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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -56.066498 0.0000000) to (34.331398 56.066498 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5373222 5.4254456 5.8134559 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -56.066498 0.0000000) to (34.331398 56.066498 8.7201838) create_atoms CPU = 0.002 seconds 1494 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5373222 5.4254456 5.8134559 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -56.066498 0.0000000) to (34.331398 56.066498 8.7201838) create_atoms CPU = 0.002 seconds 1494 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 2952 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.942 | 6.942 | 6.942 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12878.576 0 -12878.576 -2242.3003 22 0 -12951.044 0 -12951.044 -2462.9147 Loop time of 0.897836 on 1 procs for 22 steps with 2952 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 = -12878.5764695964 -12951.0332298269 -12951.0435942875 Force two-norm initial, final = 52.173410 0.47504517 Force max component initial, final = 8.5302253 0.070941931 Final line search alpha, max atom move = 1.0000000 0.070941931 Iterations, force evaluations = 22 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88876 | 0.88876 | 0.88876 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036192 | 0.0036192 | 0.0036192 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005453 | | | 0.61 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10455.0 ave 10455 max 10455 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: 515352.0 ave 515352 max 515352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515352 Ave neighs/atom = 174.57724 Neighbor list builds = 0 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.942 | 6.942 | 6.942 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -12951.044 0 -12951.044 -2462.9147 33569.939 26 0 -12951.311 0 -12951.311 -354.20103 33527.444 Loop time of 0.142534 on 1 procs for 4 steps with 2952 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 = -12951.0435942872 -12951.3058817788 -12951.3110118315 Force two-norm initial, final = 137.19869 0.59342966 Force max component initial, final = 132.62820 0.060142112 Final line search alpha, max atom move = 7.8351093e-05 4.7122002e-06 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13936 | 0.13936 | 0.13936 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047402 | 0.00047402 | 0.00047402 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002698 | | | 1.89 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10455.0 ave 10455 max 10455 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: 516516.0 ave 516516 max 516516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 516516 Ave neighs/atom = 174.97154 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.080 | 7.080 | 7.080 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12951.311 0 -12951.311 -354.20103 Loop time of 2.039e-06 on 1 procs for 0 steps with 2952 atoms 196.2% 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 | | 2.039e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10455.0 ave 10455 max 10455 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: 516528.0 ave 516528 max 516528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 516528 Ave neighs/atom = 174.97561 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.080 | 7.080 | 7.080 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 -12951.311 -12951.311 34.405257 112.133 8.690449 -354.20103 -354.20103 -2.0105165 -1058.7582 -1.8343434 2.3149018 942.13057 Loop time of 2.382e-06 on 1 procs for 0 steps with 2952 atoms 251.9% 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 | | 2.382e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10455.0 ave 10455 max 10455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 258264.0 ave 258264 max 258264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 516528.0 ave 516528 max 516528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 516528 Ave neighs/atom = 174.97561 Neighbor list builds = 0 Dangerous builds = 0 2952 -12951.3110118315 eV 2.31490179067853 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01