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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -49.103641 0.0000000) to (40.092955 49.103641 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7275650 5.6786524 6.6136224 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -49.103641 0.0000000) to (40.092955 49.103641 9.9204336) create_atoms CPU = 0.005 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7275650 5.6786524 6.6136224 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -49.103641 0.0000000) to (40.092955 49.103641 9.9204336) create_atoms CPU = 0.004 seconds 1183 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 26 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2352 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.925 | 5.925 | 5.925 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7443.2953 0 -7443.2953 17563.825 44 0 -7889.0151 0 -7889.0151 7008.1241 Loop time of 2.12718 on 1 procs for 44 steps with 2352 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 = -7443.29527175373 -7889.00902089505 -7889.01505330934 Force two-norm initial, final = 174.11401 0.15643194 Force max component initial, final = 17.213294 0.035120934 Final line search alpha, max atom move = 1.0000000 0.035120934 Iterations, force evaluations = 44 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0065 | 2.0065 | 2.0065 | 0.0 | 94.33 Neigh | 0.086873 | 0.086873 | 0.086873 | 0.0 | 4.08 Comm | 0.01395 | 0.01395 | 0.01395 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01988 | | | 0.93 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7045.00 ave 7045 max 7045 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: 305616.0 ave 305616 max 305616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305616 Ave neighs/atom = 129.93878 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -7889.0151 0 -7889.0151 7008.1241 39060.916 54 0 -7890.2505 0 -7890.2505 24.278022 39404.898 Loop time of 0.321208 on 1 procs for 10 steps with 2352 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 = -7889.01505330934 -7890.243252627 -7890.25053912635 Force two-norm initial, final = 318.36894 1.2818620 Force max component initial, final = 265.59908 1.0636840 Final line search alpha, max atom move = 8.8887393e-05 9.4548094e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30998 | 0.30998 | 0.30998 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018141 | 0.0018141 | 0.0018141 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009419 | | | 2.93 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7027.00 ave 7027 max 7027 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: 305912.0 ave 305912 max 305912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305912 Ave neighs/atom = 130.06463 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.064 | 6.064 | 6.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7890.2505 0 -7890.2505 24.278022 Loop time of 7.377e-06 on 1 procs for 0 steps with 2352 atoms 162.7% 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 | | 7.377e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7027.00 ave 7027 max 7027 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: 304932.0 ave 304932 max 304932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304932 Ave neighs/atom = 129.64796 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.064 | 6.064 | 6.064 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 -7890.2505 -7890.2505 40.098953 99.175245 9.9086363 24.278022 24.278022 4.964321 24.672505 43.197239 2.6273513 2011.9553 Loop time of 7.057e-06 on 1 procs for 0 steps with 2352 atoms 269.2% 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 | | 7.057e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7027.00 ave 7027 max 7027 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152466.0 ave 152466 max 152466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 304932.0 ave 304932 max 304932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304932 Ave neighs/atom = 129.64796 Neighbor list builds = 0 Dangerous builds = 0 2352 -7890.25053912635 eV 2.62735132558454 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03