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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -37.414399 0.0000000) to (45.823094 37.414399 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8320301 5.4420944 5.8254141 Created 1315 atoms using lattice units in orthogonal box = (0.0000000 -37.414399 0.0000000) to (45.823094 37.414399 8.7381211) create_atoms CPU = 0.002 seconds 1315 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8320301 5.4420944 5.8254141 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -37.414399 0.0000000) to (45.823094 37.414399 8.7381211) create_atoms CPU = 0.002 seconds 1321 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 17 27 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2605 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 17 27 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10506.343 0 -10506.343 24719.076 474 0 -10988.431 0 -10988.431 41665.041 Loop time of 57.2053 on 1 procs for 474 steps with 2605 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10506.3428249114 -10988.4213200509 -10988.4305797846 Force two-norm initial, final = 480.00770 0.53296947 Force max component initial, final = 93.336514 0.10470050 Final line search alpha, max atom move = 1.0000000 0.10470050 Iterations, force evaluations = 474 914 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.972 | 56.972 | 56.972 | 0.0 | 99.59 Neigh | 0.070125 | 0.070125 | 0.070125 | 0.0 | 0.12 Comm | 0.057853 | 0.057853 | 0.057853 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1049 | | | 0.18 Nlocal: 2605.00 ave 2605 max 2605 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5870.00 ave 5870 max 5870 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: 159762.0 ave 159762 max 159762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159762 Ave neighs/atom = 61.328983 Neighbor list builds = 5 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 17 27 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 474 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press Volume 474 0 -10988.431 0 -10988.431 41665.041 29962.03 487 0 -10995.452 0 -10995.452 -1930.3631 30501.885 Loop time of 1.0805 on 1 procs for 13 steps with 2605 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 = -10988.4305797845 -10995.4486570315 -10995.4520251413 Force two-norm initial, final = 1356.5714 64.835880 Force max component initial, final = 888.04622 47.676310 Final line search alpha, max atom move = 1.4948754e-05 0.00071270142 Iterations, force evaluations = 13 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0733 | 1.0733 | 1.0733 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081165 | 0.00081165 | 0.00081165 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006382 | | | 0.59 Nlocal: 2605.00 ave 2605 max 2605 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5870.00 ave 5870 max 5870 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: 159722.0 ave 159722 max 159722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159722 Ave neighs/atom = 61.313628 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 17 27 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.262 | 5.262 | 5.262 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10995.452 0 -10995.452 -1930.3631 Loop time of 2.515e-06 on 1 procs for 0 steps with 2605 atoms 159.0% 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 | | 2.515e-06 | | |100.00 Nlocal: 2605.00 ave 2605 max 2605 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5837.00 ave 5837 max 5837 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: 153434.0 ave 153434 max 153434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153434 Ave neighs/atom = 58.899808 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 17 27 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.262 | 5.262 | 5.262 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 -10995.452 -10995.452 45.999608 75.266281 8.8099225 -1930.3631 -1930.3631 -1742.0319 -1524.1798 -2524.8777 2.2119756 5578.4632 Loop time of 2.73e-06 on 1 procs for 0 steps with 2605 atoms 256.4% 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 | | 2.73e-06 | | |100.00 Nlocal: 2605.00 ave 2605 max 2605 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5837.00 ave 5837 max 5837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76717.0 ave 76717 max 76717 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 153434.0 ave 153434 max 153434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153434 Ave neighs/atom = 58.899808 Neighbor list builds = 0 Dangerous builds = 0 2605 -10995.4520251413 eV 2.2119755649058 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:58