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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247507 71.442777 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3457703 6.4115313 7.0055407 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247507 71.442777 7.0055407) create_atoms CPU = 0.009 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3457703 6.4115313 7.0055407 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -71.442777 0.0000000) to (41.247507 71.442777 7.0055407) create_atoms CPU = 0.008 seconds 1250 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 36 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2490 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_793141037706_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.116 | 6.116 | 6.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7925.4388 0 -7925.4388 21924.956 90 0 -8344.313 0 -8344.313 1637.6838 Loop time of 70.5326 on 1 procs for 90 steps with 2490 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 = -7925.43883625395 -8344.30491974209 -8344.31301029929 Force two-norm initial, final = 432.67798 0.24843500 Force max component initial, final = 75.642932 0.050876674 Final line search alpha, max atom move = 1.0000000 0.050876674 Iterations, force evaluations = 90 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.252 | 70.252 | 70.252 | 0.0 | 99.60 Neigh | 0.18769 | 0.18769 | 0.18769 | 0.0 | 0.27 Comm | 0.046393 | 0.046393 | 0.046393 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04663 | | | 0.07 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10262.0 ave 10262 max 10262 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: 331762.0 ave 331762 max 331762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331762 Ave neighs/atom = 133.23775 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.117 | 6.117 | 6.117 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -8344.313 0 -8344.313 1637.6838 41288.365 94 0 -8344.4716 0 -8344.4716 -202.63475 41384.566 Loop time of 2.7899 on 1 procs for 4 steps with 2490 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 = -8344.31301029928 -8344.46542025861 -8344.47158797337 Force two-norm initial, final = 94.947384 9.4158344 Force max component initial, final = 91.038546 6.3195670 Final line search alpha, max atom move = 7.0200725e-05 0.00044363819 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7822 | 2.7822 | 2.7822 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014744 | 0.0014744 | 0.0014744 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006259 | | | 0.22 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10316.0 ave 10316 max 10316 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: 331806.0 ave 331806 max 331806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331806 Ave neighs/atom = 133.25542 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.255 | 6.255 | 6.255 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8344.4716 0 -8344.4716 -202.63475 Loop time of 5.683e-06 on 1 procs for 0 steps with 2490 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 | | 5.683e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10316.0 ave 10316 max 10316 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: 331714.0 ave 331714 max 331714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331714 Ave neighs/atom = 133.21847 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.255 | 6.255 | 6.255 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 -8344.4716 -8344.4716 41.233071 143.42328 6.9979859 -202.63475 -202.63475 -244.57229 -123.00969 -240.32226 2.5127685 1122.6559 Loop time of 8.399e-06 on 1 procs for 0 steps with 2490 atoms 250.0% 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 | | 8.399e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10316.0 ave 10316 max 10316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165857.0 ave 165857 max 165857 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 331714.0 ave 331714 max 331714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331714 Ave neighs/atom = 133.21847 Neighbor list builds = 0 Dangerous builds = 0 2490 -8344.47158797337 eV 2.51276848876906 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:15