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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -73.348318 0.0000000) to (42.345559 73.348318 6.3360136) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6882094 5.8383809 6.3360136 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -73.348318 0.0000000) to (42.345559 73.348318 6.3360136) create_atoms CPU = 0.004 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6882094 5.8383809 6.3360136 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -73.348318 0.0000000) to (42.345559 73.348318 6.3360136) create_atoms CPU = 0.004 seconds 1610 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3182 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.651 | 6.651 | 6.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12321.296 0 -12321.296 -2376.9156 356 0 -12489.662 0 -12489.662 -62971.344 Loop time of 15.5789 on 1 procs for 356 steps with 3182 atoms 94.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12321.2958642604 -12489.6510089699 -12489.6617288832 Force two-norm initial, final = 18.847567 0.79516965 Force max component initial, final = 3.4657774 0.34016216 Final line search alpha, max atom move = 0.94762364 0.32234570 Iterations, force evaluations = 356 682 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.141 | 15.141 | 15.141 | 0.0 | 97.19 Neigh | 0.21265 | 0.21265 | 0.21265 | 0.0 | 1.37 Comm | 0.10105 | 0.10105 | 0.10105 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1237 | | | 0.79 Nlocal: 3182.00 ave 3182 max 3182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12386.0 ave 12386 max 12386 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: 428602.0 ave 428602 max 428602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428602 Ave neighs/atom = 134.69579 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 356 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.651 | 6.651 | 6.651 Mbytes Step Temp E_pair E_mol TotEng Press Volume 356 0 -12489.662 0 -12489.662 -62971.344 39359.006 400 0 -12538.69 0 -12538.69 -7642.3186 37672.814 Loop time of 1.28143 on 1 procs for 44 steps with 3182 atoms 81.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12489.661728883 -12538.6873241887 -12538.6897077892 Force two-norm initial, final = 2365.6172 6.3287939 Force max component initial, final = 2141.9753 2.5346328 Final line search alpha, max atom move = 6.7661376e-05 0.00017149674 Iterations, force evaluations = 44 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2073 | 1.2073 | 1.2073 | 0.0 | 94.22 Neigh | 0.025998 | 0.025998 | 0.025998 | 0.0 | 2.03 Comm | 0.0051042 | 0.0051042 | 0.0051042 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04302 | | | 3.36 Nlocal: 3182.00 ave 3182 max 3182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12612.0 ave 12612 max 12612 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: 444022.0 ave 444022 max 444022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444022 Ave neighs/atom = 139.54180 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.790 | 6.790 | 6.790 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12538.69 0 -12538.69 -7642.3186 Loop time of 1.662e-06 on 1 procs for 0 steps with 3182 atoms 120.3% 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 | | 1.662e-06 | | |100.00 Nlocal: 3182.00 ave 3182 max 3182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12591.0 ave 12591 max 12591 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: 448226.0 ave 448226 max 448226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448226 Ave neighs/atom = 140.86298 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.790 | 6.790 | 6.790 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 -12538.69 -12538.69 40.549616 146.69664 6.3331702 -7642.3186 -7642.3186 -22.607338 -22796.602 -107.74631 2.1822511 7620.4775 Loop time of 1.868e-06 on 1 procs for 0 steps with 3182 atoms 214.1% 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 | | 1.868e-06 | | |100.00 Nlocal: 3182.00 ave 3182 max 3182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12591.0 ave 12591 max 12591 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224113.0 ave 224113 max 224113 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 448226.0 ave 448226 max 448226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448226 Ave neighs/atom = 140.86298 Neighbor list builds = 0 Dangerous builds = 0 3182 -12088.6861004973 eV 2.18225107981481 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17