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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -49.643742 0.0000000) to (13.511315 49.643742 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7905637 5.5159714 5.8968214 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.643742 0.0000000) to (13.511315 49.643742 8.8452321) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7905637 5.5159714 5.8968214 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.643742 0.0000000) to (13.511315 49.643742 8.8452321) create_atoms CPU = 0.001 seconds 507 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 20 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3526.399 0 -3526.399 82683.905 52 0 -4167.8967 0 -4167.8967 6252.637 Loop time of 1.41753 on 1 procs for 52 steps with 1008 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 = -3526.39896006124 -4167.89324881897 -4167.89668142778 Force two-norm initial, final = 898.38296 0.25171568 Force max component initial, final = 191.95252 0.040394387 Final line search alpha, max atom move = 1.0000000 0.040394387 Iterations, force evaluations = 52 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3524 | 1.3524 | 1.3524 | 0.0 | 95.41 Neigh | 0.047096 | 0.047096 | 0.047096 | 0.0 | 3.32 Comm | 0.010817 | 0.010817 | 0.010817 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007181 | | | 0.51 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9214.00 ave 9214 max 9214 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: 383764.0 ave 383764 max 383764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383764 Ave neighs/atom = 380.71825 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4167.8967 0 -4167.8967 6252.637 11865.919 56 0 -4168.0193 0 -4168.0193 -16.108256 11909.163 Loop time of 0.104604 on 1 procs for 4 steps with 1008 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 = -4167.89668142778 -4168.01901988407 -4168.01931580078 Force two-norm initial, final = 88.702392 0.76126990 Force max component initial, final = 66.335907 0.61796239 Final line search alpha, max atom move = 0.00026474038 0.00016359960 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10218 | 0.10218 | 0.10218 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005019 | 0.0005019 | 0.0005019 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001917 | | | 1.83 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9136.00 ave 9136 max 9136 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: 383176.0 ave 383176 max 383176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383176 Ave neighs/atom = 380.13492 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.102 | 6.102 | 6.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4168.0193 0 -4168.0193 -16.108256 Loop time of 2.195e-06 on 1 procs for 0 steps with 1008 atoms 182.2% 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 | | 2.195e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9116.00 ave 9116 max 9116 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: 383022.0 ave 383022 max 383022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383022 Ave neighs/atom = 379.98214 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.102 | 6.102 | 6.102 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 -4168.0193 -4168.0193 13.541196 99.475402 8.8411456 -16.108256 -16.108256 -83.320243 47.050486 -12.055012 2.3258272 372.399 Loop time of 2.522e-06 on 1 procs for 0 steps with 1008 atoms 198.3% 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 | | 2.522e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9116.00 ave 9116 max 9116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 191511.0 ave 191511 max 191511 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 383022.0 ave 383022 max 383022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383022 Ave neighs/atom = 379.98214 Neighbor list builds = 0 Dangerous builds = 0 1008 -4168.01931580078 eV 2.32582715302274 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01