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 = 3.6147282 3.6147282 3.6147282 Created orthogonal box = (0.0000000 -37.565357 0.0000000) to (8.8542395 37.565357 5.1119976) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9028264 6.2608928 5.1119976 Created 143 atoms using lattice units in orthogonal box = (0.0000000 -37.565357 0.0000000) to (8.8542395 37.565357 5.1119976) create_atoms CPU = 0.002 seconds 143 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9028264 6.2608928 5.1119976 Created 151 atoms using lattice units in orthogonal box = (0.0000000 -37.565357 0.0000000) to (8.8542395 37.565357 5.1119976) create_atoms CPU = 0.002 seconds 151 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 18 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 288 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_942551040047_005#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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1013.8614 0 -1013.8614 1894.5139 32 0 -1015.0851 0 -1015.0851 -16.889418 Loop time of 0.479006 on 1 procs for 32 steps with 288 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 = -1013.86135821569 -1015.0843902951 -1015.08509617263 Force two-norm initial, final = 4.5442633 0.066635669 Force max component initial, final = 2.5805949 0.0099304596 Final line search alpha, max atom move = 1.0000000 0.0099304596 Iterations, force evaluations = 32 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46786 | 0.46786 | 0.46786 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069343 | 0.0069343 | 0.0069343 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004216 | | | 0.88 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 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: 64674.0 ave 64674 max 64674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64674 Ave neighs/atom = 224.56250 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1015.0851 0 -1015.0851 -16.889418 3400.6303 33 0 -1015.0851 0 -1015.0851 23.484498 3400.5328 Loop time of 0.0222877 on 1 procs for 1 steps with 288 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1015.08509617263 -1015.08509617263 -1015.08509810597 Force two-norm initial, final = 0.12016954 0.10976367 Force max component initial, final = 0.098121707 0.059046510 Final line search alpha, max atom move = 0.010191425 0.00060176807 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021285 | 0.021285 | 0.021285 | 0.0 | 95.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027048 | 0.00027048 | 0.00027048 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007321 | | | 3.28 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 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: 64608.0 ave 64608 max 64608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64608 Ave neighs/atom = 224.33333 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1015.0851 0 -1015.0851 23.484498 Loop time of 6.625e-06 on 1 procs for 0 steps with 288 atoms 166.0% 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 | | 6.625e-06 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 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: 64608.0 ave 64608 max 64608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64608 Ave neighs/atom = 224.33333 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 3 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.633 | 4.633 | 4.633 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 -1015.0851 -1015.0851 8.8541982 75.128748 5.1120086 23.484498 23.484498 23.53257 19.100831 27.820092 2.5506562 104.38193 Loop time of 6.435e-06 on 1 procs for 0 steps with 288 atoms 310.8% 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 | | 6.435e-06 | | |100.00 Nlocal: 288.000 ave 288 max 288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32304.0 ave 32304 max 32304 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64608.0 ave 64608 max 64608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64608 Ave neighs/atom = 224.33333 Neighbor list builds = 0 Dangerous builds = 0 288 -1015.08509810597 eV 2.55065619182616 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00