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 -43.600814 0.0000000) to (53.399873 43.600814 8.8388099) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1205358 5.3754428 5.8925399 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -43.600814 0.0000000) to (53.399873 43.600814 8.8388099) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1205358 5.3754428 5.8925399 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.600814 0.0000000) to (53.399873 43.600814 8.8388099) create_atoms CPU = 0.002 seconds 1754 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 = 18 30 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 8 atoms, new total = 3494 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 = 18 30 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) = 5.630 | 5.630 | 5.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13689.298 0 -13689.298 91262.858 557 0 -14872.827 0 -14872.827 -1855.2098 Loop time of 127.28 on 1 procs for 557 steps with 3494 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 = -13689.2980502689 -14872.8134623051 -14872.8274175845 Force two-norm initial, final = 1956.9028 0.36834754 Force max component initial, final = 366.63663 0.066523531 Final line search alpha, max atom move = 1.0000000 0.066523531 Iterations, force evaluations = 557 1089 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 126.7 | 126.7 | 126.7 | 0.0 | 99.55 Neigh | 0.29927 | 0.29927 | 0.29927 | 0.0 | 0.24 Comm | 0.10901 | 0.10901 | 0.10901 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1702 | | | 0.13 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7923.00 ave 7923 max 7923 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: 255822.0 ave 255822 max 255822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255822 Ave neighs/atom = 73.217516 Neighbor list builds = 14 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 = 18 30 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 : 557 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 557 0 -14872.827 0 -14872.827 -1855.2098 41158.412 567 0 -14874.686 0 -14874.686 -1.671572 41111.904 Loop time of 1.26255 on 1 procs for 10 steps with 3494 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 = -14872.8274175845 -14874.6813398919 -14874.6860852274 Force two-norm initial, final = 333.15872 1.2623345 Force max component initial, final = 310.05568 0.66942246 Final line search alpha, max atom move = 8.6868628e-05 5.8151810e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2559 | 1.2559 | 1.2559 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078774 | 0.00078774 | 0.00078774 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005821 | | | 0.46 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7932.00 ave 7932 max 7932 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: 255922.0 ave 255922 max 255922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255922 Ave neighs/atom = 73.246136 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 = 18 30 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) = 5.768 | 5.768 | 5.768 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14874.686 0 -14874.686 -1.671572 Loop time of 2.095e-06 on 1 procs for 0 steps with 3494 atoms 190.9% 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 | | 2.095e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7923.00 ave 7923 max 7923 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: 255784.0 ave 255784 max 255784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255784 Ave neighs/atom = 73.206640 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 = 18 30 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) = 5.768 | 5.768 | 5.768 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 -14874.686 -14874.686 52.897384 87.702891 8.8617497 -1.671572 -1.671572 11.350154 9.7909735 -26.155844 2.2402238 12749.996 Loop time of 2.492e-06 on 1 procs for 0 steps with 3494 atoms 240.8% 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 | | 2.492e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7923.00 ave 7923 max 7923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127892.0 ave 127892 max 127892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255784.0 ave 255784 max 255784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255784 Ave neighs/atom = 73.206640 Neighbor list builds = 0 Dangerous builds = 0 3494 -14874.6860852274 eV 2.24022380925376 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:09