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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -36.421871 0.0000000) to (25.754152 36.421871 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5448503 5.7132346 5.1000820 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.421871 0.0000000) to (25.754152 36.421871 5.1000820) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5448503 5.7132346 5.1000820 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.421871 0.0000000) to (25.754152 36.421871 5.1000820) create_atoms CPU = 0.001 seconds 410 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 818 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.623 | 6.623 | 6.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3112.3379 0 -3112.3379 84801.465 125 0 -3410.8262 0 -3410.8262 13404.485 Loop time of 5.27229 on 1 procs for 125 steps with 818 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 = -3112.33789492369 -3410.82289236464 -3410.82622563691 Force two-norm initial, final = 244.96708 0.25757196 Force max component initial, final = 46.925508 0.057377916 Final line search alpha, max atom move = 0.58423334 0.033522091 Iterations, force evaluations = 125 237 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.21 | 5.21 | 5.21 | 0.0 | 98.82 Neigh | 0.021884 | 0.021884 | 0.021884 | 0.0 | 0.42 Comm | 0.026744 | 0.026744 | 0.026744 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01367 | | | 0.26 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11301.0 ave 11301 max 11301 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: 507844.0 ave 507844 max 507844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507844 Ave neighs/atom = 620.83619 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.622 | 6.622 | 6.622 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -3410.8262 0 -3410.8262 13404.485 9567.9007 133 0 -3411.2303 0 -3411.2303 -1.4392523 9642.1119 Loop time of 0.24086 on 1 procs for 8 steps with 818 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 = -3410.8262256369 -3411.22829188041 -3411.23032789804 Force two-norm initial, final = 142.74198 0.57913498 Force max component initial, final = 107.60350 0.093353529 Final line search alpha, max atom move = 0.00013958604 1.3030849e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23635 | 0.23635 | 0.23635 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093422 | 0.00093422 | 0.00093422 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003579 | | | 1.49 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11157.0 ave 11157 max 11157 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: 505192.0 ave 505192 max 505192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505192 Ave neighs/atom = 617.59413 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.760 | 6.760 | 6.760 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3411.2303 0 -3411.2303 -1.4392523 Loop time of 1.882e-06 on 1 procs for 0 steps with 818 atoms 159.4% 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 | | 1.882e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11157.0 ave 11157 max 11157 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: 501316.0 ave 501316 max 501316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501316 Ave neighs/atom = 612.85575 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.760 | 6.760 | 6.760 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 -3411.2303 -3411.2303 25.940699 72.846041 5.102518 -1.4392523 -1.4392523 -6.2630966 -5.1964563 7.141796 2.3106363 912.13203 Loop time of 2.152e-06 on 1 procs for 0 steps with 818 atoms 185.9% 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 | | 2.152e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11157.0 ave 11157 max 11157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 250658.0 ave 250658 max 250658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 501316.0 ave 501316 max 501316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501316 Ave neighs/atom = 612.85575 Neighbor list builds = 0 Dangerous builds = 0 818 -3411.23032789804 eV 2.31063631337398 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06