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 -67.368191 0.0000000) to (38.895043 67.368191 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7386129 5.1538507 6.0992294 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.368191 0.0000000) to (38.895043 67.368191 6.0992294) create_atoms CPU = 0.010 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7386129 5.1538507 6.0992294 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.368191 0.0000000) to (38.895043 67.368191 6.0992294) create_atoms CPU = 0.012 seconds 1466 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 = 13 44 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 4 atoms, new total = 2926 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 = 13 44 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) = 5.793 | 5.793 | 5.793 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12348.82 0 -12348.82 74458.899 139 0 -12977.812 0 -12977.812 8126.2446 Loop time of 64.7473 on 1 procs for 139 steps with 2926 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 = -12348.8200373992 -12977.8006300635 -12977.8118325208 Force two-norm initial, final = 1331.6041 0.39769534 Force max component initial, final = 394.25460 0.087446949 Final line search alpha, max atom move = 1.0000000 0.087446949 Iterations, force evaluations = 139 253 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 64.426 | 64.426 | 64.426 | 0.0 | 99.50 Neigh | 0.181 | 0.181 | 0.181 | 0.0 | 0.28 Comm | 0.061548 | 0.061548 | 0.061548 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07915 | | | 0.12 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9713.00 ave 9713 max 9713 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: 251300.0 ave 251300 max 251300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251300 Ave neighs/atom = 85.885167 Neighbor list builds = 4 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 = 13 44 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 : 139 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.793 | 5.793 | 5.793 Mbytes Step Temp E_pair E_mol TotEng Press Volume 139 0 -12977.812 0 -12977.812 8126.2446 31963.484 144 0 -12978.484 0 -12978.484 356.17759 32096.174 Loop time of 1.66615 on 1 procs for 5 steps with 2926 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 = -12977.8118325208 -12978.4717106601 -12978.4843757325 Force two-norm initial, final = 328.12570 12.904523 Force max component initial, final = 300.69158 9.3963957 Final line search alpha, max atom move = 4.2768930e-05 0.00040187379 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6582 | 1.6582 | 1.6582 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014797 | 0.0014797 | 0.0014797 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006473 | | | 0.39 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9713.00 ave 9713 max 9713 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: 251288.0 ave 251288 max 251288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251288 Ave neighs/atom = 85.881066 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 = 13 44 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) = 5.931 | 5.931 | 5.931 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12978.484 0 -12978.484 356.17759 Loop time of 6.616e-06 on 1 procs for 0 steps with 2926 atoms 196.5% 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 | | 6.616e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719.00 ave 9719 max 9719 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: 251156.0 ave 251156 max 251156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251156 Ave neighs/atom = 85.835954 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 = 13 44 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) = 5.931 | 5.931 | 5.931 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 -12978.484 -12978.484 38.879721 135.33695 6.0997738 356.17759 356.17759 210.00611 471.13991 387.38674 2.2113529 1177.1471 Loop time of 7.547e-06 on 1 procs for 0 steps with 2926 atoms 278.3% 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 | | 7.547e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719.00 ave 9719 max 9719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125578.0 ave 125578 max 125578 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 251156.0 ave 251156 max 251156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251156 Ave neighs/atom = 85.835954 Neighbor list builds = 0 Dangerous builds = 0 2926 -12978.4843757325 eV 2.21135292349567 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:08