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 = 3.5196184 3.5196184 3.5196184 Created orthogonal box = (0.0000000 -67.334264 0.0000000) to (38.875456 67.334264 6.0961579) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7357230 5.1512552 6.0961579 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.334264 0.0000000) to (38.875456 67.334264 6.0961579) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7357230 5.1512552 6.0961579 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.334264 0.0000000) to (38.875456 67.334264 6.0961579) create_atoms CPU = 0.009 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 11 36 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 7.565005302429199 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_110256178378_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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12433.088 0 -12433.088 41974.291 104 0 -12984.414 0 -12984.414 5839.2905 Loop time of 9.74149 on 1 procs for 104 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 = -12433.0878296372 -12984.401500921 -12984.4144141702 Force two-norm initial, final = 797.29373 0.43917025 Force max component initial, final = 221.66249 0.10653853 Final line search alpha, max atom move = 1.0000000 0.10653853 Iterations, force evaluations = 104 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4308 | 9.4308 | 9.4308 | 0.0 | 96.81 Neigh | 0.19523 | 0.19523 | 0.19523 | 0.0 | 2.00 Comm | 0.059005 | 0.059005 | 0.059005 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05643 | | | 0.58 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12134.0 ave 12134 max 12134 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: 508852.0 ave 508852 max 508852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508852 Ave neighs/atom = 173.90704 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -12984.414 0 -12984.414 5839.2905 31915.218 108 0 -12984.684 0 -12984.684 74.773312 32019.685 Loop time of 2.17833 on 1 procs for 4 steps with 2926 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -12984.4144141704 -12984.6839347001 -12984.6839347001 Force two-norm initial, final = 218.40154 4.5133939 Force max component initial, final = 185.15292 4.2140488 Final line search alpha, max atom move = 4.7309169e-10 1.9936315e-09 Iterations, force evaluations = 4 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1259 | 2.1259 | 2.1259 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01219 | 0.01219 | 0.01219 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04023 | | | 1.85 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12132.0 ave 12132 max 12132 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: 509556.0 ave 509556 max 509556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509556 Ave neighs/atom = 174.14764 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 7.132 | 7.132 | 7.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12984.684 0 -12984.684 74.773312 Loop time of 6.886e-06 on 1 procs for 0 steps with 2926 atoms 203.3% 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 | | 6.886e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12125.0 ave 12125 max 12125 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: 509244.0 ave 509244 max 509244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509244 Ave neighs/atom = 174.04101 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 = 7.5650053 ghost atom cutoff = 7.5650053 binsize = 3.7825027, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.565005302429199 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) = 7.132 | 7.132 | 7.132 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 -12984.684 -12984.684 38.880876 135.04429 6.0982441 74.773312 74.773312 -47.714975 61.103401 210.93151 2.2314629 904.46276 Loop time of 6.876e-06 on 1 procs for 0 steps with 2926 atoms 276.3% 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 | | 6.876e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12125.0 ave 12125 max 12125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 254622.0 ave 254622 max 254622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 509244.0 ave 509244 max 509244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509244 Ave neighs/atom = 174.04101 Neighbor list builds = 0 Dangerous builds = 0 2926 -12984.6846323129 eV 2.23146288730232 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12