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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -38.555982 0.0000000) to (27.263196 38.555982 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2613186 6.0877866 5.1068646 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.555982 0.0000000) to (27.263196 38.555982 5.1068646) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2613186 6.0877866 5.1068646 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.555982 0.0000000) to (27.263196 38.555982 5.1068646) 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 ghost atom cutoff = 6 binsize = 3, bins = 10 26 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_179158257180_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 = 10 26 2 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3460.6709 0 -3460.6709 105897.64 629 0 -3889.8833 0 -3889.8833 8940.1625 Loop time of 38.2377 on 1 procs for 629 steps with 914 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 = -3460.67093099226 -3889.87976620192 -3889.88334843599 Force two-norm initial, final = 309.70700 0.21335696 Force max component initial, final = 69.499497 0.042960239 Final line search alpha, max atom move = 0.81018699 0.034805827 Iterations, force evaluations = 629 1185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.013 | 38.013 | 38.013 | 0.0 | 99.41 Neigh | 0.11089 | 0.11089 | 0.11089 | 0.0 | 0.29 Comm | 0.056187 | 0.056187 | 0.056187 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05723 | | | 0.15 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4170.00 ave 4170 max 4170 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: 60524.0 ave 60524 max 60524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60524 Ave neighs/atom = 66.218818 Neighbor list builds = 21 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 = 10 26 2 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 : 629 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 629 0 -3889.8833 0 -3889.8833 8940.1625 10736.256 658 0 -3900.3507 0 -3900.3507 -12.077114 10772.495 Loop time of 0.950985 on 1 procs for 29 steps with 914 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 = -3889.88334843599 -3900.34716061491 -3900.35067151939 Force two-norm initial, final = 540.74674 1.8225533 Force max component initial, final = 404.59112 0.75136218 Final line search alpha, max atom move = 0.00013258643 9.9620431e-05 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93195 | 0.93195 | 0.93195 | 0.0 | 98.00 Neigh | 0.010614 | 0.010614 | 0.010614 | 0.0 | 1.12 Comm | 0.0014345 | 0.0014345 | 0.0014345 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006986 | | | 0.73 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4239.00 ave 4239 max 4239 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: 59444.0 ave 59444 max 59444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59444 Ave neighs/atom = 65.037199 Neighbor list builds = 2 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 = 10 27 2 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) = 4.701 | 4.701 | 4.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3900.3507 0 -3900.3507 -12.077114 Loop time of 4.262e-06 on 1 procs for 0 steps with 914 atoms 211.2% 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 | | 4.262e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4239.00 ave 4239 max 4239 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: 59444.0 ave 59444 max 59444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59444 Ave neighs/atom = 65.037199 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 = 10 27 2 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) = 4.701 | 4.701 | 4.701 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 -3900.3507 -3900.3507 27.324541 79.294348 4.9718863 -12.077114 -12.077114 -97.304185 -47.722485 108.79533 2.3327852 1422.3604 Loop time of 2.602e-06 on 1 procs for 0 steps with 914 atoms 192.2% 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 | | 2.602e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4239.00 ave 4239 max 4239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29722.0 ave 29722 max 29722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59444.0 ave 59444 max 59444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59444 Ave neighs/atom = 65.037199 Neighbor list builds = 0 Dangerous builds = 0 914 -3900.35067151939 eV 2.33278517074659 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:39