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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -63.363763 0.0000000) to (44.802458 63.363763 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0842844 5.8666892 4.9780508 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.363763 0.0000000) to (44.802458 63.363763 4.9780508) create_atoms CPU = 0.011 seconds 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0842844 5.8666892 4.9780508 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.363763 0.0000000) to (44.802458 63.363763 4.9780508) create_atoms CPU = 0.010 seconds 1299 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 = 11 30 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 18 atoms, new total = 2580 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 30 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11401.576 0 -11401.576 2760.3667 78 0 -11447.897 0 -11447.897 -1975.3088 Loop time of 10.2584 on 1 procs for 78 steps with 2580 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 = -11401.5763390212 -11447.8864012327 -11447.8972567012 Force two-norm initial, final = 31.030738 0.35974942 Force max component initial, final = 6.0033361 0.038771570 Final line search alpha, max atom move = 1.0000000 0.038771570 Iterations, force evaluations = 78 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.066 | 10.066 | 10.066 | 0.0 | 98.13 Neigh | 0.086017 | 0.086017 | 0.086017 | 0.0 | 0.84 Comm | 0.061137 | 0.061137 | 0.061137 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04502 | | | 0.44 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15537.0 ave 15537 max 15537 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: 578982.0 ave 578982 max 578982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578982 Ave neighs/atom = 224.41163 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 30 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -11447.897 0 -11447.897 -1975.3088 28263.902 79 0 -11447.902 0 -11447.902 -1158.6273 28250.934 Loop time of 0.208059 on 1 procs for 1 steps with 2580 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 = -11447.8972567012 -11447.8972567012 -11447.902342484 Force two-norm initial, final = 26.198722 5.9692036 Force max component initial, final = 25.628746 5.8172550 Final line search alpha, max atom move = 3.9018686e-05 0.00022698165 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20332 | 0.20332 | 0.20332 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012998 | 0.0012998 | 0.0012998 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003442 | | | 1.65 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15591.0 ave 15591 max 15591 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: 578604.0 ave 578604 max 578604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578604 Ave neighs/atom = 224.26512 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 = 11 30 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) = 10.36 | 10.36 | 10.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11447.902 0 -11447.902 -1158.6273 Loop time of 6.325e-06 on 1 procs for 0 steps with 2580 atoms 189.7% 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 | | 6.325e-06 | | |100.00 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15591.0 ave 15591 max 15591 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: 578632.0 ave 578632 max 578632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578632 Ave neighs/atom = 224.27597 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 = 11 30 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) = 10.36 | 10.36 | 10.36 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 -11447.902 -11447.902 44.78549 126.72753 4.9776519 -1158.6273 -1158.6273 -73.064771 -3732.7007 329.88369 2.2702007 1132.8914 Loop time of 6.525e-06 on 1 procs for 0 steps with 2580 atoms 306.5% 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 | | 6.525e-06 | | |100.00 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15591.0 ave 15591 max 15591 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289316.0 ave 289316 max 289316 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 578632.0 ave 578632 max 578632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578632 Ave neighs/atom = 224.27597 Neighbor list builds = 0 Dangerous builds = 0 2580 -11377.5679259639 eV 2.2702006710448 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11