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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -67.305622 0.0000000) to (38.858919 67.305622 6.0935647) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7332832 5.1490640 6.0935647 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.305622 0.0000000) to (38.858919 67.305622 6.0935647) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7332832 5.1490640 6.0935647 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.305622 0.0000000) to (38.858919 67.305622 6.0935647) create_atoms CPU = 0.008 seconds 1466 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 31 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.71 | 11.71 | 11.71 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11422.821 0 -11422.821 106593.69 123 0 -12792.017 0 -12792.017 4393.3772 Loop time of 21.6278 on 1 procs for 123 steps with 2926 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 = -11422.8205683089 -12792.0054832394 -12792.0170313636 Force two-norm initial, final = 2454.3048 0.36299241 Force max component initial, final = 753.29931 0.066759089 Final line search alpha, max atom move = 1.0000000 0.066759089 Iterations, force evaluations = 123 220 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.175 | 21.175 | 21.175 | 0.0 | 97.91 Neigh | 0.29627 | 0.29627 | 0.29627 | 0.0 | 1.37 Comm | 0.088142 | 0.088142 | 0.088142 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06859 | | | 0.32 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16190.0 ave 16190 max 16190 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: 723340.0 ave 723340 max 723340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 723340 Ave neighs/atom = 247.21121 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 123 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.71 | 11.71 | 11.71 Mbytes Step Temp E_pair E_mol TotEng Press Volume 123 0 -12792.017 0 -12792.017 4393.3772 31874.508 126 0 -12792.166 0 -12792.166 -1.722396 31955.202 Loop time of 0.556669 on 1 procs for 3 steps with 2926 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 = -12792.0170313636 -12792.1612752503 -12792.1656838461 Force two-norm initial, final = 160.76403 0.50689578 Force max component initial, final = 127.09791 0.22884857 Final line search alpha, max atom move = 4.2690868e-05 9.7697441e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54794 | 0.54794 | 0.54794 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021091 | 0.0021091 | 0.0021091 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006623 | | | 1.19 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16194.0 ave 16194 max 16194 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: 723480.0 ave 723480 max 723480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 723480 Ave neighs/atom = 247.25906 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.23 | 11.23 | 11.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12792.166 0 -12792.166 -1.722396 Loop time of 7.127e-06 on 1 procs for 0 steps with 2926 atoms 182.4% 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 | | 7.127e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16194.0 ave 16194 max 16194 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: 723084.0 ave 723084 max 723084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 723084 Ave neighs/atom = 247.12372 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.23 | 11.23 | 11.23 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 -12792.166 -12792.166 38.854351 134.8651 6.0982093 -1.722396 -1.722396 -9.0839285 -7.5660619 11.482802 2.1671442 776.93572 Loop time of 6.716e-06 on 1 procs for 0 steps with 2926 atoms 312.7% 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 | | 6.716e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16194.0 ave 16194 max 16194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 361542.0 ave 361542 max 361542 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 723084.0 ave 723084 max 723084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 723084 Ave neighs/atom = 247.12372 Neighbor list builds = 0 Dangerous builds = 0 2926 -12792.1656838461 eV 2.16714424607525 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23