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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -44.864974 0.0000000) to (15.862164 44.864974 5.1463654) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8439550 4.7226288 5.1463654 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -44.864974 0.0000000) to (15.862164 44.864974 5.1463654) create_atoms CPU = 0.002 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8439550 4.7226288 5.1463654 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -44.864974 0.0000000) to (15.862164 44.864974 5.1463654) create_atoms CPU = 0.002 seconds 306 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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 610 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_748636486270_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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1276.2607 0 -1276.2607 278848.2 89 0 -2079.3256 0 -2079.3256 10256.355 Loop time of 2.20944 on 1 procs for 89 steps with 610 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1276.26065184847 -2079.32360421518 -2079.32558944351 Force two-norm initial, final = 1873.4257 0.12291230 Force max component initial, final = 763.99127 0.022587040 Final line search alpha, max atom move = 1.0000000 0.022587040 Iterations, force evaluations = 89 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.136 | 2.136 | 2.136 | 0.0 | 96.67 Neigh | 0.036028 | 0.036028 | 0.036028 | 0.0 | 1.63 Comm | 0.021828 | 0.021828 | 0.021828 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01562 | | | 0.71 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 107520.0 ave 107520 max 107520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107520 Ave neighs/atom = 176.26230 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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -2079.3256 0 -2079.3256 10256.355 7324.879 99 0 -2079.611 0 -2079.611 -55.635677 7376.3146 Loop time of 0.166216 on 1 procs for 10 steps with 610 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 = -2079.3255894435 -2079.61080115951 -2079.6109684207 Force two-norm initial, final = 86.558434 0.51483810 Force max component initial, final = 70.125410 0.28172163 Final line search alpha, max atom move = 0.0011830703 0.00033329649 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16007 | 0.16007 | 0.16007 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014457 | 0.0014457 | 0.0014457 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004702 | | | 2.83 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5492.00 ave 5492 max 5492 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: 107408.0 ave 107408 max 107408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107408 Ave neighs/atom = 176.07869 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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2079.611 0 -2079.611 -55.635677 Loop time of 9.572e-06 on 1 procs for 0 steps with 610 atoms 156.7% 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 | | 9.572e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5474.00 ave 5474 max 5474 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: 106968.0 ave 106968 max 106968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106968 Ave neighs/atom = 175.35738 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 ghost atom cutoff = 8 binsize = 4, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.078 | 5.078 | 5.078 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 -2079.611 -2079.611 15.832465 90.562474 5.1444935 -55.635677 -55.635677 -48.993122 -61.759246 -56.154663 2.3434115 487.03126 Loop time of 6.896e-06 on 1 procs for 0 steps with 610 atoms 246.5% 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 | | 6.896e-06 | | |100.00 Nlocal: 610.000 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5474.00 ave 5474 max 5474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53484.0 ave 53484 max 53484 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106968.0 ave 106968 max 106968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106968 Ave neighs/atom = 175.35738 Neighbor list builds = 0 Dangerous builds = 0 610 -2079.6109684207 eV 2.34341149690605 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02