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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -48.159948 0.0000000) to (24.078433 48.159948 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3420124 4.3420124 3.0829274 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -48.159948 0.0000000) to (24.078433 48.159948 3.0829274) create_atoms CPU = 0.000 seconds 245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3420124 4.3420124 3.0829274 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -48.159948 0.0000000) to (24.078433 48.159948 3.0829274) create_atoms CPU = 0.000 seconds 245 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 29 1 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 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 482 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_152208847456_000#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.240 | 5.240 | 5.240 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3076.3142 0 -3076.3142 12207.75 120 0 -3127.64 0 -3127.64 -21086.573 Loop time of 12.9296 on 1 procs for 120 steps with 482 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 = -3076.3141802033 -3127.63726894037 -3127.63999266321 Force two-norm initial, final = 117.91904 0.24164438 Force max component initial, final = 52.204550 0.079450968 Final line search alpha, max atom move = 0.84115926 0.066830917 Iterations, force evaluations = 120 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.911 | 12.911 | 12.911 | 0.0 | 99.86 Neigh | 0.0087819 | 0.0087819 | 0.0087819 | 0.0 | 0.07 Comm | 0.0068869 | 0.0068869 | 0.0068869 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002939 | | | 0.02 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4085.00 ave 4085 max 4085 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: 34712.0 ave 34712 max 34712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34712 Ave neighs/atom = 72.016598 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.237 | 5.237 | 5.237 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -3127.64 0 -3127.64 -21086.573 7150.0242 130 0 -3128.3065 0 -3128.3065 2303.9689 7068.6331 Loop time of 0.636732 on 1 procs for 10 steps with 482 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 = -3127.63999266322 -3128.30353986148 -3128.30646829305 Force two-norm initial, final = 158.89259 4.5755786 Force max component initial, final = 112.42918 3.3498775 Final line search alpha, max atom move = 0.00024363404 0.00081614417 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63581 | 0.63581 | 0.63581 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002163 | 0.0002163 | 0.0002163 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007104 | | | 0.11 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3778.00 ave 3778 max 3778 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: 34678.0 ave 34678 max 34678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34678 Ave neighs/atom = 71.946058 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.375 | 5.375 | 5.375 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3128.3065 0 -3128.3065 2303.9689 Loop time of 1.8e-06 on 1 procs for 0 steps with 482 atoms 111.1% 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 | | 1.8e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3778.00 ave 3778 max 3778 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: 35712.0 ave 35712 max 35712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35712 Ave neighs/atom = 74.091286 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.375 | 5.375 | 5.375 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 -3128.3065 -3128.3065 24.037563 96.319896 3.0530155 2303.9689 2303.9689 -694.20711 8358.0301 -751.91639 2.5099411 658.81373 Loop time of 2.4e-06 on 1 procs for 0 steps with 482 atoms 166.7% 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 | | 2.4e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3778.00 ave 3778 max 3778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17856.0 ave 17856 max 17856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35712.0 ave 35712 max 35712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35712 Ave neighs/atom = 74.091286 Neighbor list builds = 0 Dangerous builds = 0 482 -3128.30646829305 eV 2.50994112741047 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13