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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -35.897105 0.0000000) to (17.948553 35.897105 3.5200008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1419737 4.1419737 3.5200008 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -35.897105 0.0000000) to (17.948553 35.897105 3.5200008) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1419737 4.1419737 3.5200008 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -35.897105 0.0000000) to (17.948553 35.897105 3.5200008) create_atoms CPU = 0.000 seconds 210 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 19 1 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.486 | 4.486 | 4.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1804.896 0 -1804.896 4996.592 50 0 -1821.7591 0 -1821.7591 -3335.093 Loop time of 0.371132 on 1 procs for 50 steps with 412 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1804.89603707186 -1821.7576785247 -1821.75913349697 Force two-norm initial, final = 47.533124 0.14916137 Force max component initial, final = 16.026425 0.031521030 Final line search alpha, max atom move = 1.0000000 0.031521030 Iterations, force evaluations = 50 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36156 | 0.36156 | 0.36156 | 0.0 | 97.42 Neigh | 0.0042389 | 0.0042389 | 0.0042389 | 0.0 | 1.14 Comm | 0.0033465 | 0.0033465 | 0.0033465 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001988 | | | 0.54 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 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: 72900.0 ave 72900 max 72900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72900 Ave neighs/atom = 176.94175 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.486 | 4.486 | 4.486 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -1821.7591 0 -1821.7591 -3335.093 4535.8806 54 0 -1821.7872 0 -1821.7872 99.271222 4527.5892 Loop time of 0.0236649 on 1 procs for 4 steps with 412 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1821.75913349698 -1821.78626338423 -1821.7872116929 Force two-norm initial, final = 19.921723 0.65596041 Force max component initial, final = 17.915717 0.56975231 Final line search alpha, max atom move = 0.00019461075 0.00011087993 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022718 | 0.022718 | 0.022718 | 0.0 | 96.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019903 | 0.00019903 | 0.00019903 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000748 | | | 3.16 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 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: 72664.0 ave 72664 max 72664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72664 Ave neighs/atom = 176.36893 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1821.7872 0 -1821.7872 99.271222 Loop time of 1.662e-06 on 1 procs for 0 steps with 412 atoms 120.3% 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 | | 1.662e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 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: 72732.0 ave 72732 max 72732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72732 Ave neighs/atom = 176.53398 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.624 | 4.624 | 4.624 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 -1821.7872 -1821.7872 17.940034 71.57368 3.5260658 99.271222 99.271222 49.496288 46.351921 201.96546 2.318383 184.88953 Loop time of 2.518e-06 on 1 procs for 0 steps with 412 atoms 238.3% 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 | | 2.518e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36366.0 ave 36366 max 36366 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72732.0 ave 72732 max 72732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72732 Ave neighs/atom = 176.53398 Neighbor list builds = 0 Dangerous builds = 0 412 -1821.7872116929 eV 2.31838296579178 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00