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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -39.953426 0.0000000) to (34.597289 39.953426 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2097699 6.1460782 6.7850866 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -39.953426 0.0000000) to (34.597289 39.953426 6.7850866) create_atoms CPU = 0.004 seconds 630 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2097699 6.1460782 6.7850866 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -39.953426 0.0000000) to (34.597289 39.953426 6.7850866) create_atoms CPU = 0.003 seconds 630 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1232 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_070797404269_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7010.6258 0 -7010.6258 6154.8069 26 0 -7061.6363 0 -7061.6363 -7737.3805 Loop time of 2.22517 on 1 procs for 26 steps with 1232 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 = -7010.62576265957 -7061.6296308798 -7061.63629108163 Force two-norm initial, final = 66.374169 0.31663516 Force max component initial, final = 15.829258 0.064383839 Final line search alpha, max atom move = 1.0000000 0.064383839 Iterations, force evaluations = 26 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2142 | 2.2142 | 2.2142 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0045486 | 0.0045486 | 0.0045486 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006444 | | | 0.29 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3965.00 ave 3965 max 3965 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: 94632.0 ave 94632 max 94632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94632 Ave neighs/atom = 76.811688 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -7061.6363 0 -7061.6363 -7737.3805 18757.782 29 0 -7061.7845 0 -7061.7845 -1806.5755 18695.113 Loop time of 0.237989 on 1 procs for 3 steps with 1232 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7061.63629108161 -7061.7800809871 -7061.78454139957 Force two-norm initial, final = 116.40314 6.5730012 Force max component initial, final = 102.91473 6.4593527 Final line search alpha, max atom move = 5.9435277e-05 0.00038391342 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2356 | 0.2356 | 0.2356 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045945 | 0.00045945 | 0.00045945 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001933 | | | 0.81 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3998.00 ave 3998 max 3998 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: 94788.0 ave 94788 max 94788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94788 Ave neighs/atom = 76.938312 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.744 | 4.744 | 4.744 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7061.7845 0 -7061.7845 -1806.5755 Loop time of 6.194e-06 on 1 procs for 0 steps with 1232 atoms 193.7% 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 | | 6.194e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4004.00 ave 4004 max 4004 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: 94808.0 ave 94808 max 94808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94808 Ave neighs/atom = 76.954545 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.744 | 4.744 | 4.744 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 -7061.7845 -7061.7845 34.568528 79.906852 6.7680442 -1806.5755 -1806.5755 553.10818 -6072.2661 99.431525 2.4938828 1090.6007 Loop time of 7.196e-06 on 1 procs for 0 steps with 1232 atoms 291.8% 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 | | 7.196e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4004.00 ave 4004 max 4004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47404.0 ave 47404 max 47404 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94808.0 ave 94808 max 94808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94808 Ave neighs/atom = 76.954545 Neighbor list builds = 0 Dangerous builds = 0 1232 -7061.78454139957 eV 2.49388283544659 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03