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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -49.863918 0.0000000) to (35.256344 49.863918 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5289527 6.7711112 5.5400000 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -49.863918 0.0000000) to (35.256344 49.863918 5.5400000) create_atoms CPU = 0.005 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5289527 6.7711112 5.5400000 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -49.863918 0.0000000) to (35.256344 49.863918 5.5400000) create_atoms CPU = 0.004 seconds 650 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1294 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_070797404269_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7365.8987 0 -7365.8987 17377.632 21 0 -7448.2245 0 -7448.2245 2710.8855 Loop time of 1.66007 on 1 procs for 21 steps with 1294 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 = -7365.89869501338 -7448.21827351642 -7448.22449267869 Force two-norm initial, final = 89.381054 0.31240885 Force max component initial, final = 19.296829 0.064879178 Final line search alpha, max atom move = 1.0000000 0.064879178 Iterations, force evaluations = 21 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6499 | 1.6499 | 1.6499 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047077 | 0.0047077 | 0.0047077 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005435 | | | 0.33 Nlocal: 1294.00 ave 1294 max 1294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5741.00 ave 5741 max 5741 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: 100456.0 ave 100456 max 100456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100456 Ave neighs/atom = 77.632148 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -7448.2245 0 -7448.2245 2710.8855 19478.856 22 0 -7448.2309 0 -7448.2309 1450.6848 19492.399 Loop time of 0.139853 on 1 procs for 1 steps with 1294 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 = -7448.22449267869 -7448.22449267869 -7448.23085622872 Force two-norm initial, final = 25.746741 1.9219337 Force max component initial, final = 20.526371 1.5630356 Final line search alpha, max atom move = 4.8717818e-05 7.6147682e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13821 | 0.13821 | 0.13821 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034303 | 0.00034303 | 0.00034303 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001297 | | | 0.93 Nlocal: 1294.00 ave 1294 max 1294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5741.00 ave 5741 max 5741 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: 100232.0 ave 100232 max 100232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100232 Ave neighs/atom = 77.459042 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.174 | 5.174 | 5.174 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7448.2309 0 -7448.2309 1450.6848 Loop time of 5.974e-06 on 1 procs for 0 steps with 1294 atoms 150.7% 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 | | 5.974e-06 | | |100.00 Nlocal: 1294.00 ave 1294 max 1294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5741.00 ave 5741 max 5741 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: 100228.0 ave 100228 max 100228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100228 Ave neighs/atom = 77.455951 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.174 | 5.174 | 5.174 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 -7448.2309 -7448.2309 35.270294 99.727836 5.5416594 1450.6848 1450.6848 88.289672 4392.2769 -128.51209 2.5790533 604.26534 Loop time of 6.716e-06 on 1 procs for 0 steps with 1294 atoms 268.0% 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 | | 6.716e-06 | | |100.00 Nlocal: 1294.00 ave 1294 max 1294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5741.00 ave 5741 max 5741 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50114.0 ave 50114 max 50114 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100228.0 ave 100228 max 100228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100228 Ave neighs/atom = 77.455951 Neighbor list builds = 0 Dangerous builds = 0 1294 -7448.23085622872 eV 2.57905330350708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02