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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -55.433015 0.0000000) to (33.945651 55.433015 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751049 5.3644853 5.7481359 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -55.433015 0.0000000) to (33.945651 55.433015 8.6222039) create_atoms CPU = 0.003 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751049 5.3644853 5.7481359 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -55.433015 0.0000000) to (33.945651 55.433015 8.6222039) create_atoms CPU = 0.002 seconds 1492 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 33 3 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2978 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.468 | 6.468 | 6.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12990.652 0 -12990.652 18289.349 90 0 -13217.468 0 -13217.468 10398.961 Loop time of 2.8846 on 1 procs for 90 steps with 2978 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12990.6517338892 -13217.4560962388 -13217.4679179375 Force two-norm initial, final = 97.543364 0.39115103 Force max component initial, final = 10.004365 0.066863513 Final line search alpha, max atom move = 1.0000000 0.066863513 Iterations, force evaluations = 90 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7829 | 2.7829 | 2.7829 | 0.0 | 96.47 Neigh | 0.056718 | 0.056718 | 0.056718 | 0.0 | 1.97 Comm | 0.018206 | 0.018206 | 0.018206 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02678 | | | 0.93 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9194.00 ave 9194 max 9194 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: 395332.0 ave 395332 max 395332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395332 Ave neighs/atom = 132.75084 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.468 | 6.468 | 6.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -13217.468 0 -13217.468 10398.961 32448.97 96 0 -13218.417 0 -13218.417 -194.06599 32642.312 Loop time of 0.132114 on 1 procs for 6 steps with 2978 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 = -13217.4679179376 -13218.4151602115 -13218.4168045413 Force two-norm initial, final = 397.72215 7.8815445 Force max component initial, final = 329.41487 5.7772530 Final line search alpha, max atom move = 7.7151141e-05 0.00044572167 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12764 | 0.12764 | 0.12764 | 0.0 | 96.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061563 | 0.00061563 | 0.00061563 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003854 | | | 2.92 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9147.00 ave 9147 max 9147 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: 395434.0 ave 395434 max 395434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395434 Ave neighs/atom = 132.78509 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.606 | 6.606 | 6.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13218.417 0 -13218.417 -194.06599 Loop time of 2.012e-06 on 1 procs for 0 steps with 2978 atoms 248.5% 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 | | 2.012e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9100.00 ave 9100 max 9100 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: 395184.0 ave 395184 max 395184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395184 Ave neighs/atom = 132.70114 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.606 | 6.606 | 6.606 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 -13218.417 -13218.417 33.990271 111.44814 8.6169476 -194.06599 -194.06599 -283.93656 -39.321253 -258.94016 2.2202108 934.60305 Loop time of 2.479e-06 on 1 procs for 0 steps with 2978 atoms 242.0% 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 | | 2.479e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9100.00 ave 9100 max 9100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 197592.0 ave 197592 max 197592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 395184.0 ave 395184 max 395184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395184 Ave neighs/atom = 132.70114 Neighbor list builds = 0 Dangerous builds = 0 2978 -13218.4168045413 eV 2.22021075844491 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03