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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -42.068600 0.0000000) to (21.034300 42.068600 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9492471 4.9492471 3.6073527 Created 271 atoms using lattice units in orthogonal box = (0.0000000 -42.068600 0.0000000) to (21.034300 42.068600 3.6073527) create_atoms CPU = 0.001 seconds 271 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9492471 4.9492471 3.6073527 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -42.068600 0.0000000) to (21.034300 42.068600 3.6073527) create_atoms CPU = 0.000 seconds 273 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 544 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.773 | 5.773 | 5.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1751.6605 0 -1751.6605 49755.354 56 0 -1909.0263 0 -1909.0263 6731.4141 Loop time of 1.60509 on 1 procs for 56 steps with 544 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1751.66048812181 -1909.024729302 -1909.02633168695 Force two-norm initial, final = 270.29304 0.14900365 Force max component initial, final = 72.948974 0.020222208 Final line search alpha, max atom move = 1.0000000 0.020222208 Iterations, force evaluations = 56 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5726 | 1.5726 | 1.5726 | 0.0 | 97.97 Neigh | 0.016526 | 0.016526 | 0.016526 | 0.0 | 1.03 Comm | 0.011001 | 0.011001 | 0.011001 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005002 | | | 0.31 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11110.0 ave 11110 max 11110 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: 342702.0 ave 342702 max 342702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342702 Ave neighs/atom = 629.96691 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.779 | 5.779 | 5.779 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -1909.0263 0 -1909.0263 6731.4141 6384.1742 64 0 -1909.2169 0 -1909.2169 -66.389528 6415.0705 Loop time of 0.155582 on 1 procs for 8 steps with 544 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 = -1909.02633168695 -1909.21607564434 -1909.21692027864 Force two-norm initial, final = 59.850960 0.66180970 Force max component initial, final = 45.509942 0.43181784 Final line search alpha, max atom move = 0.00016718988 7.2195572e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15169 | 0.15169 | 0.15169 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081467 | 0.00081467 | 0.00081467 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003079 | | | 1.98 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11520.0 ave 11520 max 11520 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: 341686.0 ave 341686 max 341686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341686 Ave neighs/atom = 628.09926 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.917 | 5.917 | 5.917 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1909.2169 0 -1909.2169 -66.389528 Loop time of 1.776e-06 on 1 procs for 0 steps with 544 atoms 112.6% 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 | | 1.776e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11600.0 ave 11600 max 11600 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: 341404.0 ave 341404 max 341404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341404 Ave neighs/atom = 627.58088 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.917 | 5.917 | 5.917 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 -1909.2169 -1909.2169 20.945776 84.304391 3.6329112 -66.389528 -66.389528 -78.18127 -108.06166 -12.925652 2.2718882 250.33931 Loop time of 3.565e-06 on 1 procs for 0 steps with 544 atoms 196.4% 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 | | 3.565e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11600.0 ave 11600 max 11600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170702.0 ave 170702 max 170702 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 341404.0 ave 341404 max 341404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341404 Ave neighs/atom = 627.58088 Neighbor list builds = 0 Dangerous builds = 0 544 -1909.21692027864 eV 2.27188824076111 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02