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 -58.672632 0.0000000) to (11.976501 58.672632 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4438641 5.3338757 5.8968214 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.672632 0.0000000) to (11.976501 58.672632 8.8452321) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4438641 5.3338757 5.8968214 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.672632 0.0000000) to (11.976501 58.672632 8.8452321) create_atoms CPU = 0.001 seconds 530 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 23 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 = 1056 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 23 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) = 6.399 | 6.399 | 6.399 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3995.6929 0 -3995.6929 56187.509 84 0 -4367.758 0 -4367.758 6239.1733 Loop time of 2.57179 on 1 procs for 84 steps with 1056 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3995.69286705125 -4367.75366929517 -4367.75801586814 Force two-norm initial, final = 550.11909 0.31339507 Force max component initial, final = 155.71078 0.065232288 Final line search alpha, max atom move = 1.0000000 0.065232288 Iterations, force evaluations = 84 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5182 | 2.5182 | 2.5182 | 0.0 | 97.91 Neigh | 0.023004 | 0.023004 | 0.023004 | 0.0 | 0.89 Comm | 0.019012 | 0.019012 | 0.019012 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01161 | | | 0.45 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10140.0 ave 10140 max 10140 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: 401444.0 ave 401444 max 401444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401444 Ave neighs/atom = 380.15530 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 3 23 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.401 | 6.401 | 6.401 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -4367.758 0 -4367.758 6239.1733 12430.963 89 0 -4367.9662 0 -4367.9662 233.71762 12474.254 Loop time of 0.115799 on 1 procs for 5 steps with 1056 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 = -4367.75801586812 -4367.96382214355 -4367.96622928694 Force two-norm initial, final = 105.07558 3.3712508 Force max component initial, final = 99.515398 2.5193001 Final line search alpha, max atom move = 0.00015056101 0.00037930837 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11273 | 0.11273 | 0.11273 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057163 | 0.00057163 | 0.00057163 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002498 | | | 2.16 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10218.0 ave 10218 max 10218 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: 400612.0 ave 400612 max 400612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400612 Ave neighs/atom = 379.36742 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 23 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) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4367.9662 0 -4367.9662 233.71762 Loop time of 2.06e-06 on 1 procs for 0 steps with 1056 atoms 145.6% 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 | | 2.06e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10208.0 ave 10208 max 10208 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: 400276.0 ave 400276 max 400276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400276 Ave neighs/atom = 379.04924 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 23 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) = 6.539 | 6.539 | 6.539 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 -4367.9662 -4367.9662 11.97106 117.85414 8.8417277 233.71762 233.71762 122.02039 255.68516 323.44733 2.2547257 416.53003 Loop time of 5.034e-06 on 1 procs for 0 steps with 1056 atoms 238.4% 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 | | 5.034e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10208.0 ave 10208 max 10208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 200138.0 ave 200138 max 200138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 400276.0 ave 400276 max 400276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400276 Ave neighs/atom = 379.04924 Neighbor list builds = 0 Dangerous builds = 0 1056 -4367.96622928694 eV 2.25472570375751 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03