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 = 3.5878716 3.5878716 3.5878716 Created orthogonal box = (0.0000000 -56.501859 0.0000000) to (34.600181 56.501859 8.7884547) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5806743 5.4679218 5.8589698 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -56.501859 0.0000000) to (34.600181 56.501859 8.7884547) create_atoms CPU = 0.003 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5806743 5.4679218 5.8589698 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -56.501859 0.0000000) to (34.600181 56.501859 8.7884547) create_atoms CPU = 0.002 seconds 1494 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 28 3 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 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2976 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_228059236215_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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 7.368 | 7.368 | 7.368 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9972.2689 0 -9972.2689 37968.121 77 0 -10452.107 0 -10452.107 5127.8227 Loop time of 9.34301 on 1 procs for 77 steps with 2976 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9972.26886443926 -10452.0975427034 -10452.1066913043 Force two-norm initial, final = 571.92314 0.29548907 Force max component initial, final = 109.46984 0.036735099 Final line search alpha, max atom move = 1.0000000 0.036735099 Iterations, force evaluations = 77 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.2608 | 9.2608 | 9.2608 | 0.0 | 99.12 Neigh | 0.035886 | 0.035886 | 0.035886 | 0.0 | 0.38 Comm | 0.020325 | 0.020325 | 0.020325 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02603 | | | 0.28 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11401.0 ave 11401 max 11401 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: 593532.0 ave 593532 max 593532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593532 Ave neighs/atom = 199.43952 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.371 | 7.371 | 7.371 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -10452.107 0 -10452.107 5127.8227 34362.41 81 0 -10452.398 0 -10452.398 -57.896948 34487.19 Loop time of 0.383585 on 1 procs for 4 steps with 2976 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 = -10452.1066913043 -10452.3968527263 -10452.3984157589 Force two-norm initial, final = 204.91409 3.3911709 Force max component initial, final = 153.63253 3.3609674 Final line search alpha, max atom move = 8.2208547e-05 0.00027630024 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37905 | 0.37905 | 0.37905 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062917 | 0.00062917 | 0.00062917 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003905 | | | 1.02 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11664.0 ave 11664 max 11664 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: 593808.0 ave 593808 max 593808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593808 Ave neighs/atom = 199.53226 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 7.508 | 7.508 | 7.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10452.398 0 -10452.398 -57.896948 Loop time of 2.394e-06 on 1 procs for 0 steps with 2976 atoms 208.9% 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 | | 2.394e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11616.0 ave 11616 max 11616 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: 593268.0 ave 593268 max 593268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593268 Ave neighs/atom = 199.35081 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 7.508 | 7.508 | 7.508 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 -10452.398 -10452.398 34.690025 113.20343 8.7820036 -57.896948 -57.896948 -15.41738 -2.2471217 -156.02634 2.2990601 993.44987 Loop time of 2.859e-06 on 1 procs for 0 steps with 2976 atoms 314.8% 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 | | 2.859e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11616.0 ave 11616 max 11616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296634.0 ave 296634 max 296634 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 593268.0 ave 593268 max 593268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593268 Ave neighs/atom = 199.35081 Neighbor list builds = 0 Dangerous builds = 0 2976 -10452.3984157589 eV 2.29906008827707 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11