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 = 4.0415970 4.0415970 4.0415970 Created orthogonal box = (0.0000000 -43.152448 0.0000000) to (24.914077 43.152448 7.0002514) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5563361 6.0564839 7.0002514 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -43.152448 0.0000000) to (24.914077 43.152448 7.0002514) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5563361 6.0564839 7.0002514 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.152448 0.0000000) to (24.914077 43.152448 7.0002514) create_atoms CPU = 0.001 seconds 458 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 9 29 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, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_736419017411_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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.924 | 4.924 | 4.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2906.4866 0 -2906.4866 25594.353 95 0 -3058.1787 0 -3058.1787 17533.821 Loop time of 14.7559 on 1 procs for 95 steps with 912 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2906.48656039522 -3058.17588359571 -3058.17870424853 Force two-norm initial, final = 179.18400 0.15472454 Force max component initial, final = 45.861769 0.014084912 Final line search alpha, max atom move = 1.0000000 0.014084912 Iterations, force evaluations = 95 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.686 | 14.686 | 14.686 | 0.0 | 99.53 Neigh | 0.052375 | 0.052375 | 0.052375 | 0.0 | 0.35 Comm | 0.0073697 | 0.0073697 | 0.0073697 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009937 | | | 0.07 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3192.00 ave 3192 max 3192 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: 48928.0 ave 48928 max 48928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48928 Ave neighs/atom = 53.649123 Neighbor list builds = 3 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.924 | 4.924 | 4.924 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -3058.1787 0 -3058.1787 17533.821 15051.988 108 0 -3059.5382 0 -3059.5382 -68.081258 15212.25 Loop time of 1.13727 on 1 procs for 13 steps with 912 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 = -3058.17870424851 -3059.53799848643 -3059.53822360454 Force two-norm initial, final = 310.43406 1.3231486 Force max component initial, final = 261.84032 0.89694121 Final line search alpha, max atom move = 0.00075211935 0.00067460684 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1166 | 1.1166 | 1.1166 | 0.0 | 98.18 Neigh | 0.016659 | 0.016659 | 0.016659 | 0.0 | 1.46 Comm | 0.00062379 | 0.00062379 | 0.00062379 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003387 | | | 0.30 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3185.00 ave 3185 max 3185 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: 48872.0 ave 48872 max 48872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48872 Ave neighs/atom = 53.587719 Neighbor list builds = 1 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3059.5382 0 -3059.5382 -68.081258 Loop time of 2.665e-06 on 1 procs for 0 steps with 912 atoms 187.6% 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 | | 2.665e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3185.00 ave 3185 max 3185 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: 48872.0 ave 48872 max 48872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48872 Ave neighs/atom = 53.587719 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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) = 5.062 | 5.062 | 5.062 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 -3059.5382 -3059.5382 24.900655 87.331478 6.9953892 -68.081258 -68.081258 -94.416269 -50.529674 -59.297831 2.5006276 677.74392 Loop time of 2.311e-06 on 1 procs for 0 steps with 912 atoms 302.9% 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 | | 2.311e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3185.00 ave 3185 max 3185 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24436.0 ave 24436 max 24436 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48872.0 ave 48872 max 48872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48872 Ave neighs/atom = 53.587719 Neighbor list builds = 0 Dangerous builds = 0 912 -3059.53822360454 eV 2.50062759954222 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16