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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -50.275656 0.0000000) to (35.550257 50.275656 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5765109 4.4360873 4.9780317 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -50.275656 0.0000000) to (35.550257 50.275656 4.9780317) create_atoms CPU = 0.002 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5765109 4.4360873 4.9780317 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -50.275656 0.0000000) to (35.550257 50.275656 4.9780317) create_atoms CPU = 0.001 seconds 821 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1632 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7102.4641 0 -7102.4641 12957.723 66 0 -7242.0894 0 -7242.0894 11942.846 Loop time of 1.13912 on 1 procs for 66 steps with 1632 atoms 95.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7102.46410438115 -7242.08369529157 -7242.0894224183 Force two-norm initial, final = 63.024703 0.26057410 Force max component initial, final = 9.3102249 0.032817450 Final line search alpha, max atom move = 1.0000000 0.032817450 Iterations, force evaluations = 66 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.098 | 1.098 | 1.098 | 0.0 | 96.39 Neigh | 0.024379 | 0.024379 | 0.024379 | 0.0 | 2.14 Comm | 0.0085176 | 0.0085176 | 0.0085176 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008225 | | | 0.72 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7965.00 ave 7965 max 7965 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: 215902.0 ave 215902 max 215902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215902 Ave neighs/atom = 132.29289 Neighbor list builds = 2 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -7242.0894 0 -7242.0894 11942.846 17794.597 75 0 -7242.913 0 -7242.913 235.82141 17911.087 Loop time of 0.102742 on 1 procs for 9 steps with 1632 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7242.0894224183 -7242.91071901511 -7242.91303429296 Force two-norm initial, final = 250.95950 4.6460514 Force max component initial, final = 212.90985 3.2473830 Final line search alpha, max atom move = 0.00017471042 0.00056735164 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09869 | 0.09869 | 0.09869 | 0.0 | 96.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065853 | 0.00065853 | 0.00065853 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003394 | | | 3.30 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7968.00 ave 7968 max 7968 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: 215992.0 ave 215992 max 215992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215992 Ave neighs/atom = 132.34804 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.659 | 5.659 | 5.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7242.913 0 -7242.913 235.82141 Loop time of 1.907e-06 on 1 procs for 0 steps with 1632 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7968.00 ave 7968 max 7968 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: 215858.0 ave 215858 max 215858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215858 Ave neighs/atom = 132.26593 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.659 | 5.659 | 5.659 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 -7242.913 -7242.913 35.497218 101.39635 4.9762856 235.82141 235.82141 197.65091 292.92505 216.88827 2.3606679 1093.9239 Loop time of 2.967e-06 on 1 procs for 0 steps with 1632 atoms 269.6% 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 | | 2.967e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7968.00 ave 7968 max 7968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 107929.0 ave 107929 max 107929 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 215858.0 ave 215858 max 215858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215858 Ave neighs/atom = 132.26593 Neighbor list builds = 0 Dangerous builds = 0 1632 -7242.91303429296 eV 2.36066794940547 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01