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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -56.445408 0.0000000) to (28.220898 56.445408 3.6133157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0890143 5.0890143 3.6133157 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.445408 0.0000000) to (28.220898 56.445408 3.6133157) create_atoms CPU = 0.002 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0890143 5.0890143 3.6133157 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.445408 0.0000000) to (28.220898 56.445408 3.6133157) create_atoms CPU = 0.002 seconds 490 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 972 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_380272712420_001#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3392.7062 0 -3392.7062 13540.089 79 0 -3433.8767 0 -3433.8767 -2306.1247 Loop time of 20.2617 on 1 procs for 79 steps with 972 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 = -3392.7062060791 -3433.87338132279 -3433.87669005785 Force two-norm initial, final = 42.172887 0.17740211 Force max component initial, final = 11.578336 0.041156453 Final line search alpha, max atom move = 1.0000000 0.041156453 Iterations, force evaluations = 79 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.192 | 20.192 | 20.192 | 0.0 | 99.66 Neigh | 0.022399 | 0.022399 | 0.022399 | 0.0 | 0.11 Comm | 0.028018 | 0.028018 | 0.028018 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.019 | | | 0.09 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8584.00 ave 8584 max 8584 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: 172216.0 ave 172216 max 172216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172216 Ave neighs/atom = 177.17695 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.037 | 5.037 | 5.037 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3433.8767 0 -3433.8767 -2306.1247 11511.591 81 0 -3433.889 0 -3433.889 -249.63824 11494.77 Loop time of 0.764804 on 1 procs for 2 steps with 972 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3433.87669005784 -3433.88879279899 -3433.88895419061 Force two-norm initial, final = 23.848889 0.18099199 Force max component initial, final = 17.435312 0.044075493 Final line search alpha, max atom move = 0.00099866807 4.4016788e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76136 | 0.76136 | 0.76136 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092383 | 0.00092383 | 0.00092383 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002519 | | | 0.33 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8566.00 ave 8566 max 8566 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: 172068.0 ave 172068 max 172068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172068 Ave neighs/atom = 177.02469 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.175 | 5.175 | 5.175 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3433.889 0 -3433.889 -249.63824 Loop time of 7.808e-06 on 1 procs for 0 steps with 972 atoms 204.9% 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 | | 7.808e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8571.00 ave 8571 max 8571 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: 172144.0 ave 172144 max 172144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172144 Ave neighs/atom = 177.10288 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.175 | 5.175 | 5.175 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 -3433.889 -3433.889 28.204436 112.89082 3.6101416 -249.63824 -249.63824 -6.139795 -743.15009 0.37516239 2.3066499 159.70449 Loop time of 1.1256e-05 on 1 procs for 0 steps with 972 atoms 0.0% 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 | | 1.126e-05 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8571.00 ave 8571 max 8571 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86072.0 ave 86072 max 86072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172144.0 ave 172144 max 172144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172144 Ave neighs/atom = 177.10288 Neighbor list builds = 0 Dangerous builds = 0 972 -3433.88895419061 eV 2.30664989683838 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22