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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -42.700545 0.0000000) to (52.292288 42.700545 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6553821 6.2103963 6.6478321 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -42.700545 0.0000000) to (52.292288 42.700545 9.9717481) create_atoms CPU = 0.002 seconds 1321 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6553821 6.2103963 6.6478321 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -42.700545 0.0000000) to (52.292288 42.700545 9.9717481) create_atoms CPU = 0.002 seconds 1321 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 43 atoms, new total = 2599 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8697.2773 0 -8697.2773 -2109.9159 35 0 -8715.1341 0 -8715.1341 -8699.691 Loop time of 4.05677 on 1 procs for 35 steps with 2599 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 = -8697.27726315813 -8715.12633125917 -8715.13409532831 Force two-norm initial, final = 16.398569 0.34053200 Force max component initial, final = 3.8194691 0.17776251 Final line search alpha, max atom move = 0.90623338 0.16109432 Iterations, force evaluations = 35 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0329 | 4.0329 | 4.0329 | 0.0 | 99.41 Neigh | 0.012091 | 0.012091 | 0.012091 | 0.0 | 0.30 Comm | 0.0039301 | 0.0039301 | 0.0039301 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007846 | | | 0.19 Nlocal: 2599.00 ave 2599 max 2599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5613.00 ave 5613 max 5613 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: 139252.0 ave 139252 max 139252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139252 Ave neighs/atom = 53.579069 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -8715.1341 0 -8715.1341 -8699.691 44532.017 40 0 -8715.8226 0 -8715.8226 -2115.2821 44234.544 Loop time of 0.510794 on 1 procs for 5 steps with 2599 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 = -8715.1340953283 -8715.82252549019 -8715.82258084864 Force two-norm initial, final = 298.40701 0.68570179 Force max component initial, final = 216.58285 0.42022028 Final line search alpha, max atom move = 0.0010902768 0.00045815644 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50782 | 0.50782 | 0.50782 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036499 | 0.00036499 | 0.00036499 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002605 | | | 0.51 Nlocal: 2599.00 ave 2599 max 2599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5613.00 ave 5613 max 5613 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: 139230.0 ave 139230 max 139230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139230 Ave neighs/atom = 53.570604 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.234 | 5.234 | 5.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8715.8226 0 -8715.8226 -2115.2821 Loop time of 2.311e-06 on 1 procs for 0 steps with 2599 atoms 173.1% 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 | | 2.311e-06 | | |100.00 Nlocal: 2599.00 ave 2599 max 2599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5613.00 ave 5613 max 5613 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: 139260.0 ave 139260 max 139260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139260 Ave neighs/atom = 53.582147 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.234 | 5.234 | 5.234 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 -8715.8226 -8715.8226 52.107909 85.401091 9.9401855 -2115.2821 -2115.2821 15.166725 -6363.6594 2.6462547 2.5304459 2034.584 Loop time of 2.294e-06 on 1 procs for 0 steps with 2599 atoms 218.0% 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 | | 2.294e-06 | | |100.00 Nlocal: 2599.00 ave 2599 max 2599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5613.00 ave 5613 max 5613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69630.0 ave 69630 max 69630 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139260.0 ave 139260 max 139260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139260 Ave neighs/atom = 53.582147 Neighbor list builds = 0 Dangerous builds = 0 2599 -8715.82258084864 eV 2.53044591167608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05