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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -65.395997 0.0000000) to (13.348902 65.395997 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0676827 5.9450906 6.5725450 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -65.395997 0.0000000) to (13.348902 65.395997 9.8588175) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0676827 5.9450906 6.5725450 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.395997 0.0000000) to (13.348902 65.395997 9.8588175) create_atoms CPU = 0.001 seconds 530 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 32 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1048 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_149316865608_005#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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2724.7738 0 -2724.7738 2707.7029 104 0 -2765.9015 0 -2765.9015 -1710.7151 Loop time of 1.59581 on 1 procs for 104 steps with 1048 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 = -2724.77375567257 -2765.899118745 -2765.90153161506 Force two-norm initial, final = 76.473093 0.12007037 Force max component initial, final = 26.845633 0.023024864 Final line search alpha, max atom move = 1.0000000 0.023024864 Iterations, force evaluations = 104 197 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5584 | 1.5584 | 1.5584 | 0.0 | 97.66 Neigh | 0.018974 | 0.018974 | 0.018974 | 0.0 | 1.19 Comm | 0.0092994 | 0.0092994 | 0.0092994 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009093 | | | 0.57 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5948.00 ave 5948 max 5948 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: 146720.0 ave 146720 max 146720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146720 Ave neighs/atom = 140.00000 Neighbor list builds = 2 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -2765.9015 0 -2765.9015 -1710.7151 17212.8 107 0 -2765.9349 0 -2765.9349 98.883567 17173.266 Loop time of 0.0406091 on 1 procs for 3 steps with 1048 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 = -2765.90153161506 -2765.93452688096 -2765.93491030206 Force two-norm initial, final = 34.375471 1.9960097 Force max component initial, final = 23.850164 1.6818426 Final line search alpha, max atom move = 0.00056590491 0.00095176300 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039444 | 0.039444 | 0.039444 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021951 | 0.00021951 | 0.00021951 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009456 | | | 2.33 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6072.00 ave 6072 max 6072 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: 146572.0 ave 146572 max 146572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146572 Ave neighs/atom = 139.85878 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.197 | 5.197 | 5.197 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2765.9349 0 -2765.9349 98.883567 Loop time of 1.738e-06 on 1 procs for 0 steps with 1048 atoms 115.1% 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 | | 1.738e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6072.00 ave 6072 max 6072 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: 146584.0 ave 146584 max 146584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146584 Ave neighs/atom = 139.87023 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 4 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.197 | 5.197 | 5.197 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 -2765.9349 -2765.9349 13.327448 130.89993 9.8438836 98.883567 98.883567 61.527221 157.03667 78.08681 2.5920006 530.77238 Loop time of 1.875e-06 on 1 procs for 0 steps with 1048 atoms 213.3% 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 | | 1.875e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6072.00 ave 6072 max 6072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73292.0 ave 73292 max 73292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146584.0 ave 146584 max 146584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146584 Ave neighs/atom = 139.87023 Neighbor list builds = 0 Dangerous builds = 0 1048 -2733.72540256787 eV 2.5920005648055 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01