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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -33.883251 0.0000000) to (41.498337 33.883251 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7426671 4.3564179 4.6763329 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -33.883251 0.0000000) to (41.498337 33.883251 7.0144993) create_atoms CPU = 0.002 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7426671 4.3564179 4.6763329 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -33.883251 0.0000000) to (41.498337 33.883251 7.0144993) create_atoms CPU = 0.001 seconds 841 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 = 15 25 3 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 = 1676 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 = 15 25 3 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6751.1176 0 -6751.1176 56822.764 65 0 -7145.4873 0 -7145.4873 6335.4888 Loop time of 4.5274 on 1 procs for 65 steps with 1676 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6751.11763893826 -7145.48192313493 -7145.4872613419 Force two-norm initial, final = 425.68830 0.28287776 Force max component initial, final = 91.808828 0.072272554 Final line search alpha, max atom move = 1.0000000 0.072272554 Iterations, force evaluations = 65 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4985 | 4.4985 | 4.4985 | 0.0 | 99.36 Neigh | 0.0096709 | 0.0096709 | 0.0096709 | 0.0 | 0.21 Comm | 0.007209 | 0.007209 | 0.007209 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01202 | | | 0.27 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4921.00 ave 4921 max 4921 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: 97686.0 ave 97686 max 97686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97686 Ave neighs/atom = 58.285203 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 25 3 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -7145.4873 0 -7145.4873 6335.4888 19726.155 71 0 -7145.9557 0 -7145.9557 -25.841646 19797.331 Loop time of 0.305141 on 1 procs for 6 steps with 1676 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7145.4872613419 -7145.95545426725 -7145.95567057549 Force two-norm initial, final = 183.11853 1.3711952 Force max component initial, final = 165.18728 0.93417493 Final line search alpha, max atom move = 0.00024158707 0.00022568458 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30217 | 0.30217 | 0.30217 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047586 | 0.00047586 | 0.00047586 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002499 | | | 0.82 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4902.00 ave 4902 max 4902 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: 97854.0 ave 97854 max 97854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97854 Ave neighs/atom = 58.385442 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 = 15 25 3 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) = 4.792 | 4.792 | 4.792 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7145.9557 0 -7145.9557 -25.841646 Loop time of 2.399e-06 on 1 procs for 0 steps with 1676 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 | | 2.399e-06 | | |100.00 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4902.00 ave 4902 max 4902 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: 97796.0 ave 97796 max 97796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97796 Ave neighs/atom = 58.350835 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 = 15 25 3 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) = 4.792 | 4.792 | 4.792 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 -7145.9557 -7145.9557 41.543253 68.105782 6.9971657 -25.841646 -25.841646 -75.68359 46.713722 -48.55507 2.2620172 1888.3295 Loop time of 2.622e-06 on 1 procs for 0 steps with 1676 atoms 228.8% 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 | | 2.622e-06 | | |100.00 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4902.00 ave 4902 max 4902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48898.0 ave 48898 max 48898 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97796.0 ave 97796 max 97796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97796 Ave neighs/atom = 58.350835 Neighbor list builds = 0 Dangerous builds = 0 1676 -7145.95567057549 eV 2.26201721110982 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05