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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -43.565199 0.0000000) to (21.782600 43.565199 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7556206 3.7556206 2.8601955 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -43.565199 0.0000000) to (21.782600 43.565199 2.8601955) create_atoms CPU = 0.002 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7556206 3.7556206 2.8601955 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -43.565199 0.0000000) to (21.782600 43.565199 2.8601955) create_atoms CPU = 0.001 seconds 234 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 466 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.827 | 4.827 | 4.827 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1824.9822 0 -1824.9822 66400.012 84 0 -1983.889 0 -1983.889 14548.368 Loop time of 12.6978 on 1 procs for 84 steps with 466 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 = -1824.98217350678 -1983.88717011177 -1983.88900581553 Force two-norm initial, final = 291.82439 0.18058402 Force max component initial, final = 66.600046 0.040934855 Final line search alpha, max atom move = 1.0000000 0.040934855 Iterations, force evaluations = 84 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.676 | 12.676 | 12.676 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011021 | 0.011021 | 0.011021 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01084 | | | 0.09 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3030.00 ave 3030 max 3030 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: 27016.0 ave 27016 max 27016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27016 Ave neighs/atom = 57.974249 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.831 | 4.831 | 4.831 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -1983.889 0 -1983.889 14548.368 5428.441 97 0 -1984.3773 0 -1984.3773 -288.00368 5471.8057 Loop time of 1.19938 on 1 procs for 13 steps with 466 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 = -1983.88900581553 -1984.37690461361 -1984.37730594966 Force two-norm initial, final = 100.76920 1.8674172 Force max component initial, final = 92.764947 1.0784525 Final line search alpha, max atom move = 0.0010811044 0.0011659197 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1668 | 1.1668 | 1.1668 | 0.0 | 97.28 Neigh | 0.027247 | 0.027247 | 0.027247 | 0.0 | 2.27 Comm | 0.0012564 | 0.0012564 | 0.0012564 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004123 | | | 0.34 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409.00 ave 3409 max 3409 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: 26800.0 ave 26800 max 26800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26800 Ave neighs/atom = 57.510730 Neighbor list builds = 1 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1984.3773 0 -1984.3773 -288.00368 Loop time of 6.315e-06 on 1 procs for 0 steps with 466 atoms 190.0% 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 | | 6.315e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409.00 ave 3409 max 3409 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: 26800.0 ave 26800 max 26800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26800 Ave neighs/atom = 57.510730 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.968 | 4.968 | 4.968 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 -1984.3773 -1984.3773 21.820515 88.122565 2.8456307 -288.00368 -288.00368 -316.3268 -248.07464 -299.6096 2.3142204 286.33924 Loop time of 7.187e-06 on 1 procs for 0 steps with 466 atoms 250.5% 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 | | 7.187e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3409.00 ave 3409 max 3409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13400.0 ave 13400 max 13400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26800.0 ave 26800 max 26800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26800 Ave neighs/atom = 57.510730 Neighbor list builds = 0 Dangerous builds = 0 466 -1984.37730594966 eV 2.31422035068684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14