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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -32.337098 0.0000000) to (39.600919 32.337098 7.5515990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0401170 4.7031295 5.0343993 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -32.337098 0.0000000) to (39.600919 32.337098 7.5515990) create_atoms CPU = 0.000 seconds 662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0401170 4.7031295 5.0343993 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -32.337098 0.0000000) to (39.600919 32.337098 7.5515990) create_atoms CPU = 0.000 seconds 662 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 12 20 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 20 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.745 | 5.745 | 5.745 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7960.6716 0 -7960.6716 75726.748 177 0 -8445.5623 0 -8445.5623 -14007.964 Loop time of 46.2708 on 1 procs for 177 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 = -7960.67156221681 -8445.55385516841 -8445.56229701192 Force two-norm initial, final = 661.20844 0.45648475 Force max component initial, final = 129.52135 0.14322163 Final line search alpha, max atom move = 0.40015900 0.057311426 Iterations, force evaluations = 177 331 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 46.192 | 46.192 | 46.192 | 0.0 | 99.83 Neigh | 0.059931 | 0.059931 | 0.059931 | 0.0 | 0.13 Comm | 0.010032 | 0.010032 | 0.010032 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008578 | | | 0.02 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4598.00 ave 4598 max 4598 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: 95394.0 ave 95394 max 95394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95394 Ave neighs/atom = 73.154908 Neighbor list builds = 5 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 177 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.748 | 5.748 | 5.748 Mbytes Step Temp E_pair E_mol TotEng Press Volume 177 0 -8445.5623 0 -8445.5623 -14007.964 19340.835 184 0 -8446.5695 0 -8446.5695 2319.583 19189.762 Loop time of 1.50369 on 1 procs for 7 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 = -8445.56229701192 -8446.5680110764 -8446.56951412937 Force two-norm initial, final = 328.75732 1.0304164 Force max component initial, final = 282.57456 0.15732178 Final line search alpha, max atom move = 8.2272401e-05 1.2943240e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5025 | 1.5025 | 1.5025 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002302 | 0.0002302 | 0.0002302 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001006 | | | 0.07 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4595.00 ave 4595 max 4595 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: 95354.0 ave 95354 max 95354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95354 Ave neighs/atom = 73.124233 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.886 | 5.886 | 5.886 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8446.5695 0 -8446.5695 2319.583 Loop time of 6.9e-06 on 1 procs for 0 steps with 1304 atoms 115.9% 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 | | 6.9e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4600.00 ave 4600 max 4600 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: 97372.0 ave 97372 max 97372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97372 Ave neighs/atom = 74.671779 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.886 | 5.886 | 5.886 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 -8446.5695 -8446.5695 39.526776 64.674196 7.5066671 2319.583 2319.583 -11.371496 6971.3592 -1.238604 2.4565037 3808.2422 Loop time of 2.6e-06 on 1 procs for 0 steps with 1304 atoms 192.3% 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 | | 2.6e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4600.00 ave 4600 max 4600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48686.0 ave 48686 max 48686 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97372.0 ave 97372 max 97372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97372 Ave neighs/atom = 74.671779 Neighbor list builds = 0 Dangerous builds = 0 1304 -8446.56951412937 eV 2.45650371879008 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:48