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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -58.290126 0.0000000) to (29.145063 58.290126 3.6150002) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9322414 4.9322414 3.6150002 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.290126 0.0000000) to (29.145063 58.290126 3.6150002) create_atoms CPU = 0.003 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9322414 4.9322414 3.6150002 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.290126 0.0000000) to (29.145063 58.290126 3.6150002) create_atoms CPU = 0.002 seconds 522 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 31 1 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1040 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3576.9354 0 -3576.9354 10539.317 70 0 -3669.8588 0 -3669.8588 5285.8955 Loop time of 2.33612 on 1 procs for 70 steps with 1040 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 = -3576.93535277307 -3669.85529944853 -3669.85878053023 Force two-norm initial, final = 53.924431 0.17768857 Force max component initial, final = 8.7113380 0.027564148 Final line search alpha, max atom move = 1.0000000 0.027564148 Iterations, force evaluations = 70 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2688 | 2.2688 | 2.2688 | 0.0 | 97.12 Neigh | 0.023037 | 0.023037 | 0.023037 | 0.0 | 0.99 Comm | 0.025991 | 0.025991 | 0.025991 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01832 | | | 0.78 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8315.00 ave 8315 max 8315 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: 175864.0 ave 175864 max 175864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175864 Ave neighs/atom = 169.10000 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -3669.8588 0 -3669.8588 5285.8955 12282.826 75 0 -3670.0034 0 -3670.0034 -44.188072 12330.266 Loop time of 0.123947 on 1 procs for 5 steps with 1040 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 = -3669.85878053023 -3670.0023130582 -3670.00337184444 Force two-norm initial, final = 78.903718 0.87153304 Force max component initial, final = 66.023381 0.80738460 Final line search alpha, max atom move = 0.00013892925 0.00011216934 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11907 | 0.11907 | 0.11907 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010984 | 0.0010984 | 0.0010984 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003774 | | | 3.05 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7930.00 ave 7930 max 7930 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: 178888.0 ave 178888 max 178888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178888 Ave neighs/atom = 172.00769 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3670.0034 0 -3670.0034 -44.188072 Loop time of 6.586e-06 on 1 procs for 0 steps with 1040 atoms 182.2% 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 | | 6.586e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7945.00 ave 7945 max 7945 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: 177976.0 ave 177976 max 177976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177976 Ave neighs/atom = 171.13077 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.179 | 5.179 | 5.179 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 -3670.0034 -3670.0034 29.10613 117.03368 3.619738 -44.188072 -44.188072 -104.77022 3.6191948 -31.413196 2.2865792 359.63137 Loop time of 7.167e-06 on 1 procs for 0 steps with 1040 atoms 223.2% 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 | | 7.167e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7945.00 ave 7945 max 7945 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88988.0 ave 88988 max 88988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 177976.0 ave 177976 max 177976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177976 Ave neighs/atom = 171.13077 Neighbor list builds = 0 Dangerous builds = 0 1040 -3670.00337184444 eV 2.28657918361503 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02