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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -57.193243 0.0000000) to (11.674522 57.193243 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3066008 5.1993857 5.7481372 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.193243 0.0000000) to (11.674522 57.193243 8.6222058) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3066008 5.1993857 5.7481372 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.193243 0.0000000) to (11.674522 57.193243 8.6222058) create_atoms CPU = 0.001 seconds 530 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 30 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.119 | 5.119 | 5.119 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4551.2089 0 -4551.2089 42417.696 94 0 -4689.0918 0 -4689.0918 11784.612 Loop time of 1.72558 on 1 procs for 94 steps with 1058 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4551.20891438577 -4689.0873689424 -4689.09181316338 Force two-norm initial, final = 271.12876 0.29356131 Force max component initial, final = 63.254005 0.072249308 Final line search alpha, max atom move = 1.0000000 0.072249308 Iterations, force evaluations = 94 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.693 | 1.693 | 1.693 | 0.0 | 98.11 Neigh | 0.013328 | 0.013328 | 0.013328 | 0.0 | 0.77 Comm | 0.010098 | 0.010098 | 0.010098 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00912 | | | 0.53 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6860.00 ave 6860 max 6860 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: 188760.0 ave 188760 max 188760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188760 Ave neighs/atom = 178.41210 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.116 | 5.116 | 5.116 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -4689.0918 0 -4689.0918 11784.612 11514.158 102 0 -4689.6102 0 -4689.6102 -78.817908 11586.556 Loop time of 0.107869 on 1 procs for 8 steps with 1058 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 = -4689.09181316338 -4689.6100355686 -4689.61021881968 Force two-norm initial, final = 170.12667 1.4844296 Force max component initial, final = 155.04391 1.1111472 Final line search alpha, max atom move = 0.00035124225 0.00039028185 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10476 | 0.10476 | 0.10476 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057514 | 0.00057514 | 0.00057514 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002536 | | | 2.35 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6623.00 ave 6623 max 6623 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: 187664.0 ave 187664 max 187664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187664 Ave neighs/atom = 177.37618 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.254 | 5.254 | 5.254 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4689.6102 0 -4689.6102 -78.817908 Loop time of 1.717e-06 on 1 procs for 0 steps with 1058 atoms 174.7% 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 | | 1.717e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6623.00 ave 6623 max 6623 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: 186480.0 ave 186480 max 186480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186480 Ave neighs/atom = 176.25709 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.254 | 5.254 | 5.254 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 -4689.6102 -4689.6102 11.665109 115.1929 8.6226324 -78.817908 -78.817908 -153.52436 -111.76024 28.830877 2.2517425 397.17077 Loop time of 2.458e-06 on 1 procs for 0 steps with 1058 atoms 203.4% 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 | | 2.458e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6623.00 ave 6623 max 6623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93240.0 ave 93240 max 93240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186480.0 ave 186480 max 186480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186480 Ave neighs/atom = 176.25709 Neighbor list builds = 0 Dangerous builds = 0 1058 -4689.61021881968 eV 2.25174249515824 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02