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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -35.143007 0.0000000) to (12.423922 35.143007 4.0308524) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5772343 3.6989639 4.0308524 Created 153 atoms using lattice units in orthogonal box = (0.0000000 -35.143007 0.0000000) to (12.423922 35.143007 4.0308524) create_atoms CPU = 0.001 seconds 153 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5772343 3.6989639 4.0308524 Created 153 atoms using lattice units in orthogonal box = (0.0000000 -35.143007 0.0000000) to (12.423922 35.143007 4.0308524) create_atoms CPU = 0.000 seconds 153 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 = 5 24 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 300 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 = 5 24 2 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) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1267.1596 0 -1267.1596 3320.0743 50 0 -1279.5036 0 -1279.5036 -12645.654 Loop time of 1.85806 on 1 procs for 50 steps with 300 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1267.15960912823 -1279.50243252079 -1279.50362816332 Force two-norm initial, final = 29.214870 0.099925731 Force max component initial, final = 9.4157411 0.032162865 Final line search alpha, max atom move = 1.0000000 0.032162865 Iterations, force evaluations = 50 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8525 | 1.8525 | 1.8525 | 0.0 | 99.70 Neigh | 0.0015327 | 0.0015327 | 0.0015327 | 0.0 | 0.08 Comm | 0.0022178 | 0.0022178 | 0.0022178 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001814 | | | 0.10 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2488.00 ave 2488 max 2488 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: 19508.0 ave 19508 max 19508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19508 Ave neighs/atom = 65.026667 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 24 2 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -1279.5036 0 -1279.5036 -12645.654 3519.8529 55 0 -1279.597 0 -1279.597 -1521.0829 3495.7832 Loop time of 0.161011 on 1 procs for 5 steps with 300 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 = -1279.50362816332 -1279.59701103683 -1279.59702406766 Force two-norm initial, final = 38.289204 0.12865471 Force max component initial, final = 28.025905 0.040675169 Final line search alpha, max atom move = 0.0043555242 0.00017716168 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16018 | 0.16018 | 0.16018 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015988 | 0.00015988 | 0.00015988 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006706 | | | 0.42 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2484.00 ave 2484 max 2484 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: 19472.0 ave 19472 max 19472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19472 Ave neighs/atom = 64.906667 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 = 5 24 2 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) = 4.564 | 4.564 | 4.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1279.597 0 -1279.597 -1521.0829 Loop time of 1.841e-06 on 1 procs for 0 steps with 300 atoms 163.0% 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 | | 1.841e-06 | | |100.00 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 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: 19472.0 ave 19472 max 19472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19472 Ave neighs/atom = 64.906667 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 = 5 24 2 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) = 4.564 | 4.564 | 4.564 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 -1279.597 -1279.597 12.384407 70.286014 4.0160617 -1521.0829 -1521.0829 -18.582825 -4555.9699 11.304036 2.3036584 248.76355 Loop time of 1.624e-06 on 1 procs for 0 steps with 300 atoms 123.2% 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 | | 1.624e-06 | | |100.00 Nlocal: 300.000 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9736.00 ave 9736 max 9736 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19472.0 ave 19472 max 19472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19472 Ave neighs/atom = 64.906667 Neighbor list builds = 0 Dangerous builds = 0 300 -1279.59702406766 eV 2.30365842796904 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02