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 -59.562272 0.0000000) to (48.632392 59.562272 9.8588175) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9957743 5.7114508 6.5725450 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -59.562272 0.0000000) to (48.632392 59.562272 9.8588175) create_atoms CPU = 0.003 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9957743 5.7114508 6.5725450 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -59.562272 0.0000000) to (48.632392 59.562272 9.8588175) create_atoms CPU = 0.002 seconds 1757 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 = 12 29 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 0 atoms, new total = 3506 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 = 12 29 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) = 7.006 | 7.006 | 7.006 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8550.4709 0 -8550.4709 27105.297 81 0 -9248.7448 0 -9248.7448 5303.3983 Loop time of 3.59119 on 1 procs for 81 steps with 3506 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 = -8550.47089882035 -9248.73732311279 -9248.74483386039 Force two-norm initial, final = 636.10925 0.22885538 Force max component initial, final = 159.18998 0.035970678 Final line search alpha, max atom move = 1.0000000 0.035970678 Iterations, force evaluations = 81 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4847 | 3.4847 | 3.4847 | 0.0 | 97.03 Neigh | 0.067415 | 0.067415 | 0.067415 | 0.0 | 1.88 Comm | 0.016189 | 0.016189 | 0.016189 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02289 | | | 0.64 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11256.0 ave 11256 max 11256 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: 491272.0 ave 491272 max 491272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491272 Ave neighs/atom = 140.12322 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 = 12 29 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.006 | 7.006 | 7.006 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -9248.7448 0 -9248.7448 5303.3983 57115.201 92 0 -9250.3539 0 -9250.3539 16.355238 57485.104 Loop time of 0.35155 on 1 procs for 11 steps with 3506 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 = -9248.74483386039 -9250.35369824553 -9250.35388208913 Force two-norm initial, final = 390.60953 1.2012930 Force max component initial, final = 362.86155 0.61195113 Final line search alpha, max atom move = 0.00054532128 0.00033370998 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31063 | 0.31063 | 0.31063 | 0.0 | 88.36 Neigh | 0.032589 | 0.032589 | 0.032589 | 0.0 | 9.27 Comm | 0.0013425 | 0.0013425 | 0.0013425 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00699 | | | 1.99 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11197.0 ave 11197 max 11197 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: 489958.0 ave 489958 max 489958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489958 Ave neighs/atom = 139.74843 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 = 12 29 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) = 6.762 | 6.762 | 6.762 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9250.3539 0 -9250.3539 16.355238 Loop time of 1.989e-06 on 1 procs for 0 steps with 3506 atoms 201.1% 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 | | 1.989e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11207.0 ave 11207 max 11207 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: 489926.0 ave 489926 max 489926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489926 Ave neighs/atom = 139.73930 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 = 12 29 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) = 6.762 | 6.762 | 6.762 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 -9250.3539 -9250.3539 48.526581 120.32674 9.8449489 16.355238 16.355238 16.763438 15.270482 17.031795 2.575735 2208.6956 Loop time of 2.853e-06 on 1 procs for 0 steps with 3506 atoms 280.4% 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 | | 2.853e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11207.0 ave 11207 max 11207 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244963.0 ave 244963 max 244963 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 489926.0 ave 489926 max 489926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489926 Ave neighs/atom = 139.73930 Neighbor list builds = 0 Dangerous builds = 0 3506 -9142.59955564248 eV 2.5757350442572 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04