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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -36.584036 0.0000000) to (3.6584036 36.584036 3.6584036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6584036 3.6584036 3.6584036 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -36.584036 0.0000000) to (3.6584036 36.584036 3.6584036) create_atoms CPU = 0.000 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6584036 3.6584036 3.6584036 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -36.584036 0.0000000) to (3.6584036 36.584036 3.6584036) create_atoms CPU = 0.000 seconds 42 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 82 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.395 | 4.395 | 4.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 13.800413 0 13.800413 826327.66 56 0 -318.90462 0 -318.90462 19314.124 Loop time of 0.173377 on 1 procs for 56 steps with 82 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 13.8004132975179 -318.904326271758 -318.904622050109 Force two-norm initial, final = 1423.0594 0.066289911 Force max component initial, final = 711.47585 0.020099723 Final line search alpha, max atom move = 1.0000000 0.020099723 Iterations, force evaluations = 56 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16598 | 0.16598 | 0.16598 | 0.0 | 95.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050095 | 0.0050095 | 0.0050095 | 0.0 | 2.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002386 | | | 1.38 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2318.00 ave 2318 max 2318 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: 11220.0 ave 11220 max 11220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11220 Ave neighs/atom = 136.82927 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.396 | 4.396 | 4.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -318.90462 0 -318.90462 19314.124 979.27539 351 0 -328.4524 0 -328.4524 160.20233 955.22863 Loop time of 0.61643 on 1 procs for 295 steps with 82 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 = -318.904622050109 -328.452233810438 -328.452398722358 Force two-norm initial, final = 21.212716 0.37728024 Force max component initial, final = 15.119116 0.17395200 Final line search alpha, max atom move = 0.0013677842 0.00023792879 Iterations, force evaluations = 295 314 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53307 | 0.53307 | 0.53307 | 0.0 | 86.48 Neigh | 0.024021 | 0.024021 | 0.024021 | 0.0 | 3.90 Comm | 0.016586 | 0.016586 | 0.016586 | 0.0 | 2.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04275 | | | 6.94 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2348.00 ave 2348 max 2348 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: 11360.0 ave 11360 max 11360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11360 Ave neighs/atom = 138.53659 Neighbor list builds = 14 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -328.4524 0 -328.4524 160.20233 Loop time of 6.415e-06 on 1 procs for 0 steps with 82 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2338.00 ave 2338 max 2338 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: 11360.0 ave 11360 max 11360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11360 Ave neighs/atom = 138.53659 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.533 | 4.533 | 4.533 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 -328.4524 -328.4524 4.0376147 58.531253 4.0419844 160.20233 160.20233 170.01926 -11.768058 322.35579 2.4263469 235.87792 Loop time of 6.304e-06 on 1 procs for 0 steps with 82 atoms 222.1% 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 | | 6.304e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2338.00 ave 2338 max 2338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5680.00 ave 5680 max 5680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11360.0 ave 11360 max 11360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11360 Ave neighs/atom = 138.53659 Neighbor list builds = 0 Dangerous builds = 0 82 -328.452398722358 eV 2.42634691922819 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02