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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -38.889785 0.0000000) to (38.886127 38.889785 3.6580991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1618753 5.1618753 3.6580991 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.889785 0.0000000) to (38.886127 38.889785 3.6580991) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1618753 5.1618753 3.6580991 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.889785 0.0000000) to (38.886127 38.889785 3.6580991) create_atoms CPU = 0.000 seconds 454 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 904 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3454.4474 0 -3454.4474 22578.566 202 0 -3522.4148 0 -3522.4148 -10529.268 Loop time of 2.40479 on 1 procs for 202 steps with 904 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 = -3454.44736122741 -3522.41151409283 -3522.41482108769 Force two-norm initial, final = 48.642038 0.16777595 Force max component initial, final = 11.015717 0.022690179 Final line search alpha, max atom move = 1.0000000 0.022690179 Iterations, force evaluations = 202 386 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3506 | 2.3506 | 2.3506 | 0.0 | 97.75 Neigh | 0.02139 | 0.02139 | 0.02139 | 0.0 | 0.89 Comm | 0.017928 | 0.017928 | 0.017928 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01486 | | | 0.62 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6556.00 ave 6556 max 6556 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: 126236.0 ave 126236 max 126236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126236 Ave neighs/atom = 139.64159 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 202 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press Volume 202 0 -3522.4148 0 -3522.4148 -10529.268 11064.09 255 0 -3538.3825 0 -3538.3825 -17265.465 11103.768 Loop time of 0.361884 on 1 procs for 53 steps with 904 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 = -3522.41482108769 -3538.38120024133 -3538.38253490907 Force two-norm initial, final = 462.50106 3.6176389 Force max component initial, final = 362.23983 1.8432789 Final line search alpha, max atom move = 0.00021483803 0.00039600641 Iterations, force evaluations = 53 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33967 | 0.33967 | 0.33967 | 0.0 | 93.86 Neigh | 0.0070678 | 0.0070678 | 0.0070678 | 0.0 | 1.95 Comm | 0.0026183 | 0.0026183 | 0.0026183 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01253 | | | 3.46 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6636.00 ave 6636 max 6636 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: 126658.0 ave 126658 max 126658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126658 Ave neighs/atom = 140.10841 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.099 | 5.099 | 5.099 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3538.3825 0 -3538.3825 -17265.465 Loop time of 3.373e-06 on 1 procs for 0 steps with 904 atoms 148.2% 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 | | 3.373e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 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: 127012.0 ave 127012 max 127012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127012 Ave neighs/atom = 140.50000 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.099 | 5.099 | 5.099 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 -3538.3825 -3538.3825 37.265589 77.779571 3.830865 -17265.465 -17265.465 -143.47019 -51374.395 -278.53027 2.3040659 332.07439 Loop time of 1.526e-06 on 1 procs for 0 steps with 904 atoms 196.6% 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 | | 1.526e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6656.00 ave 6656 max 6656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63506.0 ave 63506 max 63506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127012.0 ave 127012 max 127012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127012 Ave neighs/atom = 140.50000 Neighbor list builds = 0 Dangerous builds = 0 904 -3410.5373868915 eV 2.30406589038798 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03