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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -69.084383 0.0000000) to (39.885887 69.084383 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8848030 5.2851440 6.2546061 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.084383 0.0000000) to (39.885887 69.084383 6.2546061) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8848030 5.2851440 6.2546061 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.084383 0.0000000) to (39.885887 69.084383 6.2546061) create_atoms CPU = 0.003 seconds 1466 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.187 | 6.187 | 6.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11990.037 0 -11990.037 32522.552 552 0 -12444.201 0 -12444.201 5755.3588 Loop time of 236.677 on 1 procs for 552 steps with 2926 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 = -11990.0370550107 -12444.1890599652 -12444.200975051 Force two-norm initial, final = 470.39488 0.36577750 Force max component initial, final = 144.10702 0.053092403 Final line search alpha, max atom move = 1.0000000 0.053092403 Iterations, force evaluations = 552 1019 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 235.94 | 235.94 | 235.94 | 0.0 | 99.69 Neigh | 0.41978 | 0.41978 | 0.41978 | 0.0 | 0.18 Comm | 0.15488 | 0.15488 | 0.15488 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1599 | | | 0.07 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10791.0 ave 10791 max 10791 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: 326860.0 ave 326860 max 326860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326860 Ave neighs/atom = 111.70882 Neighbor list builds = 18 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 552 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.192 | 6.192 | 6.192 Mbytes Step Temp E_pair E_mol TotEng Press Volume 552 0 -12444.201 0 -12444.201 5755.3588 34469.033 563 0 -12446.862 0 -12446.862 -16.325695 34583.398 Loop time of 3.55621 on 1 procs for 11 steps with 2926 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 = -12444.200975051 -12446.8573941272 -12446.8620328274 Force two-norm initial, final = 483.66909 1.9543872 Force max component initial, final = 477.26398 1.0542008 Final line search alpha, max atom move = 7.1013579e-05 7.4862568e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5474 | 3.5474 | 3.5474 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001127 | 0.001127 | 0.001127 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007642 | | | 0.21 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10672.0 ave 10672 max 10672 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: 327132.0 ave 327132 max 327132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327132 Ave neighs/atom = 111.80178 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.330 | 6.330 | 6.330 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12446.862 0 -12446.862 -16.325695 Loop time of 2.465e-06 on 1 procs for 0 steps with 2926 atoms 162.3% 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 | | 2.465e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10615.0 ave 10615 max 10615 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: 326732.0 ave 326732 max 326732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326732 Ave neighs/atom = 111.66507 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.330 | 6.330 | 6.330 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 -12446.862 -12446.862 39.78469 137.55039 6.3196037 -16.325695 -16.325695 39.408628 -48.620338 -39.765374 2.2595076 5892.4354 Loop time of 2.47e-06 on 1 procs for 0 steps with 2926 atoms 283.4% 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 | | 2.47e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10615.0 ave 10615 max 10615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 163366.0 ave 163366 max 163366 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 326732.0 ave 326732 max 326732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326732 Ave neighs/atom = 111.66507 Neighbor list builds = 0 Dangerous builds = 0 2926 -12446.8620328274 eV 2.25950756693639 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:04:01