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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -61.710090 0.0000000) to (30.853239 61.710090 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6491182 4.6491182 3.6110985 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -61.710090 0.0000000) to (30.853239 61.710090 3.6110985) create_atoms CPU = 0.002 seconds 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6491182 4.6491182 3.6110985 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -61.710090 0.0000000) to (30.853239 61.710090 3.6110985) create_atoms CPU = 0.002 seconds 586 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1160 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4890.7358 0 -4890.7358 520.18293 22 0 -4905.1967 0 -4905.1967 -5437.5221 Loop time of 5.17466 on 1 procs for 22 steps with 1160 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 = -4890.7358355816 -4905.19374178051 -4905.19674012881 Force two-norm initial, final = 24.996949 0.16254628 Force max component initial, final = 6.9026695 0.029956617 Final line search alpha, max atom move = 1.0000000 0.029956617 Iterations, force evaluations = 22 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1625 | 5.1625 | 5.1625 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064207 | 0.0064207 | 0.0064207 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005723 | | | 0.11 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7910.00 ave 7910 max 7910 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: 99632.0 ave 99632 max 99632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99632 Ave neighs/atom = 85.889655 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -4905.1967 0 -4905.1967 -5437.5221 13750.746 27 0 -4905.277 0 -4905.277 -2242.9562 13724.809 Loop time of 1.14962 on 1 procs for 5 steps with 1160 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 = -4905.19674012882 -4905.27617611673 -4905.27696377967 Force two-norm initial, final = 54.007638 4.5350412 Force max component initial, final = 49.418838 4.3746467 Final line search alpha, max atom move = 0.00026336330 0.0011521214 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1432 | 1.1432 | 1.1432 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012544 | 0.0012544 | 0.0012544 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00516 | | | 0.45 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7935.00 ave 7935 max 7935 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: 99848.0 ave 99848 max 99848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99848 Ave neighs/atom = 86.075862 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.176 | 5.176 | 5.176 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4905.277 0 -4905.277 -2242.9562 Loop time of 7.748e-06 on 1 procs for 0 steps with 1160 atoms 167.8% 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 | | 7.748e-06 | | |100.00 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7935.00 ave 7935 max 7935 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: 99880.0 ave 99880 max 99880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99880 Ave neighs/atom = 86.103448 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.176 | 5.176 | 5.176 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 -4905.277 -4905.277 30.736719 123.42018 3.6179507 -2242.9562 -2242.9562 -508.74923 -6082.6659 -137.45345 2.3022928 447.19245 Loop time of 6.715e-06 on 1 procs for 0 steps with 1160 atoms 297.8% 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 | | 6.715e-06 | | |100.00 Nlocal: 1160.00 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7935.00 ave 7935 max 7935 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49940.0 ave 49940 max 49940 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99880.0 ave 99880 max 99880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99880 Ave neighs/atom = 86.103448 Neighbor list builds = 0 Dangerous builds = 0 1160 -4905.27696377967 eV 2.30229282699218 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07