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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -53.343017 0.0000000) to (43.551448 53.343017 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3693566 5.1147382 5.8858683 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -53.343017 0.0000000) to (43.551448 53.343017 8.8288024) create_atoms CPU = 0.004 seconds 1760 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3693566 5.1147382 5.8858683 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -53.343017 0.0000000) to (43.551448 53.343017 8.8288024) create_atoms CPU = 0.004 seconds 1760 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 35 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3464 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.701 | 5.701 | 5.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14589.626 0 -14589.626 -2640.7768 77 0 -14659.711 0 -14659.711 -13605.138 Loop time of 30.9538 on 1 procs for 77 steps with 3464 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 = -14589.6255755442 -14659.7016810685 -14659.7111596894 Force two-norm initial, final = 40.105127 0.35616866 Force max component initial, final = 6.8267896 0.039818657 Final line search alpha, max atom move = 1.0000000 0.039818657 Iterations, force evaluations = 77 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.803 | 30.803 | 30.803 | 0.0 | 99.51 Neigh | 0.086348 | 0.086348 | 0.086348 | 0.0 | 0.28 Comm | 0.025378 | 0.025378 | 0.025378 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03903 | | | 0.13 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8449.00 ave 8449 max 8449 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: 269248.0 ave 269248 max 269248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269248 Ave neighs/atom = 77.727483 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.708 | 5.708 | 5.708 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -14659.711 0 -14659.711 -13605.138 41021.541 84 0 -14660.931 0 -14660.931 -2907.9422 40743.464 Loop time of 1.98969 on 1 procs for 7 steps with 3464 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 = -14659.7111596893 -14660.9283400055 -14660.9308669088 Force two-norm initial, final = 429.45735 1.0141338 Force max component initial, final = 367.28140 0.60590982 Final line search alpha, max atom move = 0.00011273839 6.8309300e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9803 | 1.9803 | 1.9803 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012449 | 0.0012449 | 0.0012449 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008094 | | | 0.41 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8388.00 ave 8388 max 8388 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: 269248.0 ave 269248 max 269248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269248 Ave neighs/atom = 77.727483 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.846 | 5.846 | 5.846 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14660.931 0 -14660.931 -2907.9422 Loop time of 3.551e-06 on 1 procs for 0 steps with 3464 atoms 169.0% 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 | | 3.551e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8403.00 ave 8403 max 8403 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: 269520.0 ave 269520 max 269520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269520 Ave neighs/atom = 77.806005 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.846 | 5.846 | 5.846 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 -14660.931 -14660.931 43.277113 106.68603 8.8245403 -2907.9422 -2907.9422 -21.424892 -8678.5867 -23.815006 2.1933205 1981.8456 Loop time of 3.421e-06 on 1 procs for 0 steps with 3464 atoms 204.6% 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 | | 3.421e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8403.00 ave 8403 max 8403 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134760.0 ave 134760 max 134760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269520.0 ave 269520 max 269520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269520 Ave neighs/atom = 77.806005 Neighbor list builds = 0 Dangerous builds = 0 3464 -14660.9308669088 eV 2.19332048240315 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34