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 = 2.8659480 2.8659480 2.8659480 Created orthogonal box = (0.0000000 -46.212023 0.0000000) to (23.106012 46.212023 2.8659480) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9102481 3.9102481 2.8659480 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -46.212023 0.0000000) to (23.106012 46.212023 2.8659480) create_atoms CPU = 0.002 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9102481 3.9102481 2.8659480 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.212023 0.0000000) to (23.106012 46.212023 2.8659480) create_atoms CPU = 0.001 seconds 261 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_650279905230_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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2126.821 0 -2126.821 63166.74 33 0 -2224.1109 0 -2224.1109 11525.928 Loop time of 0.539399 on 1 procs for 33 steps with 521 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 = -2126.8210071369 -2224.10881553098 -2224.11091480332 Force two-norm initial, final = 286.82790 0.16946547 Force max component initial, final = 186.80281 0.043749261 Final line search alpha, max atom move = 1.0000000 0.043749261 Iterations, force evaluations = 33 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52706 | 0.52706 | 0.52706 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0070661 | 0.0070661 | 0.0070661 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005277 | | | 0.98 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5491.00 ave 5491 max 5491 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: 87048.0 ave 87048 max 87048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87048 Ave neighs/atom = 167.07869 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -2224.1109 0 -2224.1109 11525.928 6120.3784 44 0 -2224.5325 0 -2224.5325 131.99192 6162.3745 Loop time of 0.128216 on 1 procs for 11 steps with 521 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2224.11091480332 -2224.53188181591 -2224.53251001476 Force two-norm initial, final = 97.017103 1.2662182 Force max component initial, final = 92.016123 1.2131834 Final line search alpha, max atom move = 0.00054102554 0.00065636319 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12152 | 0.12152 | 0.12152 | 0.0 | 94.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015257 | 0.0015257 | 0.0015257 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005166 | | | 4.03 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5461.00 ave 5461 max 5461 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: 86104.0 ave 86104 max 86104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86104 Ave neighs/atom = 165.26679 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2224.5325 0 -2224.5325 131.99192 Loop time of 6.085e-06 on 1 procs for 0 steps with 521 atoms 180.8% 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 | | 6.085e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5455.00 ave 5455 max 5455 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: 85900.0 ave 85900 max 85900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85900 Ave neighs/atom = 164.87524 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.641 | 4.641 | 4.641 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 -2224.5325 -2224.5325 23.089567 93.337905 2.8593956 131.99192 131.99192 55.274636 318.5384 22.162714 2.2950394 229.14131 Loop time of 6.976e-06 on 1 procs for 0 steps with 521 atoms 258.0% 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 | | 6.976e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5455.00 ave 5455 max 5455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42950.0 ave 42950 max 42950 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85900.0 ave 85900 max 85900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85900 Ave neighs/atom = 164.87524 Neighbor list builds = 0 Dangerous builds = 0 521 -2224.53238579868 eV 2.2950394396623 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01