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 = 3.4919386 3.4919386 3.4919386 Created orthogonal box = (0.0000000 -44.718633 0.0000000) to (31.620849 44.718633 4.9383469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3986815 5.9988410 4.9383469 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -44.718633 0.0000000) to (31.620849 44.718633 4.9383469) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3986815 5.9988410 4.9383469 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -44.718633 0.0000000) to (31.620849 44.718633 4.9383469) create_atoms CPU = 0.001 seconds 660 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 10 27 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 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_108408461881_001#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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5602.7202 0 -5602.7202 33265.371 81 0 -5774.4411 0 -5774.4411 -3302.0309 Loop time of 2.18016 on 1 procs for 81 steps with 1304 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5602.72023416955 -5774.4355978702 -5774.44109477014 Force two-norm initial, final = 311.90673 0.30666708 Force max component initial, final = 76.110032 0.040895921 Final line search alpha, max atom move = 1.0000000 0.040895921 Iterations, force evaluations = 81 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1511 | 2.1511 | 2.1511 | 0.0 | 98.66 Neigh | 0.0098551 | 0.0098551 | 0.0098551 | 0.0 | 0.45 Comm | 0.010166 | 0.010166 | 0.010166 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009085 | | | 0.42 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6779.00 ave 6779 max 6779 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: 173440.0 ave 173440 max 173440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173440 Ave neighs/atom = 133.00613 Neighbor list builds = 1 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -5774.4411 0 -5774.4411 -3302.0309 13966.051 85 0 -5774.5216 0 -5774.5216 -1.2957174 13940.288 Loop time of 0.0969507 on 1 procs for 4 steps with 1304 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 = -5774.44109477014 -5774.52086208311 -5774.52157535868 Force two-norm initial, final = 65.845126 0.47171955 Force max component initial, final = 63.844906 0.27062753 Final line search alpha, max atom move = 0.00012561874 3.3995891e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.094905 | 0.094905 | 0.094905 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037673 | 0.00037673 | 0.00037673 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001669 | | | 1.72 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7336.00 ave 7336 max 7336 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: 173704.0 ave 173704 max 173704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173704 Ave neighs/atom = 133.20859 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.210 | 5.210 | 5.210 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5774.5216 0 -5774.5216 -1.2957174 Loop time of 1.583e-06 on 1 procs for 0 steps with 1304 atoms 126.3% 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 | | 1.583e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7352.00 ave 7352 max 7352 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: 173720.0 ave 173720 max 173720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173720 Ave neighs/atom = 133.22086 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 5.210 | 5.210 | 5.210 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 -5774.5216 -5774.5216 31.537205 89.455093 4.9413256 -1.2957174 -1.2957174 8.0730007 -31.109795 19.149642 2.2929151 587.86792 Loop time of 1.681e-06 on 1 procs for 0 steps with 1304 atoms 178.5% 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 | | 1.681e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7352.00 ave 7352 max 7352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86860.0 ave 86860 max 86860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 173720.0 ave 173720 max 173720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173720 Ave neighs/atom = 133.22086 Neighbor list builds = 0 Dangerous builds = 0 1304 -5774.52157535868 eV 2.29291507205562 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02