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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -41.271459 0.0000000) to (20.635730 41.271459 4.0469996) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7620915 4.7620915 4.0469996 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.271459 0.0000000) to (20.635730 41.271459 4.0469996) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7620915 4.7620915 4.0469996 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.271459 0.0000000) to (20.635730 41.271459 4.0469996) create_atoms CPU = 0.000 seconds 210 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 416 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1274.5796 0 -1274.5796 40991.057 54 0 -1392.4041 0 -1392.4041 6652.8765 Loop time of 2.07723 on 1 procs for 54 steps with 416 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1274.57956568687 -1392.40276587816 -1392.40412985345 Force two-norm initial, final = 254.92483 0.10319694 Force max component initial, final = 72.181955 0.014324000 Final line search alpha, max atom move = 1.0000000 0.014324000 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0683 | 2.0683 | 2.0683 | 0.0 | 99.57 Neigh | 0.0026659 | 0.0026659 | 0.0026659 | 0.0 | 0.13 Comm | 0.0034406 | 0.0034406 | 0.0034406 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002868 | | | 0.14 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3285.00 ave 3285 max 3285 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: 35456.0 ave 35456 max 35456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35456 Ave neighs/atom = 85.230769 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.448 | 4.448 | 4.448 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1392.4041 0 -1392.4041 6652.8765 6893.3894 67 0 -1392.7116 0 -1392.7116 93.108939 6949.8719 Loop time of 0.350539 on 1 procs for 13 steps with 416 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 = -1392.40412985345 -1392.71148860299 -1392.71161426422 Force two-norm initial, final = 59.699073 0.95997905 Force max component initial, final = 54.472043 0.85915175 Final line search alpha, max atom move = 0.0066824705 0.0057412562 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34771 | 0.34771 | 0.34771 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048514 | 0.00048514 | 0.00048514 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002342 | | | 0.67 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3285.00 ave 3285 max 3285 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: 35456.0 ave 35456 max 35456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35456 Ave neighs/atom = 85.230769 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1392.7116 0 -1392.7116 93.108939 Loop time of 2.343e-06 on 1 procs for 0 steps with 416 atoms 213.4% 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 | | 2.343e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3285.00 ave 3285 max 3285 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: 35416.0 ave 35416 max 35416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35416 Ave neighs/atom = 85.134615 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.586 | 4.586 | 4.586 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 -1392.7116 -1392.7116 20.649769 83.522588 4.0295604 93.108939 93.108939 198.19778 55.511523 25.617511 2.4662819 441.9411 Loop time of 2.092e-06 on 1 procs for 0 steps with 416 atoms 239.0% 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 | | 2.092e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3285.00 ave 3285 max 3285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17708.0 ave 17708 max 17708 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35416.0 ave 35416 max 35416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35416 Ave neighs/atom = 85.134615 Neighbor list builds = 0 Dangerous builds = 0 416 -1392.71161426422 eV 2.46628190293641 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02