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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -46.472675 0.0000000) to (9.4861951 46.472675 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3119069 4.2247887 4.6706796 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -46.472675 0.0000000) to (9.4861951 46.472675 7.0060194) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3119069 4.2247887 4.6706796 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -46.472675 0.0000000) to (9.4861951 46.472675 7.0060194) create_atoms CPU = 0.000 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 35 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 530 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.854 | 4.854 | 4.854 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2138.4346 0 -2138.4346 49295.117 48 0 -2256.5915 0 -2256.5915 11025.184 Loop time of 2.89198 on 1 procs for 48 steps with 530 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 = -2138.4346387521 -2256.58925470722 -2256.59147443551 Force two-norm initial, final = 227.21475 0.19430834 Force max component initial, final = 86.637984 0.039795220 Final line search alpha, max atom move = 1.0000000 0.039795220 Iterations, force evaluations = 48 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8875 | 2.8875 | 2.8875 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020655 | 0.0020655 | 0.0020655 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002446 | | | 0.08 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772.00 ave 2772 max 2772 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: 30760.0 ave 30760 max 30760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30760 Ave neighs/atom = 58.037736 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.854 | 4.854 | 4.854 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -2256.5915 0 -2256.5915 11025.184 6177.1914 58 0 -2256.9803 0 -2256.9803 -52.465464 6214.24 Loop time of 0.412682 on 1 procs for 10 steps with 530 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 = -2256.59147443551 -2256.98015678642 -2256.98026226318 Force two-norm initial, final = 97.032558 0.81006289 Force max component initial, final = 94.065085 0.50213125 Final line search alpha, max atom move = 0.0013111387 0.00065836372 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4111 | 0.4111 | 0.4111 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026667 | 0.00026667 | 0.00026667 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001314 | | | 0.32 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2781.00 ave 2781 max 2781 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: 30596.0 ave 30596 max 30596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30596 Ave neighs/atom = 57.728302 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.992 | 4.992 | 4.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2256.9803 0 -2256.9803 -52.465464 Loop time of 1.589e-06 on 1 procs for 0 steps with 530 atoms 125.9% 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 | | 1.589e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2779.00 ave 2779 max 2779 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: 30584.0 ave 30584 max 30584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30584 Ave neighs/atom = 57.705660 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.992 | 4.992 | 4.992 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 -2256.9803 -2256.9803 9.466943 93.770606 7.0002175 -52.465464 -52.465464 10.040241 -38.082658 -129.35398 2.2501834 335.08585 Loop time of 1.445e-06 on 1 procs for 0 steps with 530 atoms 207.6% 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 | | 1.445e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2779.00 ave 2779 max 2779 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15292.0 ave 15292 max 15292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30584.0 ave 30584 max 30584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30584 Ave neighs/atom = 57.705660 Neighbor list builds = 0 Dangerous builds = 0 530 -2256.98026226318 eV 2.25018338280228 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03