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 = 2.8510000 2.8510000 2.8510000 Created orthogonal box = (0.0000000 -29.901541 0.0000000) to (36.621758 29.901541 6.9834953) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6609511 4.3493150 4.6556635 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -29.901541 0.0000000) to (36.621758 29.901541 6.9834953) create_atoms CPU = 0.001 seconds 659 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6609511 4.3493150 4.6556635 Created 665 atoms using lattice units in orthogonal box = (0.0000000 -29.901541 0.0000000) to (36.621758 29.901541 6.9834953) create_atoms CPU = 0.001 seconds 665 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 = 13 20 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1308 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 = 13 20 3 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) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4752.6782 0 -4752.6782 176686.94 71 0 -5579.6542 0 -5579.6542 -3737.9851 Loop time of 4.26052 on 1 procs for 71 steps with 1308 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 = -4752.67817787572 -5579.65035942004 -5579.65423074933 Force two-norm initial, final = 1733.4823 0.18200009 Force max component initial, final = 337.24786 0.043897149 Final line search alpha, max atom move = 1.0000000 0.043897149 Iterations, force evaluations = 71 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2303 | 4.2303 | 4.2303 | 0.0 | 99.29 Neigh | 0.015215 | 0.015215 | 0.015215 | 0.0 | 0.36 Comm | 0.0059572 | 0.0059572 | 0.0059572 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00903 | | | 0.21 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4249.00 ave 4249 max 4249 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: 84656.0 ave 84656 max 84656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84656 Ave neighs/atom = 64.721713 Neighbor list builds = 2 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 = 13 20 3 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 : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -5579.6542 0 -5579.6542 -3737.9851 15294.511 75 0 -5579.8073 0 -5579.8073 -204.33566 15262.673 Loop time of 0.210206 on 1 procs for 4 steps with 1308 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 = -5579.65423074934 -5579.80474179161 -5579.80725048742 Force two-norm initial, final = 90.204733 3.5206761 Force max component initial, final = 86.119308 2.3441850 Final line search alpha, max atom move = 0.00011840410 0.00027756110 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2086 | 0.2086 | 0.2086 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022567 | 0.00022567 | 0.00022567 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00138 | | | 0.66 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4232.00 ave 4232 max 4232 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: 84486.0 ave 84486 max 84486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84486 Ave neighs/atom = 64.591743 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 = 13 20 3 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) = 4.761 | 4.761 | 4.761 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5579.8073 0 -5579.8073 -204.33566 Loop time of 2.663e-06 on 1 procs for 0 steps with 1308 atoms 187.8% 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 | | 2.663e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4232.00 ave 4232 max 4232 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: 84490.0 ave 84490 max 84490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84490 Ave neighs/atom = 64.594801 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 = 13 20 3 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) = 4.761 | 4.761 | 4.761 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 -5579.8073 -5579.8073 36.609524 59.894174 6.9606843 -204.33566 -204.33566 -245.99514 -121.88939 -245.12244 2.2957199 1968.3078 Loop time of 2.155e-06 on 1 procs for 0 steps with 1308 atoms 232.0% 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 | | 2.155e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4232.00 ave 4232 max 4232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42245.0 ave 42245 max 42245 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84490.0 ave 84490 max 84490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84490 Ave neighs/atom = 64.594801 Neighbor list builds = 0 Dangerous builds = 0 1308 -5579.80725048742 eV 2.29571987370182 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04