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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -61.799299 0.0000000) to (35.679842 61.799299 6.0599198) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4892064 5.5460909 6.0599198 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -61.799299 0.0000000) to (35.679842 61.799299 6.0599198) create_atoms CPU = 0.003 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4892064 5.5460909 6.0599198 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -61.799299 0.0000000) to (35.679842 61.799299 6.0599198) create_atoms CPU = 0.003 seconds 1250 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2496 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.535 | 6.535 | 6.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9695.9793 0 -9695.9793 69894.456 125 0 -10243.309 0 -10243.309 2755.4193 Loop time of 4.93447 on 1 procs for 125 steps with 2496 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 = -9695.97930127415 -10243.3004376177 -10243.3090882856 Force two-norm initial, final = 1406.0462 0.37449713 Force max component initial, final = 348.94672 0.096314940 Final line search alpha, max atom move = 1.0000000 0.096314940 Iterations, force evaluations = 125 224 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7937 | 4.7937 | 4.7937 | 0.0 | 97.15 Neigh | 0.083795 | 0.083795 | 0.083795 | 0.0 | 1.70 Comm | 0.030042 | 0.030042 | 0.030042 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02698 | | | 0.55 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12211.0 ave 12211 max 12211 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: 436756.0 ave 436756 max 436756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436756 Ave neighs/atom = 174.98237 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.535 | 6.535 | 6.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -10243.309 0 -10243.309 2755.4193 26724.116 128 0 -10243.412 0 -10243.412 4.0341296 26783.138 Loop time of 0.130813 on 1 procs for 3 steps with 2496 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 = -10243.3090882856 -10243.4108170009 -10243.4117720533 Force two-norm initial, final = 101.06273 1.2507968 Force max component initial, final = 81.407885 0.87986047 Final line search alpha, max atom move = 0.00011018828 9.6950312e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12763 | 0.12763 | 0.12763 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056474 | 0.00056474 | 0.00056474 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002615 | | | 2.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12191.0 ave 12191 max 12191 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: 436824.0 ave 436824 max 436824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436824 Ave neighs/atom = 175.00962 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.673 | 6.673 | 6.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10243.412 0 -10243.412 4.0341296 Loop time of 1.789e-06 on 1 procs for 0 steps with 2496 atoms 167.7% 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 | | 1.789e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12191.0 ave 12191 max 12191 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: 436702.0 ave 436702 max 436702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436702 Ave neighs/atom = 174.96074 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.673 | 6.673 | 6.673 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 -10243.412 -10243.412 35.716944 123.81467 6.056407 4.0341296 4.0341296 -52.688288 35.960238 28.830438 2.2329045 1095.9657 Loop time of 2.726e-06 on 1 procs for 0 steps with 2496 atoms 256.8% 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 | | 2.726e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12191.0 ave 12191 max 12191 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218351.0 ave 218351 max 218351 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436702.0 ave 436702 max 436702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436702 Ave neighs/atom = 174.96074 Neighbor list builds = 0 Dangerous builds = 0 2496 -10243.4117720533 eV 2.23290453635404 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05