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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -67.884393 0.0000000) to (39.193073 67.884393 6.1459642) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7825845 5.1933416 6.1459642 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.884393 0.0000000) to (39.193073 67.884393 6.1459642) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7825845 5.1933416 6.1459642 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.884393 0.0000000) to (39.193073 67.884393 6.1459642) create_atoms CPU = 0.008 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 34 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 10.90 | 10.90 | 10.90 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11127.506 0 -11127.506 67014.736 74 0 -11826.284 0 -11826.284 17831.291 Loop time of 7.8725 on 1 procs for 74 steps with 2930 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 = -11127.5062089138 -11826.2739798136 -11826.2836374935 Force two-norm initial, final = 1047.8912 0.34296150 Force max component initial, final = 364.65793 0.061017187 Final line search alpha, max atom move = 0.80314858 0.049005867 Iterations, force evaluations = 74 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6317 | 7.6317 | 7.6317 | 0.0 | 96.94 Neigh | 0.15527 | 0.15527 | 0.15527 | 0.0 | 1.97 Comm | 0.045366 | 0.045366 | 0.045366 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04014 | | | 0.51 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13944.0 ave 13944 max 13944 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: 578016.0 ave 578016 max 578016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578016 Ave neighs/atom = 197.27509 Neighbor list builds = 2 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.90 | 10.90 | 10.90 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -11826.284 0 -11826.284 17831.291 32703.879 80 0 -11827.72 0 -11827.72 -8.2876269 32937.405 Loop time of 0.65023 on 1 procs for 6 steps with 2930 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 = -11826.2836374935 -11827.7193740035 -11827.7195827482 Force two-norm initial, final = 643.34110 0.82968492 Force max component initial, final = 465.06360 0.25392330 Final line search alpha, max atom move = 0.00029244692 7.4259086e-05 Iterations, force evaluations = 6 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6352 | 0.6352 | 0.6352 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033647 | 0.0033647 | 0.0033647 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01167 | | | 1.79 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13938.0 ave 13938 max 13938 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: 578068.0 ave 578068 max 578068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578068 Ave neighs/atom = 197.29283 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 10.41 | 10.41 | 10.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11827.72 0 -11827.72 -8.2876269 Loop time of 7.588e-06 on 1 procs for 0 steps with 2930 atoms 171.3% 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 | | 7.588e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13930.0 ave 13930 max 13930 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: 576876.0 ave 576876 max 576876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576876 Ave neighs/atom = 196.88601 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 10.41 | 10.41 | 10.41 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 -11827.72 -11827.72 39.262627 136.35391 6.1523697 -8.2876269 -8.2876269 -4.0542226 -8.4441759 -12.364482 2.3082168 1286.7967 Loop time of 8.359e-06 on 1 procs for 0 steps with 2930 atoms 263.2% 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 | | 8.359e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13930.0 ave 13930 max 13930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288438.0 ave 288438 max 288438 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 576876.0 ave 576876 max 576876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576876 Ave neighs/atom = 196.88601 Neighbor list builds = 0 Dangerous builds = 0 2930 -11827.7195827482 eV 2.30821676804416 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10