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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -31.013843 0.0000000) to (10.336992 31.013843 2.8669658) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9757662 3.9757662 2.8669658 Created 79 atoms using lattice units in orthogonal box = (0.0000000 -31.013843 0.0000000) to (10.336992 31.013843 2.8669658) create_atoms CPU = 0.000 seconds 79 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9757662 3.9757662 2.8669658 Created 79 atoms using lattice units in orthogonal box = (0.0000000 -31.013843 0.0000000) to (10.336992 31.013843 2.8669658) create_atoms CPU = 0.000 seconds 79 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 17 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 158 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.405 | 4.405 | 4.405 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -505.50612 0 -505.50612 447604.43 216 0 -634.64685 0 -634.64685 -55455.763 Loop time of 0.589266 on 1 procs for 216 steps with 158 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 = -505.506119121241 -634.646225928851 -634.646846483677 Force two-norm initial, final = 281.22867 0.082279887 Force max component initial, final = 99.936412 0.025089700 Final line search alpha, max atom move = 1.0000000 0.025089700 Iterations, force evaluations = 216 425 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57413 | 0.57413 | 0.57413 | 0.0 | 97.43 Neigh | 0.0016325 | 0.0016325 | 0.0016325 | 0.0 | 0.28 Comm | 0.0090723 | 0.0090723 | 0.0090723 | 0.0 | 1.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004431 | | | 0.75 Nlocal: 158.000 ave 158 max 158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3017.00 ave 3017 max 3017 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: 25944.0 ave 25944 max 25944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25944 Ave neighs/atom = 164.20253 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 216 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.405 | 4.405 | 4.405 Mbytes Step Temp E_pair E_mol TotEng Press Volume 216 0 -634.64685 0 -634.64685 -55455.763 1838.2403 492 0 -647.51971 0 -647.51971 20186.627 1653.8386 Loop time of 0.448948 on 1 procs for 276 steps with 158 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -634.646846483677 -647.519425723439 -647.519708983714 Force two-norm initial, final = 110.19170 1.0996288 Force max component initial, final = 95.158823 0.76707172 Final line search alpha, max atom move = 0.0010122620 0.00077647755 Iterations, force evaluations = 276 288 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41827 | 0.41827 | 0.41827 | 0.0 | 93.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061128 | 0.0061128 | 0.0061128 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02456 | | | 5.47 Nlocal: 158.000 ave 158 max 158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2985.00 ave 2985 max 2985 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: 25524.0 ave 25524 max 25524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25524 Ave neighs/atom = 161.54430 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -647.51971 0 -647.51971 20186.627 Loop time of 1.642e-06 on 1 procs for 0 steps with 158 atoms 182.7% 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 | | 1.642e-06 | | |100.00 Nlocal: 158.000 ave 158 max 158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3092.00 ave 3092 max 3092 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: 26702.0 ave 26702 max 26702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26702 Ave neighs/atom = 169.00000 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.543 | 4.543 | 4.543 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 -647.51971 -647.51971 10.413256 62.027687 2.5604778 20186.627 20186.627 748.59261 59665.045 146.24159 2.3069911 269.09229 Loop time of 1.441e-06 on 1 procs for 0 steps with 158 atoms 138.8% 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 | | 1.441e-06 | | |100.00 Nlocal: 158.000 ave 158 max 158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3092.00 ave 3092 max 3092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13351.0 ave 13351 max 13351 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26702.0 ave 26702 max 26702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26702 Ave neighs/atom = 169.00000 Neighbor list builds = 0 Dangerous builds = 0 158 -647.519708983715 eV 2.30699110746238 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01