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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -64.269933 0.0000000) to (37.106263 64.269933 6.3021854) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7086559 5.7678145 6.3021854 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -64.269933 0.0000000) to (37.106263 64.269933 6.3021854) create_atoms CPU = 0.002 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7086559 5.7678145 6.3021854 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -64.269933 0.0000000) to (37.106263 64.269933 6.3021854) create_atoms CPU = 0.002 seconds 1250 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2494 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7887.9752 0 -7887.9752 63273.56 117 0 -8468.2797 0 -8468.2797 2083.9541 Loop time of 9.47991 on 1 procs for 117 steps with 2494 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7887.97524239811 -8468.27179840381 -8468.27970118657 Force two-norm initial, final = 1237.9673 0.23783952 Force max component initial, final = 410.68881 0.027408116 Final line search alpha, max atom move = 0.53615852 0.014695095 Iterations, force evaluations = 117 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.2871 | 9.2871 | 9.2871 | 0.0 | 97.97 Neigh | 0.12157 | 0.12157 | 0.12157 | 0.0 | 1.28 Comm | 0.040764 | 0.040764 | 0.040764 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03051 | | | 0.32 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14894.0 ave 14894 max 14894 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: 793896.0 ave 793896 max 793896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 793896 Ave neighs/atom = 318.32237 Neighbor list builds = 3 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -8468.2797 0 -8468.2797 2083.9541 30059.119 121 0 -8468.4115 0 -8468.4115 -10.441538 30103.249 Loop time of 0.312296 on 1 procs for 4 steps with 2494 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 = -8468.27970118629 -8468.41005217464 -8468.41149224698 Force two-norm initial, final = 98.687956 1.7584248 Force max component initial, final = 97.701991 1.2043500 Final line search alpha, max atom move = 6.8763630e-05 8.2815480e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30717 | 0.30717 | 0.30717 | 0.0 | 98.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088554 | 0.00088554 | 0.00088554 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004243 | | | 1.36 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14898.0 ave 14898 max 14898 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: 793416.0 ave 793416 max 793416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 793416 Ave neighs/atom = 318.12991 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.52 | 11.52 | 11.52 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8468.4115 0 -8468.4115 -10.441538 Loop time of 2.397e-06 on 1 procs for 0 steps with 2494 atoms 208.6% 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 | | 2.397e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14898.0 ave 14898 max 14898 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: 793172.0 ave 793172 max 793172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 793172 Ave neighs/atom = 318.03208 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.52 | 11.52 | 11.52 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 -8468.4115 -8468.4115 37.072154 128.90542 6.2993302 -10.441538 -10.441538 -64.039851 -27.616405 60.331644 2.2244422 963.12682 Loop time of 2.85e-06 on 1 procs for 0 steps with 2494 atoms 280.7% 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 | | 2.85e-06 | | |100.00 Nlocal: 2494.00 ave 2494 max 2494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14898.0 ave 14898 max 14898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 396586.0 ave 396586 max 396586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 793172.0 ave 793172 max 793172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 793172 Ave neighs/atom = 318.03208 Neighbor list builds = 0 Dangerous builds = 0 2494 -8468.41149224698 eV 2.22444218071572 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10