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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009646 41.649202 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296738 5.3548973 5.7481359 Created 1660 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009646 41.649202 8.6222039) create_atoms CPU = 0.003 seconds 1660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296738 5.3548973 5.7481359 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009646 41.649202 8.6222039) create_atoms CPU = 0.003 seconds 1684 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 15 25 3 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3316 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14599.656 0 -14599.656 3152.7483 140 0 -14700.697 0 -14700.697 -9159.8075 Loop time of 4.75261 on 1 procs for 140 steps with 3316 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 = -14599.6556800119 -14700.6821236276 -14700.6967497797 Force two-norm initial, final = 57.571622 0.41944590 Force max component initial, final = 6.5546704 0.058330078 Final line search alpha, max atom move = 0.83595325 0.048761218 Iterations, force evaluations = 140 245 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4677 | 4.4677 | 4.4677 | 0.0 | 94.01 Neigh | 0.21569 | 0.21569 | 0.21569 | 0.0 | 4.54 Comm | 0.026978 | 0.026978 | 0.026978 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04222 | | | 0.89 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9342.00 ave 9342 max 9342 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: 436588.0 ave 436588 max 436588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436588 Ave neighs/atom = 131.66104 Neighbor list builds = 7 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 140 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.501 | 6.501 | 6.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 140 0 -14700.697 0 -14700.697 -9159.8075 36635.934 145 0 -14701.359 0 -14701.359 0.44870637 36440.798 Loop time of 0.137409 on 1 procs for 5 steps with 3316 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 = -14700.6967497793 -14701.358207045 -14701.3587928856 Force two-norm initial, final = 373.55277 1.1602758 Force max component initial, final = 282.08248 0.80824589 Final line search alpha, max atom move = 8.6451550e-05 6.9874110e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13311 | 0.13311 | 0.13311 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058924 | 0.00058924 | 0.00058924 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003707 | | | 2.70 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9346.00 ave 9346 max 9346 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: 436578.0 ave 436578 max 436578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436578 Ave neighs/atom = 131.65802 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.639 | 6.639 | 6.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14701.359 0 -14701.359 0.44870637 Loop time of 1.862e-06 on 1 procs for 0 steps with 3316 atoms 214.8% 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 | | 1.862e-06 | | |100.00 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9386.00 ave 9386 max 9386 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: 436924.0 ave 436924 max 436924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436924 Ave neighs/atom = 131.76236 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.639 | 6.639 | 6.639 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 -14701.359 -14701.359 50.96485 82.996391 8.6150525 0.44870637 0.44870637 -35.504583 8.5723858 28.278317 2.2397305 1751.2863 Loop time of 2.111e-06 on 1 procs for 0 steps with 3316 atoms 284.2% 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 | | 2.111e-06 | | |100.00 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9386.00 ave 9386 max 9386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218462.0 ave 218462 max 218462 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 436924.0 ave 436924 max 436924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 436924 Ave neighs/atom = 131.76236 Neighbor list builds = 0 Dangerous builds = 0 3316 -14701.3587928856 eV 2.23973048141663 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05