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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -69.619843 0.0000000) to (40.195035 69.619843 6.3030844) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9304150 5.3261082 6.3030844 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.619843 0.0000000) to (40.195035 69.619843 6.3030844) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9304150 5.3261082 6.3030844 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.619843 0.0000000) to (40.195035 69.619843 6.3030844) create_atoms CPU = 0.008 seconds 1466 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 = 11 35 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 = 2930 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_945691923444_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 = 11 35 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) = 10.89 | 10.89 | 10.89 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8904.3246 0 -8904.3246 69590.286 75 0 -9589.7003 0 -9589.7003 5428.2504 Loop time of 7.2601 on 1 procs for 75 steps with 2930 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 = -8904.32457631957 -9589.69074153054 -9589.70032153233 Force two-norm initial, final = 1107.5223 0.24571457 Force max component initial, final = 259.87684 0.028957147 Final line search alpha, max atom move = 1.0000000 0.028957147 Iterations, force evaluations = 75 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8874 | 6.8874 | 6.8874 | 0.0 | 94.87 Neigh | 0.28346 | 0.28346 | 0.28346 | 0.0 | 3.90 Comm | 0.044539 | 0.044539 | 0.044539 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04468 | | | 0.62 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13732.0 ave 13732 max 13732 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: 514912.0 ave 514912 max 514912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514912 Ave neighs/atom = 175.73788 Neighbor list builds = 4 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 = 11 35 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -9589.7003 0 -9589.7003 5428.2504 35276.751 78 0 -9589.9584 0 -9589.9584 6.798643 35410.104 Loop time of 0.345351 on 1 procs for 3 steps with 2930 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 = -9589.70032153237 -9589.95087682325 -9589.95842775845 Force two-norm initial, final = 212.21559 3.0850102 Force max component initial, final = 154.10525 2.3184575 Final line search alpha, max atom move = 5.8063612e-05 0.00013461801 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33747 | 0.33747 | 0.33747 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018356 | 0.0018356 | 0.0018356 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006048 | | | 1.75 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13721.0 ave 13721 max 13721 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: 514816.0 ave 514816 max 514816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514816 Ave neighs/atom = 175.70512 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 = 11 35 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) = 10.40 | 10.40 | 10.40 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9589.9584 0 -9589.9584 6.798643 Loop time of 6.896e-06 on 1 procs for 0 steps with 2930 atoms 188.5% 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: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13714.0 ave 13714 max 13714 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: 514460.0 ave 514460 max 514460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514460 Ave neighs/atom = 175.58362 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 = 11 35 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) = 10.40 | 10.40 | 10.40 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 -9589.9584 -9589.9584 40.239372 139.56025 6.3054235 6.798643 6.798643 -105.01735 47.376745 78.036536 2.2821709 1087.928 Loop time of 6.575e-06 on 1 procs for 0 steps with 2930 atoms 319.4% 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 | | 6.575e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13714.0 ave 13714 max 13714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257230.0 ave 257230 max 257230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 514460.0 ave 514460 max 514460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514460 Ave neighs/atom = 175.58362 Neighbor list builds = 0 Dangerous builds = 0 2930 -9589.95842775845 eV 2.28217089526556 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08