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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -39.407859 0.0000000) to (10.725461 39.407859 7.0214623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5966260 4.3786510 4.6809748 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -39.407859 0.0000000) to (10.725461 39.407859 7.0214623) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5966260 4.3786510 4.6809748 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.407859 0.0000000) to (10.725461 39.407859 7.0214623) create_atoms CPU = 0.000 seconds 254 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 4 28 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 504 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 4 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2028.7196 0 -2028.7196 28565.376 48 0 -2161.2669 0 -2161.2669 11601.721 Loop time of 0.109187 on 1 procs for 48 steps with 504 atoms 95.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2028.71959044318 -2161.26500271628 -2161.26692366518 Force two-norm initial, final = 127.06249 0.16593054 Force max component initial, final = 31.582859 0.045502767 Final line search alpha, max atom move = 1.0000000 0.045502767 Iterations, force evaluations = 48 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.098926 | 0.098926 | 0.098926 | 0.0 | 90.60 Neigh | 0.0062001 | 0.0062001 | 0.0062001 | 0.0 | 5.68 Comm | 0.0019529 | 0.0019529 | 0.0019529 | 0.0 | 1.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002109 | | | 1.93 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2684.00 ave 2684 max 2684 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: 30916.0 ave 30916 max 30916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30916 Ave neighs/atom = 61.341270 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 4 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -2161.2669 0 -2161.2669 11601.721 5935.487 58 0 -2161.6218 0 -2161.6218 113.03264 5972.2877 Loop time of 0.0185178 on 1 procs for 10 steps with 504 atoms 96.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2161.26692366518 -2161.62173699726 -2161.62176338999 Force two-norm initial, final = 93.026579 0.86362548 Force max component initial, final = 88.499487 0.45138979 Final line search alpha, max atom move = 0.0050723765 0.0022896190 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.01672 | 0.01672 | 0.01672 | 0.0 | 90.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029637 | 0.00029637 | 0.00029637 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001501 | | | 8.11 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2678.00 ave 2678 max 2678 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: 30700.0 ave 30700 max 30700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30700 Ave neighs/atom = 60.912698 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 4 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2161.6218 0 -2161.6218 113.03264 Loop time of 1.609e-06 on 1 procs for 0 steps with 504 atoms 124.3% 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 | | 1.609e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2668.00 ave 2668 max 2668 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: 30604.0 ave 30604 max 30604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30604 Ave neighs/atom = 60.722222 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 4 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.599 | 4.599 | 4.599 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 -2161.6218 -2161.6218 10.711144 79.4987 7.0136623 113.03264 113.03264 118.25117 99.887633 120.95913 2.3034338 377.5153 Loop time of 1.1017e-05 on 1 procs for 0 steps with 504 atoms 54.5% 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 | | 1.102e-05 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2668.00 ave 2668 max 2668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15302.0 ave 15302 max 15302 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30604.0 ave 30604 max 30604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30604 Ave neighs/atom = 60.722222 Neighbor list builds = 0 Dangerous builds = 0 504 -2161.62176338999 eV 2.30343378506973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00