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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -73.348805 0.0000000) to (25.932719 73.348805 5.7275794) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9575586 6.2614833 5.7275794 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -73.348805 0.0000000) to (25.932719 73.348805 5.7275794) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9575586 6.2614833 5.7275794 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -73.348805 0.0000000) to (25.932719 73.348805 5.7275794) create_atoms CPU = 0.002 seconds 658 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3984.8633 0 -3984.8633 543990.81 111 0 -4442.1425 0 -4442.1425 1336.4212 Loop time of 1.54459 on 1 procs for 111 steps with 1312 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3984.86327953847 -4442.13838844179 -4442.14247340753 Force two-norm initial, final = 16107.671 0.14107465 Force max component initial, final = 3757.8933 0.027267285 Final line search alpha, max atom move = 1.0000000 0.027267285 Iterations, force evaluations = 111 199 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4751 | 1.4751 | 1.4751 | 0.0 | 95.50 Neigh | 0.040033 | 0.040033 | 0.040033 | 0.0 | 2.59 Comm | 0.015816 | 0.015816 | 0.015816 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01364 | | | 0.88 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6757.00 ave 6757 max 6757 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: 154260.0 ave 154260 max 154260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154260 Ave neighs/atom = 117.57622 Neighbor list builds = 4 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.080 | 5.080 | 5.080 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -4442.1425 0 -4442.1425 1336.4212 21789.246 114 0 -4442.1702 0 -4442.1702 -11.694154 21827.311 Loop time of 0.0434115 on 1 procs for 3 steps with 1312 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 = -4442.14247340754 -4442.16997905405 -4442.17017632789 Force two-norm initial, final = 35.482277 0.83202612 Force max component initial, final = 29.579071 0.54012195 Final line search alpha, max atom move = 0.00038823568 0.00020969462 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041722 | 0.041722 | 0.041722 | 0.0 | 96.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031855 | 0.00031855 | 0.00031855 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001371 | | | 3.16 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6745.00 ave 6745 max 6745 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: 158260.0 ave 158260 max 158260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158260 Ave neighs/atom = 120.62500 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.218 | 5.218 | 5.218 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4442.1702 0 -4442.1702 -11.694154 Loop time of 1.668e-06 on 1 procs for 0 steps with 1312 atoms 119.9% 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 | | 1.668e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6745.00 ave 6745 max 6745 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: 153620.0 ave 153620 max 153620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153620 Ave neighs/atom = 117.08841 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.218 | 5.218 | 5.218 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 -4442.1702 -4442.1702 25.973466 146.79755 5.7246843 -11.694154 -11.694154 -39.708529 34.260833 -29.634765 2.6734686 677.5633 Loop time of 1.989e-06 on 1 procs for 0 steps with 1312 atoms 201.1% 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 | | 1.989e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6745.00 ave 6745 max 6745 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76810.0 ave 76810 max 76810 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 153620.0 ave 153620 max 153620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153620 Ave neighs/atom = 117.08841 Neighbor list builds = 0 Dangerous builds = 0 1312 -4442.17017632789 eV 2.6734685782881 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01