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 = 3.6135806 3.6135806 3.6135806 Created orthogonal box = (0.0000000 -43.663061 0.0000000) to (53.476110 43.663061 8.8514286) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1278461 5.3831171 5.9009524 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.663061 0.0000000) to (53.476110 43.663061 8.8514286) create_atoms CPU = 0.006 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1278461 5.3831171 5.9009524 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.663061 0.0000000) to (53.476110 43.663061 8.8514286) create_atoms CPU = 0.006 seconds 1756 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 15 24 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3480 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_426403318662_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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.607 | 6.607 | 6.607 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9799.2589 0 -9799.2589 151384.42 90 0 -12282.524 0 -12282.524 -4667.7093 Loop time of 7.0087 on 1 procs for 90 steps with 3480 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 = -9799.25886036074 -12282.5129040896 -12282.5244587096 Force two-norm initial, final = 3838.8580 0.32350416 Force max component initial, final = 744.67693 0.020879378 Final line search alpha, max atom move = 1.0000000 0.020879378 Iterations, force evaluations = 90 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6905 | 6.6905 | 6.6905 | 0.0 | 95.46 Neigh | 0.22601 | 0.22601 | 0.22601 | 0.0 | 3.22 Comm | 0.038093 | 0.038093 | 0.038093 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0541 | | | 0.77 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10666.0 ave 10666 max 10666 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: 491072.0 ave 491072 max 491072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491072 Ave neighs/atom = 141.11264 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.604 | 6.604 | 6.604 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -12282.524 0 -12282.524 -4667.7093 41334.943 94 0 -12282.808 0 -12282.808 70.886173 41193.325 Loop time of 0.324145 on 1 procs for 4 steps with 3480 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 = -12282.5244587096 -12282.806881052 -12282.8075604299 Force two-norm initial, final = 219.00357 5.0303677 Force max component initial, final = 167.59203 4.8774503 Final line search alpha, max atom move = 0.00010135777 0.00049436747 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31568 | 0.31568 | 0.31568 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016326 | 0.0016326 | 0.0016326 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006832 | | | 2.11 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10483.0 ave 10483 max 10483 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: 489732.0 ave 489732 max 489732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489732 Ave neighs/atom = 140.72759 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.742 | 6.742 | 6.742 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12282.808 0 -12282.808 70.886173 Loop time of 6.395e-06 on 1 procs for 0 steps with 3480 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 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: 490172.0 ave 490172 max 490172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490172 Ave neighs/atom = 140.85402 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.742 | 6.742 | 6.742 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 -12282.808 -12282.808 53.425212 87.070024 8.8554763 70.886173 70.886173 189.52339 41.786551 -18.651423 2.372352 1407.0556 Loop time of 8.369e-06 on 1 procs for 0 steps with 3480 atoms 274.8% 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 | | 8.369e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10496.0 ave 10496 max 10496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 245086.0 ave 245086 max 245086 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 490172.0 ave 490172 max 490172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490172 Ave neighs/atom = 140.85402 Neighbor list builds = 0 Dangerous builds = 0 3480 -12282.8249604299 eV 2.37235198997293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08