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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -41.626972 0.0000000) to (50.982420 41.626972 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8265623 5.3520392 5.7450679 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -41.626972 0.0000000) to (50.982420 41.626972 8.6176019) create_atoms CPU = 0.008 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8265623 5.3520392 5.7450679 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -41.626972 0.0000000) to (50.982420 41.626972 8.6176019) create_atoms CPU = 0.007 seconds 1687 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 3349 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 8.284 | 8.284 | 8.284 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13132.089 0 -13132.089 124516.32 118 0 -14620.679 0 -14620.679 3224.5832 Loop time of 18.8624 on 1 procs for 118 steps with 3349 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 = -13132.0886353215 -14620.6730224714 -14620.6790975651 Force two-norm initial, final = 1144.4083 0.25949963 Force max component initial, final = 105.92748 0.046511900 Final line search alpha, max atom move = 0.84423048 0.039266764 Iterations, force evaluations = 118 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.841 | 17.841 | 17.841 | 0.0 | 94.58 Neigh | 0.89246 | 0.89246 | 0.89246 | 0.0 | 4.73 Comm | 0.058994 | 0.058994 | 0.058994 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07017 | | | 0.37 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12926.0 ave 12926 max 12926 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: 825858.0 ave 825858 max 825858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825858 Ave neighs/atom = 246.59839 Neighbor list builds = 8 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.283 | 8.283 | 8.283 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -14620.679 0 -14620.679 3224.5832 36577.304 121 0 -14620.859 0 -14620.859 401.54961 36638.888 Loop time of 0.508059 on 1 procs for 3 steps with 3349 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14620.6790975652 -14620.8489736066 -14620.8589154242 Force two-norm initial, final = 160.61471 17.961787 Force max component initial, final = 153.10084 15.933448 Final line search alpha, max atom move = 4.5452157e-05 0.00072420959 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50127 | 0.50127 | 0.50127 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014357 | 0.0014357 | 0.0014357 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005357 | | | 1.05 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12926.0 ave 12926 max 12926 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: 825820.0 ave 825820 max 825820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825820 Ave neighs/atom = 246.58704 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 8.421 | 8.421 | 8.421 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14620.859 0 -14620.859 401.54961 Loop time of 6.866e-06 on 1 procs for 0 steps with 3349 atoms 247.6% 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 | | 6.866e-06 | | |100.00 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12929.0 ave 12929 max 12929 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: 825380.0 ave 825380 max 825380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825380 Ave neighs/atom = 246.45566 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 8.421 | 8.421 | 8.421 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 -14620.859 -14620.859 50.964123 83.442498 8.6156973 401.54961 401.54961 291.92445 698.32941 214.39496 2.1867984 1609.7195 Loop time of 6.565e-06 on 1 procs for 0 steps with 3349 atoms 289.4% 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 | | 6.565e-06 | | |100.00 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12929.0 ave 12929 max 12929 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 412690.0 ave 412690 max 412690 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 825380.0 ave 825380 max 825380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825380 Ave neighs/atom = 246.45566 Neighbor list builds = 0 Dangerous builds = 0 3349 -14620.8589154242 eV 2.18679843463051 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21