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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -43.807295 0.0000000) to (14.602432 43.807295 4.0499858) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6163198 5.6163198 4.0499858 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -43.807295 0.0000000) to (14.602432 43.807295 4.0499858) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6163198 5.6163198 4.0499858 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -43.807295 0.0000000) to (14.602432 43.807295 4.0499858) create_atoms CPU = 0.001 seconds 158 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 ghost atom cutoff = 6 binsize = 3, bins = 5 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_022920256108_001#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 ghost atom cutoff = 6 binsize = 3, bins = 5 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1021.0385 0 -1021.0385 12731.145 20 0 -1042.6189 0 -1042.6189 3989.524 Loop time of 0.687593 on 1 procs for 20 steps with 312 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 = -1021.03846113625 -1042.61850344081 -1042.6188654876 Force two-norm initial, final = 53.090404 0.44556792 Force max component initial, final = 18.611218 0.15811934 Final line search alpha, max atom move = 0.039263741 0.0062083567 Iterations, force evaluations = 20 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68195 | 0.68195 | 0.68195 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030583 | 0.0030583 | 0.0030583 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002586 | | | 0.38 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2248.00 ave 2248 max 2248 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: 16864.0 ave 16864 max 16864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16864 Ave neighs/atom = 54.051282 Neighbor list builds = 0 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 ghost atom cutoff = 6 binsize = 3, bins = 5 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -1042.6189 0 -1042.6189 3989.524 5181.4953 32 0 -1042.7506 0 -1042.7506 -149.0488 5213.4403 Loop time of 0.182799 on 1 procs for 12 steps with 312 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 = -1042.6188654876 -1042.75037753323 -1042.75056594711 Force two-norm initial, final = 28.523455 0.94323427 Force max component initial, final = 27.310723 0.64062974 Final line search alpha, max atom move = 0.0041022186 0.0026280033 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17933 | 0.17933 | 0.17933 | 0.0 | 98.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074342 | 0.00074342 | 0.00074342 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002727 | | | 1.49 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2248.00 ave 2248 max 2248 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: 16760.0 ave 16760 max 16760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16760 Ave neighs/atom = 53.717949 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 ghost atom cutoff = 6 binsize = 3, bins = 5 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1042.7506 0 -1042.7506 -149.0488 Loop time of 6.384e-06 on 1 procs for 0 steps with 312 atoms 156.6% 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 | | 6.384e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2248.00 ave 2248 max 2248 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: 16736.0 ave 16736 max 16736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16736 Ave neighs/atom = 53.641026 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 ghost atom cutoff = 6 binsize = 3, bins = 5 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.554 | 4.554 | 4.554 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 -1042.7506 -1042.7506 14.619113 88.53913 4.0278021 -149.0488 -149.0488 -197.10103 -140.90789 -109.13746 2.5426435 201.09718 Loop time of 6.726e-06 on 1 procs for 0 steps with 312 atoms 208.1% 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 | | 6.726e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2248.00 ave 2248 max 2248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8368.00 ave 8368 max 8368 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16736.0 ave 16736 max 16736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16736 Ave neighs/atom = 53.641026 Neighbor list builds = 0 Dangerous builds = 0 312 -1042.75056594711 eV 2.54264348046527 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01