dangerous builds = 0 1036 -4393.63686060296 eV 2.28579158601596 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10