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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1194 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) create_atoms CPU = 0.002 seconds 1194 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1202 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507796) create_atoms CPU = 0.002 seconds 1202 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 = 9 42 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2396 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 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) = 5.158 | 5.158 | 5.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8349.409 0 -8349.409 16377.557 84 0 -8458.7039 0 -8458.7039 1199.8555 Loop time of 6.54839 on 1 procs for 84 steps with 2396 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8349.40898742445 -8458.69582209647 -8458.70390437531 Force two-norm initial, final = 125.05418 0.27488751 Force max component initial, final = 42.250044 0.059060419 Final line search alpha, max atom move = 1.0000000 0.059060419 Iterations, force evaluations = 84 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4962 | 6.4962 | 6.4962 | 0.0 | 99.20 Neigh | 0.015933 | 0.015933 | 0.015933 | 0.0 | 0.24 Comm | 0.015299 | 0.015299 | 0.015299 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02096 | | | 0.32 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6844.00 ave 6844 max 6844 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: 185492.0 ave 185492 max 185492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185492 Ave neighs/atom = 77.417362 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.156 | 5.156 | 5.156 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -8458.7039 0 -8458.7039 1199.8555 28305.377 87 0 -8458.8051 0 -8458.8051 -35.943471 28329.752 Loop time of 0.20018 on 1 procs for 3 steps with 2396 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 = -8458.7039043753 -8458.799103809 -8458.80506749854 Force two-norm initial, final = 74.930404 1.3331446 Force max component initial, final = 74.305487 1.0304696 Final line search alpha, max atom move = 7.5669519e-05 7.7975137e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19818 | 0.19818 | 0.19818 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028567 | 0.00028567 | 0.00028567 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001717 | | | 0.86 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6700.00 ave 6700 max 6700 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: 185436.0 ave 185436 max 185436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185436 Ave neighs/atom = 77.393990 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 = 9 42 3 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) = 5.294 | 5.294 | 5.294 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8458.8051 0 -8458.8051 -35.943471 Loop time of 2.056e-06 on 1 procs for 0 steps with 2396 atoms 194.6% 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 | | 2.056e-06 | | |100.00 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6704.00 ave 6704 max 6704 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: 185416.0 ave 185416 max 185416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185416 Ave neighs/atom = 77.385643 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 = 9 42 3 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) = 5.294 | 5.294 | 5.294 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 -8458.8051 -8458.8051 25.535481 125.49334 8.8405253 -35.943471 -35.943471 -5.1221373 -44.498048 -58.210229 2.3612935 887.56429 Loop time of 2.283e-06 on 1 procs for 0 steps with 2396 atoms 262.8% 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 | | 2.283e-06 | | |100.00 Nlocal: 2396.00 ave 2396 max 2396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6704.00 ave 6704 max 6704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92708.0 ave 92708 max 92708 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185416.0 ave 185416 max 185416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185416 Ave neighs/atom = 77.385643 Neighbor list builds = 0 Dangerous builds = 0 2396 -8458.80506749854 eV 2.3612934960708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07