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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -38.030005 0.0000000) to (21.956634 38.030005 6.1692815) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7780615 5.3375446 6.1692815 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.030005 0.0000000) to (21.956634 38.030005 6.1692815) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7780615 5.3375446 6.1692815 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.030005 0.0000000) to (21.956634 38.030005 6.1692815) create_atoms CPU = 0.003 seconds 458 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 6 18 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_322509103239_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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.412 | 5.412 | 5.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3235.6966 0 -3235.6966 65820.304 74 0 -3566.0125 0 -3566.0125 5588.9127 Loop time of 2.48132 on 1 procs for 74 steps with 912 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 = -3235.69660805327 -3566.00916749749 -3566.01248001221 Force two-norm initial, final = 497.80007 0.25181093 Force max component initial, final = 143.24087 0.024411699 Final line search alpha, max atom move = 1.0000000 0.024411699 Iterations, force evaluations = 74 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4145 | 2.4145 | 2.4145 | 0.0 | 97.31 Neigh | 0.028486 | 0.028486 | 0.028486 | 0.0 | 1.15 Comm | 0.021815 | 0.021815 | 0.021815 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01647 | | | 0.66 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6809.00 ave 6809 max 6809 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: 203944.0 ave 203944 max 203944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203944 Ave neighs/atom = 223.62281 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.406 | 5.406 | 5.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -3566.0125 0 -3566.0125 5588.9127 10302.835 78 0 -3566.1354 0 -3566.1354 340.2576 10332.519 Loop time of 0.115854 on 1 procs for 4 steps with 912 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 = -3566.01248001221 -3566.1324652081 -3566.13542213962 Force two-norm initial, final = 77.034683 4.1641263 Force max component initial, final = 72.410970 3.2579436 Final line search alpha, max atom move = 0.00011903482 0.00038780873 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11238 | 0.11238 | 0.11238 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083519 | 0.00083519 | 0.00083519 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002637 | | | 2.28 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6352.00 ave 6352 max 6352 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: 204544.0 ave 204544 max 204544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204544 Ave neighs/atom = 224.28070 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3566.1354 0 -3566.1354 340.2576 Loop time of 6.265e-06 on 1 procs for 0 steps with 912 atoms 207.5% 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: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6354.00 ave 6354 max 6354 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: 204432.0 ave 204432 max 204432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204432 Ave neighs/atom = 224.15789 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.544 | 5.544 | 5.544 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 -3566.1354 -3566.1354 22.028449 76.005924 6.1712743 340.2576 340.2576 506.83414 141.60773 372.33093 2.2924796 639.43503 Loop time of 6.936e-06 on 1 procs for 0 steps with 912 atoms 259.5% 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 | | 6.936e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6354.00 ave 6354 max 6354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102216.0 ave 102216 max 102216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204432.0 ave 204432 max 204432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204432 Ave neighs/atom = 224.15789 Neighbor list builds = 0 Dangerous builds = 0 912 -3566.13542213962 eV 2.29247955714751 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03