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 -38.560170 0.0000000) to (27.263604 38.560170 5.1069410) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2180151 6.0878778 5.1069410 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.560170 0.0000000) to (27.263604 38.560170 5.1069410) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2180151 6.0878778 5.1069410 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.560170 0.0000000) to (27.263604 38.560170 5.1069410) create_atoms CPU = 0.001 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 29 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 6 atoms, new total = 910 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 = 11 29 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) = 4.931 | 4.931 | 4.931 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3798.9077 0 -3798.9077 18933.403 19 0 -3846.3947 0 -3846.3947 4812.9904 Loop time of 1.46276 on 1 procs for 19 steps with 910 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 = -3798.90766017676 -3846.39320622332 -3846.39468502364 Force two-norm initial, final = 62.468177 0.74281623 Force max component initial, final = 14.908580 0.20684017 Final line search alpha, max atom move = 0.54228356 0.11216602 Iterations, force evaluations = 19 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4603 | 1.4603 | 1.4603 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095459 | 0.00095459 | 0.00095459 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001515 | | | 0.10 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3428.00 ave 3428 max 3428 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: 48956.0 ave 48956 max 48956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48956 Ave neighs/atom = 53.797802 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 29 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.931 | 4.931 | 4.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -3846.3947 0 -3846.3947 4812.9904 10737.744 21 0 -3846.4177 0 -3846.4177 1707.5026 10758.048 Loop time of 0.167677 on 1 procs for 2 steps with 910 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 = -3846.39468502364 -3846.41730522099 -3846.41768344041 Force two-norm initial, final = 34.203251 0.93456709 Force max component initial, final = 26.500933 0.46322006 Final line search alpha, max atom move = 0.00041352355 0.00019155240 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16709 | 0.16709 | 0.16709 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010676 | 0.00010676 | 0.00010676 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004819 | | | 0.29 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3428.00 ave 3428 max 3428 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: 49064.0 ave 49064 max 49064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49064 Ave neighs/atom = 53.916484 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 = 11 29 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) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3846.4177 0 -3846.4177 1707.5026 Loop time of 1.806e-06 on 1 procs for 0 steps with 910 atoms 166.1% 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 | | 1.806e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3428.00 ave 3428 max 3428 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: 49064.0 ave 49064 max 49064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49064 Ave neighs/atom = 53.916484 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 = 11 29 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) = 5.069 | 5.069 | 5.069 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 -3846.4177 -3846.4177 27.282178 77.120341 5.1131142 1707.5026 1707.5026 -53.872145 5245.4498 -69.06991 2.3212716 274.90378 Loop time of 1.45e-06 on 1 procs for 0 steps with 910 atoms 206.9% 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 | | 1.45e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3428.00 ave 3428 max 3428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24532.0 ave 24532 max 24532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49064.0 ave 49064 max 49064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49064 Ave neighs/atom = 53.916484 Neighbor list builds = 0 Dangerous builds = 0 910 -3846.41768344041 eV 2.32127163760082 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02