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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.104128 0.0000000) to (52.791559 43.104128 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0622043 5.3142075 5.8254141 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -43.104128 0.0000000) to (52.791559 43.104128 8.7381211) create_atoms CPU = 0.006 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0622043 5.3142075 5.8254141 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.104128 0.0000000) to (52.791559 43.104128 8.7381211) create_atoms CPU = 0.005 seconds 1754 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 3466 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14089.148 0 -14089.148 22688.616 113 0 -14625.345 0 -14625.345 30203.843 Loop time of 16.2232 on 1 procs for 113 steps with 3466 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14089.1484888942 -14625.3305696267 -14625.3447093284 Force two-norm initial, final = 502.72855 0.65666241 Force max component initial, final = 95.614400 0.097042891 Final line search alpha, max atom move = 0.86756068 0.084190597 Iterations, force evaluations = 113 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.081 | 16.081 | 16.081 | 0.0 | 99.12 Neigh | 0.084842 | 0.084842 | 0.084842 | 0.0 | 0.52 Comm | 0.019472 | 0.019472 | 0.019472 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03822 | | | 0.24 Nlocal: 3466.00 ave 3466 max 3466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7245.00 ave 7245 max 7245 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: 200502.0 ave 200502 max 200502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200502 Ave neighs/atom = 57.848240 Neighbor list builds = 3 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.596 | 5.596 | 5.596 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -14625.345 0 -14625.345 30203.843 39767.786 118 0 -14628.921 0 -14628.921 -11.166838 40145.023 Loop time of 0.712563 on 1 procs for 5 steps with 3466 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 = -14625.3447093284 -14628.9086363652 -14628.9207568202 Force two-norm initial, final = 1301.2598 2.9240188 Force max component initial, final = 818.62062 1.0041606 Final line search alpha, max atom move = 3.6855283e-05 3.7008625e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70817 | 0.70817 | 0.70817 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049146 | 0.00049146 | 0.00049146 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003898 | | | 0.55 Nlocal: 3466.00 ave 3466 max 3466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7290.00 ave 7290 max 7290 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: 203128.0 ave 203128 max 203128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203128 Ave neighs/atom = 58.605886 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.734 | 5.734 | 5.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14628.921 0 -14628.921 -11.166838 Loop time of 2.564e-06 on 1 procs for 0 steps with 3466 atoms 195.0% 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 | | 2.564e-06 | | |100.00 Nlocal: 3466.00 ave 3466 max 3466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7265.00 ave 7265 max 7265 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: 197834.0 ave 197834 max 197834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197834 Ave neighs/atom = 57.078477 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.734 | 5.734 | 5.734 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 -14628.921 -14628.921 52.920477 86.45234 8.7746783 -11.166838 -11.166838 17.703768 -40.189235 -11.015046 2.3252978 1864.4804 Loop time of 2.579e-06 on 1 procs for 0 steps with 3466 atoms 232.6% 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 | | 2.579e-06 | | |100.00 Nlocal: 3466.00 ave 3466 max 3466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7265.00 ave 7265 max 7265 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98917.0 ave 98917 max 98917 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197834.0 ave 197834 max 197834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197834 Ave neighs/atom = 57.078477 Neighbor list builds = 0 Dangerous builds = 0 3466 -14628.9207568202 eV 2.32529778315939 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17