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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0763986 6.2062905 5.0973115 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0763986 6.2062905 5.0973115 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) create_atoms CPU = 0.002 seconds 916 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1812 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_492310898779_001#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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.158 | 5.158 | 5.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7641.5066 0 -7641.5066 1362.3424 243 0 -7686.2086 0 -7686.2086 -9492.5423 Loop time of 27.3075 on 1 procs for 243 steps with 1812 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 = -7641.50661299231 -7686.20145700869 -7686.20856798486 Force two-norm initial, final = 34.650893 0.24120800 Force max component initial, final = 7.0871780 0.047226673 Final line search alpha, max atom move = 1.0000000 0.047226673 Iterations, force evaluations = 243 462 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.172 | 27.172 | 27.172 | 0.0 | 99.50 Neigh | 0.051251 | 0.051251 | 0.051251 | 0.0 | 0.19 Comm | 0.043251 | 0.043251 | 0.043251 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04097 | | | 0.15 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7202.00 ave 7202 max 7202 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: 138768.0 ave 138768 max 138768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138768 Ave neighs/atom = 76.582781 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 243 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.157 | 5.157 | 5.157 Mbytes Step Temp E_pair E_mol TotEng Press Volume 243 0 -7686.2086 0 -7686.2086 -9492.5423 21353.65 246 0 -7686.2873 0 -7686.2873 -8435.3986 21339.385 Loop time of 0.297085 on 1 procs for 3 steps with 1812 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 = -7686.20856798487 -7686.28485532648 -7686.28732483696 Force two-norm initial, final = 56.118163 1.6056253 Force max component initial, final = 52.464537 1.2010384 Final line search alpha, max atom move = 0.00013787599 0.00016559435 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29522 | 0.29522 | 0.29522 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003138 | 0.0003138 | 0.0003138 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001551 | | | 0.52 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7302.00 ave 7302 max 7302 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: 138464.0 ave 138464 max 138464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138464 Ave neighs/atom = 76.415011 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.295 | 5.295 | 5.295 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7686.2873 0 -7686.2873 -8435.3986 Loop time of 1.885e-06 on 1 procs for 0 steps with 1812 atoms 212.2% 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 | | 1.885e-06 | | |100.00 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7351.00 ave 7351 max 7351 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: 138512.0 ave 138512 max 138512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138512 Ave neighs/atom = 76.441501 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.295 | 5.295 | 5.295 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 -7686.2873 -7686.2873 38.548194 108.856 5.0854045 -8435.3986 -8435.3986 -77.368696 -25138.863 -89.96419 2.4155394 1882.2611 Loop time of 1.914e-06 on 1 procs for 0 steps with 1812 atoms 261.2% 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 | | 1.914e-06 | | |100.00 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7351.00 ave 7351 max 7351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69256.0 ave 69256 max 69256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138512.0 ave 138512 max 138512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138512 Ave neighs/atom = 76.441501 Neighbor list builds = 0 Dangerous builds = 0 1812 -7686.28732483696 eV 2.41553936079524 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:28