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 = 3.9946166 3.9946166 3.9946166 Created orthogonal box = (0.0000000 -42.650834 0.0000000) to (30.158694 42.650834 5.6492410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8200989 6.7343423 5.6492410 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -42.650834 0.0000000) to (30.158694 42.650834 5.6492410) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8200989 6.7343423 5.6492410 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -42.650834 0.0000000) to (30.158694 42.650834 5.6492410) create_atoms CPU = 0.003 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 23 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 7.618764085891188 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2914.9985 0 -2914.9985 10311.883 91 0 -2986.6681 0 -2986.6681 1044.9688 Loop time of 4.38018 on 1 procs for 91 steps with 912 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 = -2914.99853174038 -2986.66529870723 -2986.66808994644 Force two-norm initial, final = 101.20462 0.11922066 Force max component initial, final = 28.240787 0.024003804 Final line search alpha, max atom move = 1.0000000 0.024003804 Iterations, force evaluations = 91 175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3193 | 4.3193 | 4.3193 | 0.0 | 98.61 Neigh | 0.018102 | 0.018102 | 0.018102 | 0.0 | 0.41 Comm | 0.021322 | 0.021322 | 0.021322 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0215 | | | 0.49 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5099.00 ave 5099 max 5099 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: 119036.0 ave 119036 max 119036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119036 Ave neighs/atom = 130.52193 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.964 | 4.964 | 4.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -2986.6681 0 -2986.6681 1044.9688 14533.164 96 0 -2986.7358 0 -2986.7358 53.997883 14570.008 Loop time of 0.190331 on 1 procs for 5 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 = -2986.66808994644 -2986.73360450406 -2986.73582678091 Force two-norm initial, final = 28.876267 0.98392347 Force max component initial, final = 28.176628 0.85573841 Final line search alpha, max atom move = 0.00029647972 0.00025370909 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18622 | 0.18622 | 0.18622 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086468 | 0.00086468 | 0.00086468 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003245 | | | 1.70 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4763.00 ave 4763 max 4763 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: 118984.0 ave 118984 max 118984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118984 Ave neighs/atom = 130.46491 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.102 | 5.102 | 5.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2986.7358 0 -2986.7358 53.997883 Loop time of 9.202e-06 on 1 procs for 0 steps with 912 atoms 184.7% 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 | | 9.202e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4760.00 ave 4760 max 4760 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: 118812.0 ave 118812 max 118812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118812 Ave neighs/atom = 130.27632 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 5.102 | 5.102 | 5.102 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 -2986.7358 -2986.7358 30.078853 85.674727 5.6538695 53.997883 53.997883 43.527075 24.289048 94.177526 2.5697026 781.74021 Loop time of 7.136e-06 on 1 procs for 0 steps with 912 atoms 238.2% 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 | | 7.136e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4760.00 ave 4760 max 4760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59406.0 ave 59406 max 59406 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118812.0 ave 118812 max 118812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118812 Ave neighs/atom = 130.27632 Neighbor list builds = 0 Dangerous builds = 0 912 -2986.73582678091 eV 2.56970261750994 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04