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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -46.579105 0.0000000) to (16.468201 46.579105 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4913274 3.5287201 4.0541907 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -46.579105 0.0000000) to (16.468201 46.579105 4.0541907) create_atoms CPU = 0.002 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4913274 3.5287201 4.0541907 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -46.579105 0.0000000) to (16.468201 46.579105 4.0541907) create_atoms CPU = 0.001 seconds 266 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 25 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 526 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1949.7092 0 -1949.7092 97107.374 68 0 -2238.5929 0 -2238.5929 4467.0715 Loop time of 1.08975 on 1 procs for 68 steps with 526 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 = -1949.70920528629 -2238.59113411794 -2238.5928887951 Force two-norm initial, final = 672.01619 0.21569835 Force max component initial, final = 232.86421 0.068987930 Final line search alpha, max atom move = 1.0000000 0.068987930 Iterations, force evaluations = 68 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0438 | 1.0438 | 1.0438 | 0.0 | 95.79 Neigh | 0.022764 | 0.022764 | 0.022764 | 0.0 | 2.09 Comm | 0.012907 | 0.012907 | 0.012907 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01025 | | | 0.94 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4753.00 ave 4753 max 4753 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: 87404.0 ave 87404 max 87404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87404 Ave neighs/atom = 166.16730 Neighbor list builds = 2 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -2238.5929 0 -2238.5929 4467.0715 6219.729 73 0 -2238.6626 0 -2238.6626 15.514827 6232.9751 Loop time of 0.0663065 on 1 procs for 5 steps with 526 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 = -2238.59288879511 -2238.66249509052 -2238.66262817717 Force two-norm initial, final = 38.809866 0.37612159 Force max component initial, final = 37.405570 0.14338713 Final line search alpha, max atom move = 0.00054902893 7.8723680e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063315 | 0.063315 | 0.063315 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006855 | 0.0006855 | 0.0006855 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002306 | | | 3.48 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4799.00 ave 4799 max 4799 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: 87536.0 ave 87536 max 87536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87536 Ave neighs/atom = 166.41825 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.657 | 4.657 | 4.657 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2238.6626 0 -2238.6626 15.514827 Loop time of 6.465e-06 on 1 procs for 0 steps with 526 atoms 170.1% 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 | | 6.465e-06 | | |100.00 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4781.00 ave 4781 max 4781 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: 87504.0 ave 87504 max 87504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87504 Ave neighs/atom = 166.35741 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.657 | 4.657 | 4.657 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 -2238.6626 -2238.6626 16.453429 93.528925 4.0503543 15.514827 15.514827 5.4301672 37.004107 4.1102077 2.3705446 218.7733 Loop time of 7.066e-06 on 1 procs for 0 steps with 526 atoms 254.7% 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 | | 7.066e-06 | | |100.00 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4781.00 ave 4781 max 4781 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43752.0 ave 43752 max 43752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87504.0 ave 87504 max 87504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87504 Ave neighs/atom = 166.35741 Neighbor list builds = 0 Dangerous builds = 0 526 -2238.66262817717 eV 2.37054463761798 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01