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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -38.031680 0.0000000) to (13.446229 38.031680 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8895380 4.3217818 4.0541907 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -38.031680 0.0000000) to (13.446229 38.031680 4.0541907) create_atoms CPU = 0.002 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8895380 4.3217818 4.0541907 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -38.031680 0.0000000) to (13.446229 38.031680 4.0541907) create_atoms CPU = 0.001 seconds 178 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 350 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1391.9406 0 -1391.9406 64607.171 76 0 -1487.6361 0 -1487.6361 813.92677 Loop time of 0.870509 on 1 procs for 76 steps with 350 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 = -1391.94063653529 -1487.63469793989 -1487.63608784275 Force two-norm initial, final = 239.60776 0.15469093 Force max component initial, final = 80.956671 0.027395053 Final line search alpha, max atom move = 1.0000000 0.027395053 Iterations, force evaluations = 76 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84307 | 0.84307 | 0.84307 | 0.0 | 96.85 Neigh | 0.0080664 | 0.0080664 | 0.0080664 | 0.0 | 0.93 Comm | 0.010946 | 0.010946 | 0.010946 | 0.0 | 1.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008432 | | | 0.97 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3725.00 ave 3725 max 3725 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: 57932.0 ave 57932 max 57932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57932 Ave neighs/atom = 165.52000 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -1487.6361 0 -1487.6361 813.92677 4146.486 81 0 -1487.6943 0 -1487.6943 12.591571 4148.8155 Loop time of 0.0516654 on 1 procs for 5 steps with 350 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 = -1487.63608784274 -1487.69426796391 -1487.69430298574 Force two-norm initial, final = 26.501598 0.69626143 Force max component initial, final = 23.538451 0.43609272 Final line search alpha, max atom move = 0.0086858808 0.0037878494 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049191 | 0.049191 | 0.049191 | 0.0 | 95.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058965 | 0.00058965 | 0.00058965 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001885 | | | 3.65 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3699.00 ave 3699 max 3699 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: 58136.0 ave 58136 max 58136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58136 Ave neighs/atom = 166.10286 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1487.6943 0 -1487.6943 12.591571 Loop time of 6.225e-06 on 1 procs for 0 steps with 350 atoms 160.6% 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 | | 6.225e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3663.00 ave 3663 max 3663 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: 58128.0 ave 58128 max 58128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58128 Ave neighs/atom = 166.08000 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.597 | 4.597 | 4.597 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 -1487.6943 -1487.6943 13.428159 76.349175 4.0467212 12.591571 12.591571 -168.18259 38.488234 167.46907 2.3191669 280.60899 Loop time of 6.715e-06 on 1 procs for 0 steps with 350 atoms 223.4% 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: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3663.00 ave 3663 max 3663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29064.0 ave 29064 max 29064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58128.0 ave 58128 max 58128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58128 Ave neighs/atom = 166.08000 Neighbor list builds = 0 Dangerous builds = 0 350 -1487.69430298574 eV 2.3191669336605 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01