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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -39.061056 0.0000000) to (22.551911 39.061056 6.3365399) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9347134 5.4822534 6.3365399 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.061056 0.0000000) to (22.551911 39.061056 6.3365399) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9347134 5.4822534 6.3365399 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.061056 0.0000000) to (22.551911 39.061056 6.3365399) create_atoms CPU = 0.001 seconds 458 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 19 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.025 | 5.025 | 5.025 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3408.6452 0 -3408.6452 47543.167 345 0 -3579.5478 0 -3579.5478 -57022.186 Loop time of 7.27876 on 1 procs for 345 steps with 912 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 = -3408.64518117632 -3579.54543717315 -3579.5477905476 Force two-norm initial, final = 233.84794 0.20510504 Force max component initial, final = 42.464136 0.059309545 Final line search alpha, max atom move = 1.0000000 0.059309545 Iterations, force evaluations = 345 677 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1276 | 7.1276 | 7.1276 | 0.0 | 97.92 Neigh | 0.072077 | 0.072077 | 0.072077 | 0.0 | 0.99 Comm | 0.045076 | 0.045076 | 0.045076 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03404 | | | 0.47 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6247.00 ave 6247 max 6247 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: 186644.0 ave 186644 max 186644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186644 Ave neighs/atom = 204.65351 Neighbor list builds = 6 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 345 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.020 | 5.020 | 5.020 Mbytes Step Temp E_pair E_mol TotEng Press Volume 345 0 -3579.5478 0 -3579.5478 -57022.186 11163.734 385 0 -3589.877 0 -3589.877 -158.0817 10699.778 Loop time of 0.577371 on 1 procs for 40 steps with 912 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 = -3579.54779054762 -3589.87355301742 -3589.87695102103 Force two-norm initial, final = 708.20736 5.2977940 Force max component initial, final = 508.09767 4.4375188 Final line search alpha, max atom move = 0.00011101395 0.00049262650 Iterations, force evaluations = 40 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53622 | 0.53622 | 0.53622 | 0.0 | 92.87 Neigh | 0.024991 | 0.024991 | 0.024991 | 0.0 | 4.33 Comm | 0.0029841 | 0.0029841 | 0.0029841 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01317 | | | 2.28 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6322.00 ave 6322 max 6322 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: 198512.0 ave 198512 max 198512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198512 Ave neighs/atom = 217.66667 Neighbor list builds = 2 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.540 | 5.540 | 5.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3589.877 0 -3589.877 -158.0817 Loop time of 2.128e-06 on 1 procs for 0 steps with 912 atoms 141.0% 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 | | 2.128e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6326.00 ave 6326 max 6326 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: 199020.0 ave 199020 max 199020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199020 Ave neighs/atom = 218.22368 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.540 | 5.540 | 5.540 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 -3589.877 -3589.877 22.225845 75.931979 6.3400368 -158.0817 -158.0817 -9.5762909 200.1685 -664.83729 2.2408544 3390.0466 Loop time of 2.84e-06 on 1 procs for 0 steps with 912 atoms 211.3% 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 | | 2.84e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6326.00 ave 6326 max 6326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99510.0 ave 99510 max 99510 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199020.0 ave 199020 max 199020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199020 Ave neighs/atom = 218.22368 Neighbor list builds = 0 Dangerous builds = 0 912 -3589.87695102104 eV 2.24085437091549 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08