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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -37.924731 0.0000000) to (37.921164 37.924731 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0337828 5.0337828 3.5673230 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.924731 0.0000000) to (37.921164 37.924731 3.5673230) create_atoms CPU = 0.002 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0337828 5.0337828 3.5673230 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.924731 0.0000000) to (37.921164 37.924731 3.5673230) create_atoms CPU = 0.002 seconds 454 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 28 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 892 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3734.5046 0 -3734.5046 -3855.8579 41 0 -3765.2328 0 -3765.2328 16100.42 Loop time of 4.52375 on 1 procs for 41 steps with 892 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 = -3734.50463620508 -3765.23004161126 -3765.23279290057 Force two-norm initial, final = 32.036494 0.19506033 Force max component initial, final = 8.7019101 0.027835196 Final line search alpha, max atom move = 1.0000000 0.027835196 Iterations, force evaluations = 41 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5053 | 4.5053 | 4.5053 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0090665 | 0.0090665 | 0.0090665 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009357 | | | 0.21 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5084.00 ave 5084 max 5084 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: 48120.0 ave 48120 max 48120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48120 Ave neighs/atom = 53.946188 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3765.2328 0 -3765.2328 16100.42 10260.691 63 0 -3768.1924 0 -3768.1924 5063.1867 10382.77 Loop time of 1.54592 on 1 procs for 22 steps with 892 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 = -3765.23279290057 -3768.18963788431 -3768.1924154466 Force two-norm initial, final = 274.05694 7.4549392 Force max component initial, final = 251.60450 6.8129492 Final line search alpha, max atom move = 8.0550904e-05 0.00054878922 Iterations, force evaluations = 22 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5317 | 1.5317 | 1.5317 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002975 | 0.002975 | 0.002975 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01127 | | | 0.73 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094.00 ave 5094 max 5094 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: 53400.0 ave 53400 max 53400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53400 Ave neighs/atom = 59.865471 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3768.1924 0 -3768.1924 5063.1867 Loop time of 6.265e-06 on 1 procs for 0 steps with 892 atoms 0.0% 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 | | 6.265e-06 | | |100.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5066.00 ave 5066 max 5066 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: 52336.0 ave 52336 max 52336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52336 Ave neighs/atom = 58.672646 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.692 | 4.692 | 4.692 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 -3768.1924 -3768.1924 38.62218 75.849462 3.5442467 5063.1867 5063.1867 371.97869 15862.094 -1044.5128 2.3163685 168.01351 Loop time of 6.355e-06 on 1 procs for 0 steps with 892 atoms 299.0% 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 | | 6.355e-06 | | |100.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5066.00 ave 5066 max 5066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26168.0 ave 26168 max 26168 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52336.0 ave 52336 max 52336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52336 Ave neighs/atom = 58.672646 Neighbor list builds = 0 Dangerous builds = 0 892 -3768.1924154466 eV 2.31636848632909 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06