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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -59.151014 0.0000000) to (41.826083 59.151014 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6041183 5.7075539 5.5400000 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -59.151014 0.0000000) to (41.826083 59.151014 5.5400000) create_atoms CPU = 0.006 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6041183 5.7075539 5.5400000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -59.151014 0.0000000) to (41.826083 59.151014 5.5400000) create_atoms CPU = 0.006 seconds 916 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 37 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1828 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10013.977 0 -10013.977 54688.279 55 0 -10513.238 0 -10513.238 10444.347 Loop time of 7.30976 on 1 procs for 55 steps with 1828 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 = -10013.9771522242 -10513.2303571342 -10513.2383230736 Force two-norm initial, final = 468.14467 0.43420534 Force max component initial, final = 102.68446 0.12016648 Final line search alpha, max atom move = 1.0000000 0.12016648 Iterations, force evaluations = 55 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2695 | 7.2695 | 7.2695 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019812 | 0.019812 | 0.019812 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02048 | | | 0.28 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7468.00 ave 7468 max 7468 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: 142696.0 ave 142696 max 142696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142696 Ave neighs/atom = 78.061269 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -10513.238 0 -10513.238 10444.347 27412.532 62 0 -10514.074 0 -10514.074 -2.6766446 27573.832 Loop time of 0.694628 on 1 procs for 7 steps with 1828 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 = -10513.2383230736 -10514.0736975265 -10514.0739447053 Force two-norm initial, final = 336.35876 0.56176790 Force max component initial, final = 286.15809 0.16638657 Final line search alpha, max atom move = 0.00018820334 3.1314507e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68624 | 0.68624 | 0.68624 | 0.0 | 98.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017065 | 0.0017065 | 0.0017065 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006677 | | | 0.96 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7435.00 ave 7435 max 7435 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: 141818.0 ave 141818 max 141818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141818 Ave neighs/atom = 77.580963 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.292 | 5.292 | 5.292 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10514.074 0 -10514.074 -2.6766446 Loop time of 6.585e-06 on 1 procs for 0 steps with 1828 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7435.00 ave 7435 max 7435 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: 141704.0 ave 141704 max 141704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141704 Ave neighs/atom = 77.518600 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.292 | 5.292 | 5.292 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 -10514.074 -10514.074 41.837434 118.99656 5.5385706 -2.6766446 -2.6766446 3.3178839 -3.6400351 -7.7077825 2.4679015 718.49943 Loop time of 6.706e-06 on 1 procs for 0 steps with 1828 atoms 298.2% 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 | | 6.706e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7435.00 ave 7435 max 7435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70852.0 ave 70852 max 70852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141704.0 ave 141704 max 141704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141704 Ave neighs/atom = 77.518600 Neighbor list builds = 0 Dangerous builds = 0 1828 -10514.0739447053 eV 2.46790145084672 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08