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 -36.111526 0.0000000) to (3.6111526 36.111526 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6111526 3.6111526 3.6111526 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -36.111526 0.0000000) to (3.6111526 36.111526 3.6111526) create_atoms CPU = 0.001 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6111526 3.6111526 3.6111526 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -36.111526 0.0000000) to (3.6111526 36.111526 3.6111526) 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 2 27 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 2 atoms, new total = 80 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 = 2 27 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) = 4.365 | 4.365 | 4.365 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -339.97079 0 -339.97079 -0.0057004807 1 0 -339.97079 0 -339.97079 -0.0057004806 Loop time of 0.0312345 on 1 procs for 1 steps with 80 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 = -339.970788731098 -339.970788731098 -339.970788731098 Force two-norm initial, final = 7.4541963e-08 2.4787810e-08 Force max component initial, final = 3.7248564e-08 1.2357542e-08 Final line search alpha, max atom move = 1.0000000 1.2357542e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030989 | 0.030989 | 0.030989 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.5025e-05 | 7.5025e-05 | 7.5025e-05 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00017 | | | 0.54 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1023.00 ave 1023 max 1023 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: 4320.00 ave 4320 max 4320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4320 Ave neighs/atom = 54.000000 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 = 2 27 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.365 | 4.365 | 4.365 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -339.97079 0 -339.97079 -0.0057004806 941.81918 2 0 -339.97079 0 -339.97079 1.2950132e-07 941.81917 Loop time of 0.0310893 on 1 procs for 1 steps with 80 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 = -339.970788731098 -339.970788731098 -339.970788731095 Force two-norm initial, final = 5.8041520e-06 3.5644228e-08 Force max component initial, final = 3.3749135e-06 2.0909266e-08 Final line search alpha, max atom move = 1.0000000 2.0909266e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030817 | 0.030817 | 0.030817 | 0.0 | 99.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.3889e-05 | 6.3889e-05 | 6.3889e-05 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002088 | | | 0.67 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1023.00 ave 1023 max 1023 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: 4320.00 ave 4320 max 4320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4320 Ave neighs/atom = 54.000000 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 = 2 27 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) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -339.97079 0 -339.97079 1.2950132e-07 Loop time of 5.894e-06 on 1 procs for 0 steps with 80 atoms 186.6% 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 | | 5.894e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1023.00 ave 1023 max 1023 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: 4320.00 ave 4320 max 4320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4320 Ave neighs/atom = 54.000000 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 = 2 27 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) = 4.503 | 4.503 | 4.503 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 -339.97079 -339.97079 3.6111526 72.223052 3.6111526 1.2950132e-07 1.2950132e-07 1.7979145e-05 -3.5569816e-05 1.7979174e-05 2.5534705 9.8718579e-17 Loop time of 6.345e-06 on 1 procs for 0 steps with 80 atoms 189.1% 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 | | 6.345e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1023.00 ave 1023 max 1023 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2160.00 ave 2160 max 2160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4320.00 ave 4320 max 4320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4320 Ave neighs/atom = 54.000000 Neighbor list builds = 0 Dangerous builds = 0 80 -339.970788731095 eV 2.55347050713682 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00