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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -42.349083 0.0000000) to (29.945324 42.349083 5.1737640) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8102868 6.3207587 5.1737640 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -42.349083 0.0000000) to (29.945324 42.349083 5.1737640) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8102868 6.3207587 5.1737640 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -42.349083 0.0000000) to (29.945324 42.349083 5.1737640) create_atoms CPU = 0.001 seconds 538 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1068 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.012 | 5.012 | 5.012 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3892.4131 0 -3892.4131 59071.969 656 0 -4224.8319 0 -4224.8319 -69617.279 Loop time of 10.3576 on 1 procs for 656 steps with 1068 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3892.41314533446 -4224.82809736673 -4224.83189783253 Force two-norm initial, final = 645.20558 0.23476571 Force max component initial, final = 205.87937 0.036814339 Final line search alpha, max atom move = 1.0000000 0.036814339 Iterations, force evaluations = 656 1229 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.047 | 10.047 | 10.047 | 0.0 | 97.00 Neigh | 0.15132 | 0.15132 | 0.15132 | 0.0 | 1.46 Comm | 0.085468 | 0.085468 | 0.085468 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07393 | | | 0.71 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6072.00 ave 6072 max 6072 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: 143976.0 ave 143976 max 143976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143976 Ave neighs/atom = 134.80899 Neighbor list builds = 16 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 656 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.010 | 5.010 | 5.010 Mbytes Step Temp E_pair E_mol TotEng Press Volume 656 0 -4224.8319 0 -4224.8319 -69617.279 13122.29 703 0 -4251.9737 0 -4251.9737 68.928621 12474.917 Loop time of 0.439085 on 1 procs for 47 steps with 1068 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 = -4224.83189783253 -4251.97235274701 -4251.97366834593 Force two-norm initial, final = 1108.3827 5.6910128 Force max component initial, final = 923.23640 4.1862326 Final line search alpha, max atom move = 0.00061375029 0.0025693015 Iterations, force evaluations = 47 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41206 | 0.41206 | 0.41206 | 0.0 | 93.84 Neigh | 0.0097773 | 0.0097773 | 0.0097773 | 0.0 | 2.23 Comm | 0.0029061 | 0.0029061 | 0.0029061 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01434 | | | 3.27 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6159.00 ave 6159 max 6159 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: 149448.0 ave 149448 max 149448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149448 Ave neighs/atom = 139.93258 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.149 | 5.149 | 5.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4251.9737 0 -4251.9737 68.928621 Loop time of 2.638e-06 on 1 procs for 0 steps with 1068 atoms 151.6% 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 | | 2.638e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6268.00 ave 6268 max 6268 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: 150612.0 ave 150612 max 150612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150612 Ave neighs/atom = 141.02247 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.149 | 5.149 | 5.149 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 -4251.9737 -4251.9737 30.291497 83.307767 4.9434646 68.928621 68.928621 -23.516325 528.81958 -298.5174 2.2522807 3023.9808 Loop time of 2.616e-06 on 1 procs for 0 steps with 1068 atoms 229.4% 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 | | 2.616e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6268.00 ave 6268 max 6268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75306.0 ave 75306 max 75306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 150612.0 ave 150612 max 150612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150612 Ave neighs/atom = 141.02247 Neighbor list builds = 0 Dangerous builds = 0 1068 -4251.97366834593 eV 2.25228067045566 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11