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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -47.361481 0.0000000) to (16.744812 47.361481 5.7434232) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8949226 6.9649237 5.7434232 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.361481 0.0000000) to (16.744812 47.361481 5.7434232) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8949226 6.9649237 5.7434232 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.361481 0.0000000) to (16.744812 47.361481 5.7434232) create_atoms CPU = 0.002 seconds 274 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 4 20 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1397.3686 0 -1397.3686 21039.833 86 0 -1468.7911 0 -1468.7911 5538.1728 Loop time of 2.80243 on 1 procs for 86 steps with 546 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 = -1397.36859177922 -1468.78982615259 -1468.79110580739 Force two-norm initial, final = 98.358629 0.10922977 Force max component initial, final = 31.125134 0.010701459 Final line search alpha, max atom move = 1.0000000 0.010701459 Iterations, force evaluations = 86 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7485 | 2.7485 | 2.7485 | 0.0 | 98.08 Neigh | 0.016968 | 0.016968 | 0.016968 | 0.0 | 0.61 Comm | 0.022257 | 0.022257 | 0.022257 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01469 | | | 0.52 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5894.00 ave 5894 max 5894 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: 124256.0 ave 124256 max 124256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124256 Ave neighs/atom = 227.57509 Neighbor list builds = 1 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -1468.7911 0 -1468.7911 5538.1728 9109.748 92 0 -1468.9576 0 -1468.9576 47.134206 9175.9612 Loop time of 0.135997 on 1 procs for 6 steps with 546 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 = -1468.79110580739 -1468.95723545458 -1468.95763045395 Force two-norm initial, final = 61.348616 0.73739797 Force max component initial, final = 51.346136 0.67387797 Final line search alpha, max atom move = 0.00040336408 0.00027181817 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13202 | 0.13202 | 0.13202 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096679 | 0.00096679 | 0.00096679 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003008 | | | 2.21 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5892.00 ave 5892 max 5892 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: 124760.0 ave 124760 max 124760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124760 Ave neighs/atom = 228.49817 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1468.9576 0 -1468.9576 47.134206 Loop time of 6.505e-06 on 1 procs for 0 steps with 546 atoms 169.1% 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 | | 6.505e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5878.00 ave 5878 max 5878 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: 124240.0 ave 124240 max 124240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124240 Ave neighs/atom = 227.54579 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.078 | 5.078 | 5.078 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 -1468.9576 -1468.9576 16.829121 94.707375 5.7571341 47.134206 47.134206 118.25546 -18.866435 42.013596 2.7148669 674.6746 Loop time of 7.056e-06 on 1 procs for 0 steps with 546 atoms 269.3% 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 | | 7.056e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5878.00 ave 5878 max 5878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62120.0 ave 62120 max 62120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124240.0 ave 124240 max 124240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124240 Ave neighs/atom = 227.54579 Neighbor list builds = 0 Dangerous builds = 0 546 -1468.95763045395 eV 2.7148669011104 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03