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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -52.361773 0.0000000) to (30.231083 52.361773 6.9971362) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4780893 6.2335443 6.9971362 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -52.361773 0.0000000) to (30.231083 52.361773 6.9971362) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4780893 6.2335443 6.9971362 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.361773 0.0000000) to (30.231083 52.361773 6.9971362) create_atoms CPU = 0.001 seconds 676 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 18 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1348 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_279544746097_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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.742 | 6.742 | 6.742 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3563.5014 0 -3563.5014 25890.954 109 0 -3870.1503 0 -3870.1503 5051.4138 Loop time of 4.90433 on 1 procs for 109 steps with 1348 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3563.50140026155 -3870.14652856505 -3870.15026403228 Force two-norm initial, final = 329.75845 0.19148117 Force max component initial, final = 73.850148 0.028863147 Final line search alpha, max atom move = 1.0000000 0.028863147 Iterations, force evaluations = 109 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7487 | 4.7487 | 4.7487 | 0.0 | 96.83 Neigh | 0.11118 | 0.11118 | 0.11118 | 0.0 | 2.27 Comm | 0.025908 | 0.025908 | 0.025908 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01859 | | | 0.38 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11368.0 ave 11368 max 11368 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: 554288.0 ave 554288 max 554288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554288 Ave neighs/atom = 411.19288 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.742 | 6.742 | 6.742 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -3870.1503 0 -3870.1503 5051.4138 22152.277 115 0 -3870.4714 0 -3870.4714 53.970717 22296.911 Loop time of 0.177069 on 1 procs for 6 steps with 1348 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 = -3870.15026403228 -3870.47083872865 -3870.47137211466 Force two-norm initial, final = 131.31964 1.9330130 Force max component initial, final = 111.14779 1.7427681 Final line search alpha, max atom move = 0.00022014544 0.00038366245 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17358 | 0.17358 | 0.17358 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067209 | 0.00067209 | 0.00067209 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002819 | | | 1.59 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11373.0 ave 11373 max 11373 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: 557856.0 ave 557856 max 557856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557856 Ave neighs/atom = 413.83976 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.880 | 6.880 | 6.880 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3870.4714 0 -3870.4714 53.970717 Loop time of 1.947e-06 on 1 procs for 0 steps with 1348 atoms 154.1% 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 | | 1.947e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11369.0 ave 11369 max 11369 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: 540360.0 ave 540360 max 540360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 540360 Ave neighs/atom = 400.86053 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 6.880 | 6.880 | 6.880 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 -3870.4714 -3870.4714 30.237901 105.24818 7.0061345 53.970717 53.970717 -17.914197 125.85646 53.969887 2.5998772 1069.1819 Loop time of 2.399e-06 on 1 procs for 0 steps with 1348 atoms 250.1% 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 | | 2.399e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11369.0 ave 11369 max 11369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 270180.0 ave 270180 max 270180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 540360.0 ave 540360 max 540360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 540360 Ave neighs/atom = 400.86053 Neighbor list builds = 0 Dangerous builds = 0 1348 -3870.47137211466 eV 2.59987723318718 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05