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 -52.791559 0.0000000) to (43.104127 52.791559 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3142075 5.0622043 5.8254140 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -52.791559 0.0000000) to (43.104127 52.791559 8.7381210) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3142075 5.0622043 5.8254140 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.791559 0.0000000) to (43.104127 52.791559 8.7381210) create_atoms CPU = 0.002 seconds 1759 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 = 16 38 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 0 atoms, new total = 3510 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 38 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14516.376 0 -14516.376 32178.337 68 0 -14776.018 0 -14776.018 44887.708 Loop time of 12.2414 on 1 procs for 68 steps with 3510 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14516.3759140256 -14776.0063494842 -14776.017972153 Force two-norm initial, final = 153.12835 0.50859610 Force max component initial, final = 23.919381 0.083461475 Final line search alpha, max atom move = 0.90315419 0.075378581 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.203 | 12.203 | 12.203 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.013429 | 0.013429 | 0.013429 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02525 | | | 0.21 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7512.00 ave 7512 max 7512 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: 191538.0 ave 191538 max 191538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191538 Ave neighs/atom = 54.569231 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 38 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.608 | 5.608 | 5.608 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -14776.018 0 -14776.018 44887.708 39767.785 102 0 -14792.359 0 -14792.359 -372.26943 40848.028 Loop time of 3.41118 on 1 procs for 34 steps with 3510 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14776.017972153 -14792.3515682457 -14792.359144726 Force two-norm initial, final = 1934.4349 17.899417 Force max component initial, final = 1215.8090 11.983482 Final line search alpha, max atom move = 4.5175923e-05 0.00054136486 Iterations, force evaluations = 34 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3663 | 3.3663 | 3.3663 | 0.0 | 98.69 Neigh | 0.019237 | 0.019237 | 0.019237 | 0.0 | 0.56 Comm | 0.0028877 | 0.0028877 | 0.0028877 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02272 | | | 0.67 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7517.00 ave 7517 max 7517 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: 198296.0 ave 198296 max 198296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198296 Ave neighs/atom = 56.494587 Neighbor list builds = 1 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 = 16 38 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) = 5.746 | 5.746 | 5.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14792.359 0 -14792.359 -372.26943 Loop time of 2.112e-06 on 1 procs for 0 steps with 3510 atoms 189.4% 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 | | 2.112e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7492.00 ave 7492 max 7492 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: 203116.0 ave 203116 max 203116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203116 Ave neighs/atom = 57.867806 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 = 16 38 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) = 5.746 | 5.746 | 5.746 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 -14792.359 -14792.359 44.496748 105.24979 8.7221105 -372.26943 -372.26943 -214.09013 -468.54255 -434.17562 2.1741596 1885.7028 Loop time of 2.499e-06 on 1 procs for 0 steps with 3510 atoms 240.1% 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 | | 2.499e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7492.00 ave 7492 max 7492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101558.0 ave 101558 max 101558 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203116.0 ave 203116 max 203116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203116 Ave neighs/atom = 57.867806 Neighbor list builds = 0 Dangerous builds = 0 3510 -14792.359144726 eV 2.17415959944029 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16