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 = 3.6150004 3.6150004 3.6150004 Created orthogonal box = (0.0000000 -38.427981 0.0000000) to (38.427981 38.427981 3.6150004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1010594 5.1010594 3.6150004 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.427981 0.0000000) to (38.427981 38.427981 3.6150004) create_atoms CPU = 0.003 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1010594 5.1010594 3.6150004 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.427981 0.0000000) to (38.427981 38.427981 3.6150004) create_atoms CPU = 0.002 seconds 454 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 12 24 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 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 904 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_762798677854_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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 12 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.561 | 4.561 | 4.561 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2419.7101 0 -2419.7101 214219.03 121 0 -3174.288 0 -3174.288 3292.507 Loop time of 1.96472 on 1 procs for 121 steps with 904 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 = -2419.71008337676 -3174.28537868614 -3174.28804637338 Force two-norm initial, final = 1937.2116 0.13644761 Force max component initial, final = 507.74783 0.029514541 Final line search alpha, max atom move = 1.0000000 0.029514541 Iterations, force evaluations = 121 217 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8663 | 1.8663 | 1.8663 | 0.0 | 94.99 Neigh | 0.041829 | 0.041829 | 0.041829 | 0.0 | 2.13 Comm | 0.02947 | 0.02947 | 0.02947 | 0.0 | 1.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02709 | | | 1.38 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6141.00 ave 6141 max 6141 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: 77952.0 ave 77952 max 77952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77952 Ave neighs/atom = 86.230088 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 12 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.566 | 4.566 | 4.566 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -3174.288 0 -3174.288 3292.507 10676.612 124 0 -3174.3358 0 -3174.3358 108.00227 10699.909 Loop time of 0.0420963 on 1 procs for 3 steps with 904 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3174.28804637338 -3174.33396087794 -3174.33577340547 Force two-norm initial, final = 44.518555 1.5883348 Force max component initial, final = 38.591312 1.4576399 Final line search alpha, max atom move = 0.00012193518 0.00017773758 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039373 | 0.039373 | 0.039373 | 0.0 | 93.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061623 | 0.00061623 | 0.00061623 | 0.0 | 1.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002107 | | | 5.01 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6141.00 ave 6141 max 6141 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: 77924.0 ave 77924 max 77924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77924 Ave neighs/atom = 86.199115 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 12 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.704 | 4.704 | 4.704 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3174.3358 0 -3174.3358 108.00227 Loop time of 6.575e-06 on 1 procs for 0 steps with 904 atoms 197.7% 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 | | 6.575e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6151.00 ave 6151 max 6151 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: 77892.0 ave 77892 max 77892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77892 Ave neighs/atom = 86.163717 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 12 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.704 | 4.704 | 4.704 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 -3174.3358 -3174.3358 38.40418 77.017683 3.6175216 108.00227 108.00227 14.21452 218.72247 91.069815 2.0502427 91.738205 Loop time of 7.177e-06 on 1 procs for 0 steps with 904 atoms 236.9% 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 | | 7.177e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6151.00 ave 6151 max 6151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38946.0 ave 38946 max 38946 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77892.0 ave 77892 max 77892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77892 Ave neighs/atom = 86.163717 Neighbor list builds = 0 Dangerous builds = 0 904 -3174.33577340547 eV 2.05024266070807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02