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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -51.865367 0.0000000) to (36.674352 51.865367 5.7275716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2614748 6.9575492 5.7275716 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.865367 0.0000000) to (36.674352 51.865367 5.7275716) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2614748 6.9575492 5.7275716 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.865367 0.0000000) to (36.674352 51.865367 5.7275716) create_atoms CPU = 0.005 seconds 660 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 9 26 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_651801486679_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4351.6568 0 -4351.6568 4461.2549 82 0 -4398.9907 0 -4398.9907 2378.2449 Loop time of 3.0098 on 1 procs for 82 steps with 1312 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 = -4351.65683337354 -4398.9880062149 -4398.99072532226 Force two-norm initial, final = 30.245702 0.11168836 Force max component initial, final = 6.1228388 0.0080117460 Final line search alpha, max atom move = 1.0000000 0.0080117460 Iterations, force evaluations = 82 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9069 | 2.9069 | 2.9069 | 0.0 | 96.58 Neigh | 0.052693 | 0.052693 | 0.052693 | 0.0 | 1.75 Comm | 0.026386 | 0.026386 | 0.026386 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02382 | | | 0.79 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6977.00 ave 6977 max 6977 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: 183160.0 ave 183160 max 183160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183160 Ave neighs/atom = 139.60366 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -4398.9907 0 -4398.9907 2378.2449 21789.157 89 0 -4399.2211 0 -4399.2211 55.244817 21852.924 Loop time of 0.177927 on 1 procs for 7 steps with 1312 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 = -4398.99072532228 -4399.22066889766 -4399.22108861948 Force two-norm initial, final = 79.407383 1.3416397 Force max component initial, final = 77.734317 0.89756179 Final line search alpha, max atom move = 0.00049921907 0.00044807996 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17158 | 0.17158 | 0.17158 | 0.0 | 96.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013285 | 0.0013285 | 0.0013285 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005022 | | | 2.82 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6977.00 ave 6977 max 6977 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: 183232.0 ave 183232 max 183232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183232 Ave neighs/atom = 139.65854 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.209 | 5.209 | 5.209 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4399.2211 0 -4399.2211 55.244817 Loop time of 6.064e-06 on 1 procs for 0 steps with 1312 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 | | 6.064e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6972.00 ave 6972 max 6972 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: 183056.0 ave 183056 max 183056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183056 Ave neighs/atom = 139.52439 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.209 | 5.209 | 5.209 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 -4399.2211 -4399.2211 36.582787 104.3734 5.7232529 55.244817 55.244817 40.706353 66.213652 58.814446 2.6607341 766.54997 Loop time of 6.826e-06 on 1 procs for 0 steps with 1312 atoms 278.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6972.00 ave 6972 max 6972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91528.0 ave 91528 max 91528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 183056.0 ave 183056 max 183056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183056 Ave neighs/atom = 139.52439 Neighbor list builds = 0 Dangerous builds = 0 1312 -4399.22108875622 eV 2.66073405358412 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03