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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -52.582787 0.0000000) to (26.289588 52.582787 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4642697 4.4642697 3.6111526 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.582787 0.0000000) to (26.289588 52.582787 3.6111526) create_atoms CPU = 0.001 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4642697 4.4642697 3.6111526 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.582787 0.0000000) to (26.289588 52.582787 3.6111526) create_atoms CPU = 0.000 seconds 426 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 14 atoms, new total = 838 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.919 | 4.919 | 4.919 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3525.3366 0 -3525.3366 -2595.5149 52 0 -3545.4156 0 -3545.4156 -12618.25 Loop time of 3.93355 on 1 procs for 52 steps with 838 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 = -3525.33664535146 -3545.41224731924 -3545.41559490315 Force two-norm initial, final = 22.369459 0.23201926 Force max component initial, final = 9.4625078 0.067077034 Final line search alpha, max atom move = 1.0000000 0.067077034 Iterations, force evaluations = 52 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.909 | 3.909 | 3.909 | 0.0 | 99.38 Neigh | 0.01753 | 0.01753 | 0.01753 | 0.0 | 0.45 Comm | 0.0030916 | 0.0030916 | 0.0030916 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003916 | | | 0.10 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3704.00 ave 3704 max 3704 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: 44928.0 ave 44928 max 44928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44928 Ave neighs/atom = 53.613365 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.919 | 4.919 | 4.919 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -3545.4156 0 -3545.4156 -12618.25 9983.9689 56 0 -3545.6093 0 -3545.6093 -3125.4481 9924.8129 Loop time of 0.264932 on 1 procs for 4 steps with 838 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 = -3545.41559490315 -3545.60870926599 -3545.60934404301 Force two-norm initial, final = 91.996558 1.2939592 Force max component initial, final = 68.693126 1.1388661 Final line search alpha, max atom move = 0.00021755184 0.00024776240 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26375 | 0.26375 | 0.26375 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019614 | 0.00019614 | 0.00019614 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009871 | | | 0.37 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3694.00 ave 3694 max 3694 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: 44916.0 ave 44916 max 44916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44916 Ave neighs/atom = 53.599045 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3545.6093 0 -3545.6093 -3125.4481 Loop time of 1.878e-06 on 1 procs for 0 steps with 838 atoms 106.5% 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 | | 1.878e-06 | | |100.00 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3704.00 ave 3704 max 3704 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: 44932.0 ave 44932 max 44932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44932 Ave neighs/atom = 53.618138 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.057 | 5.057 | 5.057 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 -3545.6093 -3545.6093 26.204854 105.16557 3.6013638 -3125.4481 -3125.4481 -87.5755 -9472.1193 183.35039 2.3134449 178.88207 Loop time of 1.781e-06 on 1 procs for 0 steps with 838 atoms 168.4% 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 | | 1.781e-06 | | |100.00 Nlocal: 838.000 ave 838 max 838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3704.00 ave 3704 max 3704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22466.0 ave 22466 max 22466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44932.0 ave 44932 max 44932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44932 Ave neighs/atom = 53.618138 Neighbor list builds = 0 Dangerous builds = 0 838 -3545.60934404301 eV 2.31344485587424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04