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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -43.580149 0.0000000) to (25.161011 43.580149 7.0696337) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6213186 6.1165122 7.0696337 Created 455 atoms using lattice units in orthogonal box = (0.0000000 -43.580149 0.0000000) to (25.161011 43.580149 7.0696337) create_atoms CPU = 0.001 seconds 455 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6213186 6.1165122 7.0696337 Created 457 atoms using lattice units in orthogonal box = (0.0000000 -43.580149 0.0000000) to (25.161011 43.580149 7.0696337) create_atoms CPU = 0.001 seconds 457 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 15 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 912 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_049243498555_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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.866 | 5.866 | 5.866 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3172.1132 0 -3172.1132 15479.947 153 0 -3256.4573 0 -3256.4573 5448.9688 Loop time of 6.3587 on 1 procs for 153 steps with 912 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 = -3172.1132359267 -3256.45438331229 -3256.45731490781 Force two-norm initial, final = 90.513156 0.10343279 Force max component initial, final = 22.516487 0.019902154 Final line search alpha, max atom move = 1.0000000 0.019902154 Iterations, force evaluations = 153 255 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1793 | 6.1793 | 6.1793 | 0.0 | 97.18 Neigh | 0.13943 | 0.13943 | 0.13943 | 0.0 | 2.19 Comm | 0.024403 | 0.024403 | 0.024403 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01553 | | | 0.24 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9006.00 ave 9006 max 9006 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: 390114.0 ave 390114 max 390114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390114 Ave neighs/atom = 427.75658 Neighbor list builds = 7 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 153 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.859 | 5.859 | 5.859 Mbytes Step Temp E_pair E_mol TotEng Press Volume 153 0 -3256.4573 0 -3256.4573 5448.9688 15503.998 159 0 -3256.6641 0 -3256.6641 -4.8421882 15595.533 Loop time of 0.215653 on 1 procs for 6 steps with 912 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 = -3256.45731490781 -3256.66254258911 -3256.66412003641 Force two-norm initial, final = 94.725698 0.57814745 Force max component initial, final = 72.730109 0.46293164 Final line search alpha, max atom move = 9.9472630e-05 4.6049028e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21247 | 0.21247 | 0.21247 | 0.0 | 98.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062763 | 0.00062763 | 0.00062763 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002553 | | | 1.18 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9012.00 ave 9012 max 9012 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: 390196.0 ave 390196 max 390196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390196 Ave neighs/atom = 427.84649 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.997 | 5.997 | 5.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3256.6641 0 -3256.6641 -4.8421882 Loop time of 1.821e-06 on 1 procs for 0 steps with 912 atoms 219.7% 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 | | 1.821e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8980.00 ave 8980 max 8980 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: 389438.0 ave 389438 max 389438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389438 Ave neighs/atom = 427.01535 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.997 | 5.997 | 5.997 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 -3256.6641 -3256.6641 25.180621 87.627904 7.0679156 -4.8421882 -4.8421882 -47.595441 1.7558175 31.313059 2.588818 796.60769 Loop time of 2.062e-06 on 1 procs for 0 steps with 912 atoms 242.5% 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 | | 2.062e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8980.00 ave 8980 max 8980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 194719.0 ave 194719 max 194719 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 389438.0 ave 389438 max 389438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389438 Ave neighs/atom = 427.01535 Neighbor list builds = 0 Dangerous builds = 0 912 -3256.66412003641 eV 2.58881803060734 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07