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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -37.862840 0.0000000) to (37.862840 37.862840 3.5618363) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0260407 5.0260407 3.5618363 Created 451 atoms using lattice units in orthogonal box = (0.0000000 -37.862840 0.0000000) to (37.862840 37.862840 3.5618363) create_atoms CPU = 0.002 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0260407 5.0260407 3.5618363 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -37.862840 0.0000000) to (37.862840 37.862840 3.5618363) create_atoms CPU = 0.002 seconds 453 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 9 18 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 903 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_322509103239_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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.394 | 5.394 | 5.394 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3020.098 0 -3020.098 90717.708 199 0 -3551.0444 0 -3551.0444 -498.43475 Loop time of 7.47091 on 1 procs for 199 steps with 903 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 = -3020.09802656057 -3551.04134150787 -3551.04444831121 Force two-norm initial, final = 679.87938 0.30372316 Force max component initial, final = 183.34680 0.11698386 Final line search alpha, max atom move = 1.0000000 0.11698386 Iterations, force evaluations = 199 363 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2672 | 7.2672 | 7.2672 | 0.0 | 97.27 Neigh | 0.081198 | 0.081198 | 0.081198 | 0.0 | 1.09 Comm | 0.074233 | 0.074233 | 0.074233 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04829 | | | 0.65 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8733.00 ave 8733 max 8733 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: 202496.0 ave 202496 max 202496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202496 Ave neighs/atom = 224.24806 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 199 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.394 | 5.394 | 5.394 Mbytes Step Temp E_pair E_mol TotEng Press Volume 199 0 -3551.0444 0 -3551.0444 -498.43475 10212.459 204 0 -3551.1187 0 -3551.1187 162.91161 10208.602 Loop time of 0.151478 on 1 procs for 5 steps with 903 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 = -3551.04444831121 -3551.11799306451 -3551.11866179349 Force two-norm initial, final = 35.819554 2.1019457 Force max component initial, final = 31.597556 1.7562597 Final line search alpha, max atom move = 0.00018636117 0.00032729861 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14581 | 0.14581 | 0.14581 | 0.0 | 96.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015068 | 0.0015068 | 0.0015068 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004163 | | | 2.75 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8733.00 ave 8733 max 8733 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: 202324.0 ave 202324 max 202324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202324 Ave neighs/atom = 224.05759 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3551.1187 0 -3551.1187 162.91161 Loop time of 6.455e-06 on 1 procs for 0 steps with 903 atoms 201.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8733.00 ave 8733 max 8733 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: 202332.0 ave 202332 max 202332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202332 Ave neighs/atom = 224.06645 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.532 | 5.532 | 5.532 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 -3551.1187 -3551.1187 37.749199 75.654047 3.5745913 162.91161 162.91161 165.08623 47.027534 276.62106 2.0827879 46.271193 Loop time of 6.836e-06 on 1 procs for 0 steps with 903 atoms 277.9% 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 | | 6.836e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8733.00 ave 8733 max 8733 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101166.0 ave 101166 max 101166 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202332.0 ave 202332 max 202332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202332 Ave neighs/atom = 224.06645 Neighbor list builds = 0 Dangerous builds = 0 903 -3551.11866179349 eV 2.08278792487607 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08