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 = 2.8659480 2.8659480 2.8659480 Created orthogonal box = (0.0000000 -45.132995 0.0000000) to (27.638202 45.132995 7.0201103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4577745 4.3677092 4.6800735 Created 741 atoms using lattice units in orthogonal box = (0.0000000 -45.132995 0.0000000) to (27.638202 45.132995 7.0201103) create_atoms CPU = 0.001 seconds 741 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4577745 4.3677092 4.6800735 Created 747 atoms using lattice units in orthogonal box = (0.0000000 -45.132995 0.0000000) to (27.638202 45.132995 7.0201103) create_atoms CPU = 0.001 seconds 747 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1488 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_650279905230_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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.523 | 5.523 | 5.523 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5925.4331 0 -5925.4331 86574.373 92 0 -6354.9846 0 -6354.9846 5003.4145 Loop time of 1.58212 on 1 procs for 92 steps with 1488 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 = -5925.43309455017 -6354.97838268411 -6354.98460338771 Force two-norm initial, final = 686.21095 0.28259140 Force max component initial, final = 190.60010 0.036700946 Final line search alpha, max atom move = 1.0000000 0.036700946 Iterations, force evaluations = 92 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5038 | 1.5038 | 1.5038 | 0.0 | 95.05 Neigh | 0.057414 | 0.057414 | 0.057414 | 0.0 | 3.63 Comm | 0.010033 | 0.010033 | 0.010033 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01091 | | | 0.69 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7014.00 ave 7014 max 7014 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: 245930.0 ave 245930 max 245930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245930 Ave neighs/atom = 165.27554 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.523 | 5.523 | 5.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -6354.9846 0 -6354.9846 5003.4145 17513.698 99 0 -6355.4808 0 -6355.4808 -65.426851 17567.152 Loop time of 0.0981591 on 1 procs for 7 steps with 1488 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 = -6354.98460338772 -6355.47763882777 -6355.48077496868 Force two-norm initial, final = 155.78925 1.4112534 Force max component initial, final = 154.82017 0.95349734 Final line search alpha, max atom move = 0.00011033237 0.00010520162 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.094663 | 0.094663 | 0.094663 | 0.0 | 96.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051347 | 0.00051347 | 0.00051347 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002983 | | | 3.04 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7020.00 ave 7020 max 7020 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: 246106.0 ave 246106 max 246106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 246106 Ave neighs/atom = 165.39382 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.662 | 5.662 | 5.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6355.4808 0 -6355.4808 -65.426851 Loop time of 1.794e-06 on 1 procs for 0 steps with 1488 atoms 167.2% 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 | | 1.794e-06 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7020.00 ave 7020 max 7020 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: 245860.0 ave 245860 max 245860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245860 Ave neighs/atom = 165.22849 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.662 | 5.662 | 5.662 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 -6355.4808 -6355.4808 27.601738 90.853039 7.0052794 -65.426851 -65.426851 -86.847064 -63.37146 -46.06203 2.2900223 934.75267 Loop time of 2.0447e-05 on 1 procs for 0 steps with 1488 atoms 24.5% 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 | | 2.045e-05 | | |100.00 Nlocal: 1488.00 ave 1488 max 1488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7020.00 ave 7020 max 7020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122930.0 ave 122930 max 122930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 245860.0 ave 245860 max 245860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245860 Ave neighs/atom = 165.22849 Neighbor list builds = 0 Dangerous builds = 0 1488 -6355.48042020185 eV 2.29002225729666 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01