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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -40.902996 0.0000000) to (28.922786 40.902996 5.7275650) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1040210 6.4161562 5.7275650 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.902996 0.0000000) to (28.922786 40.902996 5.7275650) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1040210 6.4161562 5.7275650 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.902996 0.0000000) to (28.922786 40.902996 5.7275650) create_atoms CPU = 0.003 seconds 410 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 20 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 808 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_751354403791_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2677.1667 0 -2677.1667 -64.354924 66 0 -2705.7796 0 -2705.7796 -2372.8394 Loop time of 1.48851 on 1 procs for 66 steps with 808 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 = -2677.16669510961 -2705.77744188588 -2705.77959237203 Force two-norm initial, final = 18.890739 0.11634531 Force max component initial, final = 4.4430611 0.019277896 Final line search alpha, max atom move = 1.0000000 0.019277896 Iterations, force evaluations = 66 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4271 | 1.4271 | 1.4271 | 0.0 | 95.87 Neigh | 0.033727 | 0.033727 | 0.033727 | 0.0 | 2.27 Comm | 0.014523 | 0.014523 | 0.014523 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01317 | | | 0.88 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4910.00 ave 4910 max 4910 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: 112352.0 ave 112352 max 112352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112352 Ave neighs/atom = 139.04950 Neighbor list builds = 2 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2705.7796 0 -2705.7796 -2372.8394 13551.746 71 0 -2705.8745 0 -2705.8745 -53.742743 13510.903 Loop time of 0.088955 on 1 procs for 5 steps with 808 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 = -2705.77959237202 -2705.87411021002 -2705.87447019722 Force two-norm initial, final = 43.350965 1.4523502 Force max component initial, final = 30.926524 1.3072514 Final line search alpha, max atom move = 0.00034054887 0.00044518298 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085606 | 0.085606 | 0.085606 | 0.0 | 96.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072845 | 0.00072845 | 0.00072845 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00262 | | | 2.95 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4901.00 ave 4901 max 4901 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: 112116.0 ave 112116 max 112116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112116 Ave neighs/atom = 138.75743 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.091 | 5.091 | 5.091 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2705.8745 0 -2705.8745 -53.742743 Loop time of 6.285e-06 on 1 procs for 0 steps with 808 atoms 175.0% 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 | | 6.285e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4901.00 ave 4901 max 4901 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: 112148.0 ave 112148 max 112148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112148 Ave neighs/atom = 138.79703 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.091 | 5.091 | 5.091 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 -2705.8745 -2705.8745 28.833447 82.040577 5.7116175 -53.742743 -53.742743 -154.54022 47.134312 -53.82232 2.6179153 642.43525 Loop time of 6.986e-06 on 1 procs for 0 steps with 808 atoms 229.0% 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 | | 6.986e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4901.00 ave 4901 max 4901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56074.0 ave 56074 max 56074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112148.0 ave 112148 max 112148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112148 Ave neighs/atom = 138.79703 Neighbor list builds = 0 Dangerous builds = 0 808 -2705.87447016186 eV 2.61791525028334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02