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 = 2.8553128 2.8553128 2.8553128 Created orthogonal box = (0.0000000 -44.965511 0.0000000) to (27.535639 44.965511 6.9940594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4412321 4.3515010 4.6627062 Created 743 atoms using lattice units in orthogonal box = (0.0000000 -44.965511 0.0000000) to (27.535639 44.965511 6.9940594) create_atoms CPU = 0.001 seconds 743 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4412321 4.3515010 4.6627062 Created 749 atoms using lattice units in orthogonal box = (0.0000000 -44.965511 0.0000000) to (27.535639 44.965511 6.9940594) create_atoms CPU = 0.001 seconds 749 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1488 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.518 | 5.518 | 5.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3185.6628 0 -3185.6628 349913.2 92 0 -5944.8486 0 -5944.8486 3318.101 Loop time of 1.84431 on 1 procs for 92 steps with 1488 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 = -3185.66281216926 -5944.84331011595 -5944.84860145063 Force two-norm initial, final = 4909.1294 0.29810583 Force max component initial, final = 861.56666 0.092601151 Final line search alpha, max atom move = 1.0000000 0.092601151 Iterations, force evaluations = 92 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8054 | 1.8054 | 1.8054 | 0.0 | 97.89 Neigh | 0.014097 | 0.014097 | 0.014097 | 0.0 | 0.76 Comm | 0.011674 | 0.011674 | 0.011674 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01315 | | | 0.71 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6648.00 ave 6648 max 6648 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: 204246.0 ave 204246 max 204246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204246 Ave neighs/atom = 137.26210 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.516 | 5.516 | 5.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -5944.8486 0 -5944.8486 3318.101 17319.446 98 0 -5945.1624 0 -5945.1624 -52.205967 17353.587 Loop time of 0.0794505 on 1 procs for 6 steps with 1488 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 = -5944.84860145067 -5945.16230030559 -5945.16242316061 Force two-norm initial, final = 118.89518 1.1377795 Force max component initial, final = 115.74420 0.70273877 Final line search alpha, max atom move = 0.00061425104 0.00043165802 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076975 | 0.076975 | 0.076975 | 0.0 | 96.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038261 | 0.00038261 | 0.00038261 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002093 | | | 2.63 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6560.00 ave 6560 max 6560 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: 203304.0 ave 203304 max 203304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203304 Ave neighs/atom = 136.62903 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.654 | 5.654 | 5.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5945.1624 0 -5945.1624 -52.205967 Loop time of 1.843e-06 on 1 procs for 0 steps with 1488 atoms 108.5% 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 | | 1.843e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6644.00 ave 6644 max 6644 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: 203064.0 ave 203064 max 203064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203064 Ave neighs/atom = 136.46774 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.654 | 5.654 | 5.654 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 -5945.1624 -5945.1624 27.513442 90.388163 6.9780291 -52.205967 -52.205967 -54.931646 -36.954338 -64.731918 2.2329512 914.75263 Loop time of 2.34e-06 on 1 procs for 0 steps with 1488 atoms 170.9% 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 | | 2.34e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6644.00 ave 6644 max 6644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101532.0 ave 101532 max 101532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203064.0 ave 203064 max 203064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203064 Ave neighs/atom = 136.46774 Neighbor list builds = 0 Dangerous builds = 0 1488 -5945.16242316061 eV 2.2329512076741 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02