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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -41.302047 0.0000000) to (20.651023 41.302047 4.0499989) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7656208 4.7656208 4.0499989 Created 207 atoms using lattice units in orthogonal box = (0.0000000 -41.302047 0.0000000) to (20.651023 41.302047 4.0499989) create_atoms CPU = 0.001 seconds 207 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7656208 4.7656208 4.0499989 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.302047 0.0000000) to (20.651023 41.302047 4.0499989) create_atoms CPU = 0.001 seconds 209 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 412 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_315820974149_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.446 | 4.446 | 4.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1309.4848 0 -1309.4848 24886.497 81 0 -1377.9211 0 -1377.9211 176.84076 Loop time of 4.50521 on 1 procs for 81 steps with 412 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 = -1309.48482537862 -1377.9199602808 -1377.92108425032 Force two-norm initial, final = 188.21055 0.12328027 Force max component initial, final = 67.365435 0.013427557 Final line search alpha, max atom move = 1.0000000 0.013427557 Iterations, force evaluations = 81 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4754 | 4.4754 | 4.4754 | 0.0 | 99.34 Neigh | 0.0059158 | 0.0059158 | 0.0059158 | 0.0 | 0.13 Comm | 0.012844 | 0.012844 | 0.012844 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01109 | | | 0.25 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3215.00 ave 3215 max 3215 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: 33472.0 ave 33472 max 33472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33472 Ave neighs/atom = 81.242718 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -1377.9211 0 -1377.9211 176.84076 6908.7273 85 0 -1377.9491 0 -1377.9491 81.275217 6909.8786 Loop time of 0.168486 on 1 procs for 4 steps with 412 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 = -1377.92108425032 -1377.94810806772 -1377.9490602454 Force two-norm initial, final = 11.341213 0.64547979 Force max component initial, final = 8.4527476 0.44324931 Final line search alpha, max atom move = 0.00059372708 0.00026316912 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16657 | 0.16657 | 0.16657 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041002 | 0.00041002 | 0.00041002 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001506 | | | 0.89 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 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: 32548.0 ave 32548 max 32548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32548 Ave neighs/atom = 79.000000 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1377.9491 0 -1377.9491 81.275217 Loop time of 6.616e-06 on 1 procs for 0 steps with 412 atoms 181.4% 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 | | 6.616e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 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: 32560.0 ave 32560 max 32560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32560 Ave neighs/atom = 79.029126 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.584 | 4.584 | 4.584 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 -1377.9491 -1377.9491 20.66034 82.880756 4.0353317 81.275217 81.275217 102.82149 72.485154 68.519005 2.6267426 252.19423 Loop time of 6.937e-06 on 1 procs for 0 steps with 412 atoms 259.5% 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 | | 6.937e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16280.0 ave 16280 max 16280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32560.0 ave 32560 max 32560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32560 Ave neighs/atom = 79.029126 Neighbor list builds = 0 Dangerous builds = 0 412 -1377.9490602454 eV 2.62674263388462 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05