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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -38.077724 0.0000000) to (23.315991 38.077724 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2392711 4.3266879 4.6866905 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -38.077724 0.0000000) to (23.315991 38.077724 7.0300358) create_atoms CPU = 0.002 seconds 531 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2392711 4.3266879 4.6866905 Created 531 atoms using lattice units in orthogonal box = (0.0000000 -38.077724 0.0000000) to (23.315991 38.077724 7.0300358) create_atoms CPU = 0.001 seconds 531 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 25 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 19 atoms, new total = 1043 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_024705128470_000#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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4392.9402 0 -4392.9402 6012.9765 96 0 -4437.74 0 -4437.74 -8606.9561 Loop time of 1.28476 on 1 procs for 96 steps with 1043 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 = -4392.94024239106 -4437.7355570164 -4437.73998719277 Force two-norm initial, final = 54.928058 0.23879876 Force max component initial, final = 11.011538 0.043332970 Final line search alpha, max atom move = 1.0000000 0.043332970 Iterations, force evaluations = 96 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2323 | 1.2323 | 1.2323 | 0.0 | 95.92 Neigh | 0.026462 | 0.026462 | 0.026462 | 0.0 | 2.06 Comm | 0.011983 | 0.011983 | 0.011983 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01401 | | | 1.09 Nlocal: 1043.00 ave 1043 max 1043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4208.00 ave 4208 max 4208 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: 67752.0 ave 67752 max 67752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67752 Ave neighs/atom = 64.958773 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -4437.74 0 -4437.74 -8606.9561 12482.811 100 0 -4437.9173 0 -4437.9173 -738.05009 12423.435 Loop time of 0.0490541 on 1 procs for 4 steps with 1043 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 = -4437.73998719277 -4437.91659746143 -4437.91732780019 Force two-norm initial, final = 101.72965 0.27711260 Force max component initial, final = 81.005352 0.044208124 Final line search alpha, max atom move = 0.00025040937 1.1070129e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046353 | 0.046353 | 0.046353 | 0.0 | 94.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000456 | 0.000456 | 0.000456 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002245 | | | 4.58 Nlocal: 1043.00 ave 1043 max 1043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4208.00 ave 4208 max 4208 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: 67720.0 ave 67720 max 67720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67720 Ave neighs/atom = 64.928092 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.708 | 4.708 | 4.708 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4437.9173 0 -4437.9173 -738.05009 Loop time of 3.042e-06 on 1 procs for 0 steps with 1043 atoms 131.5% 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 | | 3.042e-06 | | |100.00 Nlocal: 1043.00 ave 1043 max 1043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4208.00 ave 4208 max 4208 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: 67822.0 ave 67822 max 67822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67822 Ave neighs/atom = 65.025887 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.708 | 4.708 | 4.708 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 -4437.9173 -4437.9173 23.243884 76.155447 7.0183015 -738.05009 -738.05009 1.2251808 -2212.5388 -2.8366389 2.2820621 846.79134 Loop time of 2.927e-06 on 1 procs for 0 steps with 1043 atoms 170.8% 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 | | 2.927e-06 | | |100.00 Nlocal: 1043.00 ave 1043 max 1043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4208.00 ave 4208 max 4208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33911.0 ave 33911 max 33911 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67822.0 ave 67822 max 67822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67822 Ave neighs/atom = 65.025887 Neighbor list builds = 0 Dangerous builds = 0 1043 -4437.91722350019 eV 2.28206210842996 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01