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 = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -35.924046 0.0000000) to (17.962023 35.924046 3.5226425) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1450822 4.1450822 3.5226425 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -35.924046 0.0000000) to (17.962023 35.924046 3.5226425) create_atoms CPU = 0.002 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1450822 4.1450822 3.5226425 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -35.924046 0.0000000) to (17.962023 35.924046 3.5226425) create_atoms CPU = 0.001 seconds 210 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 1 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 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_381861218831_004#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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.346 | 5.346 | 5.346 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1675.2331 0 -1675.2331 23102.534 47 0 -1731.6868 0 -1731.6868 -6094.5603 Loop time of 3.2624 on 1 procs for 47 steps with 412 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 = -1675.2330858064 -1731.68559960956 -1731.68684457938 Force two-norm initial, final = 127.51799 0.13966079 Force max component initial, final = 43.864117 0.024221575 Final line search alpha, max atom move = 1.0000000 0.024221575 Iterations, force evaluations = 47 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2104 | 3.2104 | 3.2104 | 0.0 | 98.41 Neigh | 0.025286 | 0.025286 | 0.025286 | 0.0 | 0.78 Comm | 0.018497 | 0.018497 | 0.018497 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008232 | | | 0.25 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9071.00 ave 9071 max 9071 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: 254836.0 ave 254836 max 254836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254836 Ave neighs/atom = 618.53398 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.347 | 5.347 | 5.347 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1731.6868 0 -1731.6868 -6094.5603 4546.1007 53 0 -1731.7559 0 -1731.7559 -577.29266 4532.2964 Loop time of 0.297908 on 1 procs for 6 steps with 412 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 = -1731.68684457939 -1731.75510734796 -1731.75592771599 Force two-norm initial, final = 32.561375 3.0865043 Force max component initial, final = 23.312111 2.1391917 Final line search alpha, max atom move = 0.00039759911 0.00085054070 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29251 | 0.29251 | 0.29251 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015026 | 0.0015026 | 0.0015026 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003898 | | | 1.31 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9142.00 ave 9142 max 9142 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: 255544.0 ave 255544 max 255544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255544 Ave neighs/atom = 620.25243 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.485 | 5.485 | 5.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1731.7559 0 -1731.7559 -577.29266 Loop time of 7.337e-06 on 1 procs for 0 steps with 412 atoms 177.2% 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 | | 7.337e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9158.00 ave 9158 max 9158 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: 255796.0 ave 255796 max 255796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255796 Ave neighs/atom = 620.86408 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 = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 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) = 5.485 | 5.485 | 5.485 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 -1731.7559 -1731.7559 17.905782 71.593617 3.535499 -577.29266 -577.29266 -753.84106 -733.87799 -244.15892 2.2435959 197.87013 Loop time of 6.776e-06 on 1 procs for 0 steps with 412 atoms 295.2% 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 | | 6.776e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9158.00 ave 9158 max 9158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127898.0 ave 127898 max 127898 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255796.0 ave 255796 max 255796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255796 Ave neighs/atom = 620.86408 Neighbor list builds = 0 Dangerous builds = 0 412 -1731.75592771599 eV 2.24359586401197 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04