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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -54.660803 0.0000000) to (38.651025 54.660803 5.1194533) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1027934 5.2742880 5.1194533 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.660803 0.0000000) to (38.651025 54.660803 5.1194533) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1027934 5.2742880 5.1194533 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.660803 0.0000000) to (38.651025 54.660803 5.1194533) create_atoms CPU = 0.002 seconds 916 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 29 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.979 | 5.979 | 5.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5889.4089 0 -5889.4089 54500.168 142 0 -6444.3165 0 -6444.3165 2461.123 Loop time of 4.51197 on 1 procs for 142 steps with 1824 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5889.40889369212 -6444.31133679032 -6444.31649012254 Force two-norm initial, final = 880.04590 0.22519381 Force max component initial, final = 209.45657 0.034166879 Final line search alpha, max atom move = 1.0000000 0.034166879 Iterations, force evaluations = 142 271 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4158 | 4.4158 | 4.4158 | 0.0 | 97.87 Neigh | 0.039463 | 0.039463 | 0.039463 | 0.0 | 0.87 Comm | 0.030809 | 0.030809 | 0.030809 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02587 | | | 0.57 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10624.0 ave 10624 max 10624 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: 317000.0 ave 317000 max 317000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317000 Ave neighs/atom = 173.79386 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 142 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.982 | 5.982 | 5.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 142 0 -6444.3165 0 -6444.3165 2461.123 21631.697 148 0 -6444.5873 0 -6444.5873 104.28213 21669.015 Loop time of 0.125861 on 1 procs for 6 steps with 1824 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 = -6444.31649012254 -6444.58249269604 -6444.58727677653 Force two-norm initial, final = 96.277623 2.4850656 Force max component initial, final = 96.239516 1.5354439 Final line search alpha, max atom move = 0.00012037979 0.00018483641 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12239 | 0.12239 | 0.12239 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006109 | 0.0006109 | 0.0006109 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002859 | | | 2.27 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10625.0 ave 10625 max 10625 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: 317424.0 ave 317424 max 317424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317424 Ave neighs/atom = 174.02632 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.120 | 6.120 | 6.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6444.5873 0 -6444.5873 104.28213 Loop time of 2.016e-06 on 1 procs for 0 steps with 1824 atoms 148.8% 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 | | 2.016e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10616.0 ave 10616 max 10616 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: 316904.0 ave 316904 max 316904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316904 Ave neighs/atom = 173.74123 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.120 | 6.120 | 6.120 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 -6444.5873 -6444.5873 38.585025 109.94179 5.108079 104.28213 104.28213 99.955633 114.17261 98.718158 2.3848556 718.52231 Loop time of 2.606e-06 on 1 procs for 0 steps with 1824 atoms 230.2% 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 | | 2.606e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10616.0 ave 10616 max 10616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158452.0 ave 158452 max 158452 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316904.0 ave 316904 max 316904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316904 Ave neighs/atom = 173.74123 Neighbor list builds = 0 Dangerous builds = 0 1824 -6444.58727677653 eV 2.3848555731281 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05