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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -63.497155 0.0000000) to (38.883908 63.497155 9.8765224) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2715980 6.1448860 6.5843483 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -63.497155 0.0000000) to (38.883908 63.497155 9.8765224) create_atoms CPU = 0.007 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2715980 6.1448860 6.5843483 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -63.497155 0.0000000) to (38.883908 63.497155 9.8765224) create_atoms CPU = 0.008 seconds 1492 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 34 3 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2964 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.467 | 6.467 | 6.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9756.0791 0 -9756.0791 2029.2927 89 0 -9942.7464 0 -9942.7464 -935.26529 Loop time of 5.55582 on 1 procs for 89 steps with 2964 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9756.07907210842 -9942.73748901925 -9942.74640869618 Force two-norm initial, final = 54.161177 0.21913318 Force max component initial, final = 6.5891178 0.027210043 Final line search alpha, max atom move = 1.0000000 0.027210043 Iterations, force evaluations = 89 159 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4201 | 5.4201 | 5.4201 | 0.0 | 97.56 Neigh | 0.052744 | 0.052744 | 0.052744 | 0.0 | 0.95 Comm | 0.035193 | 0.035193 | 0.035193 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04774 | | | 0.86 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8869.00 ave 8869 max 8869 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: 388776.0 ave 388776 max 388776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388776 Ave neighs/atom = 131.16599 Neighbor list builds = 1 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.085 | 6.085 | 6.085 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -9942.7464 0 -9942.7464 -935.26529 48770.613 91 0 -9942.7716 0 -9942.7716 -0.18631951 48714.549 Loop time of 0.168488 on 1 procs for 2 steps with 2964 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 = -9942.74640869616 -9942.76726909574 -9942.77162049679 Force two-norm initial, final = 52.894041 0.50760495 Force max component initial, final = 44.044211 0.34208382 Final line search alpha, max atom move = 9.2013821e-05 3.1476439e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16358 | 0.16358 | 0.16358 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00098978 | 0.00098978 | 0.00098978 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003916 | | | 2.32 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9021.00 ave 9021 max 9021 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: 390672.0 ave 390672 max 390672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390672 Ave neighs/atom = 131.80567 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.223 | 6.223 | 6.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9942.7716 0 -9942.7716 -0.18631951 Loop time of 6.896e-06 on 1 procs for 0 steps with 2964 atoms 203.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9021.00 ave 9021 max 9021 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: 390808.0 ave 390808 max 390808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390808 Ave neighs/atom = 131.85155 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.223 | 6.223 | 6.223 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 -9942.7716 -9942.7716 38.881601 126.99956 9.8653463 -0.18631951 -0.18631951 -11.250153 9.9282346 0.76296007 2.6371449 1560.5209 Loop time of 6.816e-06 on 1 procs for 0 steps with 2964 atoms 308.1% 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 | | 6.816e-06 | | |100.00 Nlocal: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9021.00 ave 9021 max 9021 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195404.0 ave 195404 max 195404 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 390808.0 ave 390808 max 390808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390808 Ave neighs/atom = 131.85155 Neighbor list builds = 0 Dangerous builds = 0 2964 -9942.77162049679 eV 2.63714489290054 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06