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 -41.045530 0.0000000) to (35.546472 41.045530 6.9712367) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3801360 6.3146970 6.9712367 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -41.045530 0.0000000) to (35.546472 41.045530 6.9712367) create_atoms CPU = 0.004 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3801360 6.3146970 6.9712367 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -41.045530 0.0000000) to (35.546472 41.045530 6.9712367) create_atoms CPU = 0.003 seconds 628 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 = 9 20 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1249 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 = 9 20 2 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 -3130.5404 0 -3130.5404 20814.939 130 0 -3290.2178 0 -3290.2178 7675.8536 Loop time of 5.51138 on 1 procs for 130 steps with 1249 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 = -3130.54038614066 -3290.21451933031 -3290.21776593769 Force two-norm initial, final = 170.62552 0.15347537 Force max component initial, final = 39.719449 0.060119112 Final line search alpha, max atom move = 1.0000000 0.060119112 Iterations, force evaluations = 130 236 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2983 | 5.2983 | 5.2983 | 0.0 | 96.13 Neigh | 0.13795 | 0.13795 | 0.13795 | 0.0 | 2.50 Comm | 0.038893 | 0.038893 | 0.038893 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03625 | | | 0.66 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6084.00 ave 6084 max 6084 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: 175466.0 ave 175466 max 175466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175466 Ave neighs/atom = 140.48519 Neighbor list builds = 5 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 = 9 20 2 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 : 130 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 130 0 -3290.2178 0 -3290.2178 7675.8536 20342.4 144 0 -3291.2538 0 -3291.2538 8.8091229 20531.69 Loop time of 0.3957 on 1 procs for 14 steps with 1249 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 = -3290.21776593766 -3291.2537708233 -3291.25384228444 Force two-norm initial, final = 196.79158 0.92757917 Force max component initial, final = 178.60460 0.69847139 Final line search alpha, max atom move = 0.0044676088 0.0031204969 Iterations, force evaluations = 14 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35718 | 0.35718 | 0.35718 | 0.0 | 90.26 Neigh | 0.026464 | 0.026464 | 0.026464 | 0.0 | 6.69 Comm | 0.0026728 | 0.0026728 | 0.0026728 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009387 | | | 2.37 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6086.00 ave 6086 max 6086 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: 174780.0 ave 174780 max 174780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174780 Ave neighs/atom = 139.93595 Neighbor list builds = 1 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 = 9 20 2 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 -3291.2538 0 -3291.2538 8.8091229 Loop time of 6.585e-06 on 1 procs for 0 steps with 1249 atoms 182.2% 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 | | 6.585e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6089.00 ave 6089 max 6089 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: 174778.0 ave 174778 max 174778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174778 Ave neighs/atom = 139.93435 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 = 9 20 2 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 -3291.2538 -3291.2538 35.531082 83.148566 6.9496271 8.8091229 8.8091229 54.481143 1.935175 -29.988949 2.541065 1094.4184 Loop time of 6.776e-06 on 1 procs for 0 steps with 1249 atoms 265.6% 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 | | 6.776e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6089.00 ave 6089 max 6089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87389.0 ave 87389 max 87389 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174778.0 ave 174778 max 174778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174778 Ave neighs/atom = 139.93435 Neighbor list builds = 0 Dangerous builds = 0 1249 -3252.86674766611 eV 2.54106499076276 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06