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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -53.267178 0.0000000) to (26.633589 53.267178 3.6584048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5226850 4.5226850 3.6584048 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -53.267178 0.0000000) to (26.633589 53.267178 3.6584048) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5226850 4.5226850 3.6584048 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -53.267178 0.0000000) to (26.633589 53.267178 3.6584048) create_atoms CPU = 0.000 seconds 426 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 850 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_884343146310_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.964 | 4.964 | 4.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2506.1394 0 -2506.1394 195699.59 220 0 -3302.1782 0 -3302.1782 65.146712 Loop time of 2.60927 on 1 procs for 220 steps with 850 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 = -2506.13943079459 -3302.17504120338 -3302.17824397588 Force two-norm initial, final = 1827.3350 0.17009025 Force max component initial, final = 705.33970 0.033656410 Final line search alpha, max atom move = 1.0000000 0.033656410 Iterations, force evaluations = 220 421 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5558 | 2.5558 | 2.5558 | 0.0 | 97.95 Neigh | 0.013206 | 0.013206 | 0.013206 | 0.0 | 0.51 Comm | 0.022822 | 0.022822 | 0.022822 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01747 | | | 0.67 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6640.00 ave 6640 max 6640 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: 116028.0 ave 116028 max 116028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116028 Ave neighs/atom = 136.50353 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 220 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.964 | 4.964 | 4.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 220 0 -3302.1782 0 -3302.1782 65.146712 10380.33 269 0 -3309.4641 0 -3309.4641 466.36399 10338.624 Loop time of 0.364376 on 1 procs for 49 steps with 850 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 = -3302.17824397588 -3309.46219694182 -3309.46405097689 Force two-norm initial, final = 271.50275 6.0188745 Force max component initial, final = 219.86083 3.3554405 Final line search alpha, max atom move = 0.00043912356 0.0014734530 Iterations, force evaluations = 49 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32809 | 0.32809 | 0.32809 | 0.0 | 90.04 Neigh | 0.020941 | 0.020941 | 0.020941 | 0.0 | 5.75 Comm | 0.0029724 | 0.0029724 | 0.0029724 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01237 | | | 3.39 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 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: 118888.0 ave 118888 max 118888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118888 Ave neighs/atom = 139.86824 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.102 | 5.102 | 5.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3309.4641 0 -3309.4641 466.36399 Loop time of 1.712e-06 on 1 procs for 0 steps with 850 atoms 175.2% 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 | | 1.712e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 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: 118948.0 ave 118948 max 118948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118948 Ave neighs/atom = 139.93882 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.102 | 5.102 | 5.102 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 -3309.4641 -3309.4641 26.24207 103.51595 3.8059 466.36399 466.36399 512.34861 362.95639 523.78697 2.2343484 516.55624 Loop time of 2.137e-06 on 1 procs for 0 steps with 850 atoms 234.0% 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 | | 2.137e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59474.0 ave 59474 max 59474 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118948.0 ave 118948 max 118948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118948 Ave neighs/atom = 139.93882 Neighbor list builds = 0 Dangerous builds = 0 850 -3309.4640509769 eV 2.23434842296042 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03