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 = 3.1501534 3.1501534 3.1501534 Created orthogonal box = (0.0000000 -40.830654 0.0000000) to (23.573589 40.830654 5.4562257) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0514834 4.8607922 5.4562257 Created 335 atoms using lattice units in orthogonal box = (0.0000000 -40.830654 0.0000000) to (23.573589 40.830654 5.4562257) create_atoms CPU = 0.003 seconds 335 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0514834 4.8607922 5.4562257 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -40.830654 0.0000000) to (23.573589 40.830654 5.4562257) create_atoms CPU = 0.002 seconds 339 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 6 21 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 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 671 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_271256517527_005#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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3510.7952 0 -3510.7952 158160.39 69 0 -4535.8101 0 -4535.8101 7855.9276 Loop time of 1.27888 on 1 procs for 69 steps with 671 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 = -3510.79524870628 -4535.80592192826 -4535.8101154222 Force two-norm initial, final = 2168.9181 0.24321219 Force max component initial, final = 573.33429 0.027112549 Final line search alpha, max atom move = 1.0000000 0.027112549 Iterations, force evaluations = 69 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2245 | 1.2245 | 1.2245 | 0.0 | 95.75 Neigh | 0.02864 | 0.02864 | 0.02864 | 0.0 | 2.24 Comm | 0.013702 | 0.013702 | 0.013702 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01199 | | | 0.94 Nlocal: 671.000 ave 671 max 671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4701.00 ave 4701 max 4701 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: 92898.0 ave 92898 max 92898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92898 Ave neighs/atom = 138.44709 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4535.8101 0 -4535.8101 7855.9276 10503.508 71 0 -4535.8934 0 -4535.8934 -464.74721 10537.412 Loop time of 0.043366 on 1 procs for 2 steps with 671 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 = -4535.8101154222 -4535.88997539526 -4535.89337814132 Force two-norm initial, final = 90.326782 7.7861590 Force max component initial, final = 58.197819 7.7126807 Final line search alpha, max atom move = 9.0206324e-05 0.00069573258 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041705 | 0.041705 | 0.041705 | 0.0 | 96.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039963 | 0.00039963 | 0.00039963 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001262 | | | 2.91 Nlocal: 671.000 ave 671 max 671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4715.00 ave 4715 max 4715 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: 92356.0 ave 92356 max 92356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92356 Ave neighs/atom = 137.63934 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4535.8934 0 -4535.8934 -464.74721 Loop time of 5.624e-06 on 1 procs for 0 steps with 671 atoms 195.6% 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 | | 5.624e-06 | | |100.00 Nlocal: 671.000 ave 671 max 671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4715.00 ave 4715 max 4715 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: 92244.0 ave 92244 max 92244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92244 Ave neighs/atom = 137.47243 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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.100217342376709 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) = 4.675 | 4.675 | 4.675 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 -4535.8934 -4535.8934 23.588505 81.769079 5.4631666 -464.74721 -464.74721 -1173.428 -124.72067 -96.092963 2.4640885 568.80028 Loop time of 6.255e-06 on 1 procs for 0 steps with 671 atoms 255.8% 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 | | 6.255e-06 | | |100.00 Nlocal: 671.000 ave 671 max 671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4715.00 ave 4715 max 4715 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46122.0 ave 46122 max 46122 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92244.0 ave 92244 max 92244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92244 Ave neighs/atom = 137.47243 Neighbor list builds = 0 Dangerous builds = 0 671 -4535.89273822585 eV 2.46408848445539 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01