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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -43.418155 0.0000000) to (15.349391 43.418155 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6550387 4.5699614 4.9800000 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.418155 0.0000000) to (15.349391 43.418155 4.9800000) create_atoms CPU = 0.001 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6550387 4.5699614 4.9800000 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.418155 0.0000000) to (15.349391 43.418155 4.9800000) create_atoms CPU = 0.000 seconds 306 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 606 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2654.978 0 -2654.978 20433.116 32 0 -2684.4494 0 -2684.4494 4597.7306 Loop time of 1.33502 on 1 procs for 32 steps with 606 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 = -2654.97803646741 -2684.44691757505 -2684.44944786774 Force two-norm initial, final = 46.186410 0.20219137 Force max component initial, final = 10.459555 0.046384694 Final line search alpha, max atom move = 1.0000000 0.046384694 Iterations, force evaluations = 32 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3298 | 1.3298 | 1.3298 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026624 | 0.0026624 | 0.0026624 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002513 | | | 0.19 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3727.00 ave 3727 max 3727 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: 52324.0 ave 52324 max 52324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52324 Ave neighs/atom = 86.343234 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.516 | 4.516 | 4.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -2684.4494 0 -2684.4494 4597.7306 6637.7645 34 0 -2684.4651 0 -2684.4651 1039.1352 6650.4596 Loop time of 0.0857145 on 1 procs for 2 steps with 606 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 = -2684.44944786774 -2684.46508474801 -2684.465115307 Force two-norm initial, final = 23.244230 0.30349970 Force max component initial, final = 17.731868 0.21808429 Final line search alpha, max atom move = 0.0011517928 0.00025118790 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085083 | 0.085083 | 0.085083 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012145 | 0.00012145 | 0.00012145 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005101 | | | 0.60 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3811.00 ave 3811 max 3811 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: 52104.0 ave 52104 max 52104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52104 Ave neighs/atom = 85.980198 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.654 | 4.654 | 4.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2684.4651 0 -2684.4651 1039.1352 Loop time of 1.97e-06 on 1 procs for 0 steps with 606 atoms 152.3% 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 | | 1.97e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3804.00 ave 3804 max 3804 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: 52100.0 ave 52100 max 52100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52100 Ave neighs/atom = 85.973597 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.654 | 4.654 | 4.654 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 -2684.4651 -2684.4651 15.365768 86.836309 4.9842067 1039.1352 1039.1352 -14.422119 3184.4113 -52.583535 2.3242652 297.79769 Loop time of 1.852e-06 on 1 procs for 0 steps with 606 atoms 162.0% 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 | | 1.852e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3804.00 ave 3804 max 3804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26050.0 ave 26050 max 26050 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52100.0 ave 52100 max 52100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52100 Ave neighs/atom = 85.973597 Neighbor list builds = 0 Dangerous builds = 0 606 -2684.465115307 eV 2.32426518515906 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01