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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -41.054366 0.0000000) to (23.702749 41.054366 5.4861205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0791606 4.8874246 5.4861205 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -41.054366 0.0000000) to (23.702749 41.054366 5.4861205) create_atoms CPU = 0.001 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0791606 4.8874246 5.4861205 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -41.054366 0.0000000) to (23.702749 41.054366 5.4861205) create_atoms CPU = 0.001 seconds 339 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 21 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 672 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_269937397263_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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4500.7226 0 -4500.7226 22794.893 38 0 -4548.3643 0 -4548.3643 9615.9506 Loop time of 4.75533 on 1 procs for 38 steps with 672 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4500.72259101179 -4548.36134123649 -4548.36433853089 Force two-norm initial, final = 57.027489 0.17056496 Force max component initial, final = 12.634690 0.021496468 Final line search alpha, max atom move = 1.0000000 0.021496468 Iterations, force evaluations = 38 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7498 | 4.7498 | 4.7498 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002842 | 0.002842 | 0.002842 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002698 | | | 0.06 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4392.00 ave 4392 max 4392 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: 90976.0 ave 90976 max 90976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90976 Ave neighs/atom = 135.38095 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -4548.3643 0 -4548.3643 9615.9506 10677.103 43 0 -4548.5709 0 -4548.5709 -6.705446 10719.257 Loop time of 0.780749 on 1 procs for 5 steps with 672 atoms 77.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4548.36433853089 -4548.5685186075 -4548.57086277549 Force two-norm initial, final = 120.40127 0.82744860 Force max component initial, final = 100.11946 0.58445093 Final line search alpha, max atom move = 6.9485269e-05 4.0610730e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77884 | 0.77884 | 0.77884 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032584 | 0.00032584 | 0.00032584 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001584 | | | 0.20 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4506.00 ave 4506 max 4506 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: 90642.0 ave 90642 max 90642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90642 Ave neighs/atom = 134.88393 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.670 | 4.670 | 4.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4548.5709 0 -4548.5709 -6.705446 Loop time of 2.256e-06 on 1 procs for 0 steps with 672 atoms 177.3% 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 | | 2.256e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4464.00 ave 4464 max 4464 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: 90592.0 ave 90592 max 90592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90592 Ave neighs/atom = 134.80952 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.670 | 4.670 | 4.670 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 -4548.5709 -4548.5709 23.724285 82.433583 5.4810954 -6.705446 -6.705446 87.435569 -47.173078 -60.378829 2.4825871 491.20167 Loop time of 2.3e-06 on 1 procs for 0 steps with 672 atoms 217.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4464.00 ave 4464 max 4464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45296.0 ave 45296 max 45296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90592.0 ave 90592 max 90592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90592 Ave neighs/atom = 134.80952 Neighbor list builds = 0 Dangerous builds = 0 672 -4548.57086277549 eV 2.4825870785341 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06