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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -57.963281 0.0000000) to (28.981641 57.963281 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4324862 4.4324862 3.1435003 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -57.963281 0.0000000) to (28.981641 57.963281 3.1435003) create_atoms CPU = 0.001 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4324862 4.4324862 3.1435003 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -57.963281 0.0000000) to (28.981641 57.963281 3.1435003) create_atoms CPU = 0.000 seconds 341 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 24 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 677 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3204.5855 0 -3204.5855 207553.57 166 0 -4521.8649 0 -4521.8649 -7498.132 Loop time of 2.61021 on 1 procs for 166 steps with 677 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3204.58550108805 -4521.8604934335 -4521.86488302631 Force two-norm initial, final = 2974.2007 0.39392069 Force max component initial, final = 1394.1680 0.068898344 Final line search alpha, max atom move = 0.45470134 0.031328169 Iterations, force evaluations = 166 306 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.54 | 2.54 | 2.54 | 0.0 | 97.31 Neigh | 0.033622 | 0.033622 | 0.033622 | 0.0 | 1.29 Comm | 0.023316 | 0.023316 | 0.023316 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01326 | | | 0.51 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8738.00 ave 8738 max 8738 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: 186002.0 ave 186002 max 186002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186002 Ave neighs/atom = 274.74446 Neighbor list builds = 3 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 166 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.980 | 4.980 | 4.980 Mbytes Step Temp E_pair E_mol TotEng Press Volume 166 0 -4521.8649 0 -4521.8649 -7498.132 10561.35 216 0 -4530.5175 0 -4530.5175 -815.24347 10526.786 Loop time of 0.469198 on 1 procs for 50 steps with 677 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 = -4521.86488302631 -4530.51326212893 -4530.51748603471 Force two-norm initial, final = 245.90899 10.246746 Force max component initial, final = 226.03191 5.9184681 Final line search alpha, max atom move = 0.00028357138 0.0016783082 Iterations, force evaluations = 50 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42884 | 0.42884 | 0.42884 | 0.0 | 91.40 Neigh | 0.020781 | 0.020781 | 0.020781 | 0.0 | 4.43 Comm | 0.0041649 | 0.0041649 | 0.0041649 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01541 | | | 3.28 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9907.00 ave 9907 max 9907 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: 183998.0 ave 183998 max 183998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183998 Ave neighs/atom = 271.78434 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4530.5175 0 -4530.5175 -815.24347 Loop time of 1.58e-06 on 1 procs for 0 steps with 677 atoms 189.9% 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 | | 1.58e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9795.00 ave 9795 max 9795 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: 183592.0 ave 183592 max 183592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183592 Ave neighs/atom = 271.18464 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.126 | 5.126 | 5.126 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 -4530.5175 -4530.5175 29.721984 118.55348 2.9874709 -815.24347 -815.24347 -892.61151 -921.20274 -631.91616 2.6157 182.2985 Loop time of 1.853e-06 on 1 procs for 0 steps with 677 atoms 215.9% 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 | | 1.853e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9795.00 ave 9795 max 9795 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 91796.0 ave 91796 max 91796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 183592.0 ave 183592 max 183592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183592 Ave neighs/atom = 271.18464 Neighbor list builds = 0 Dangerous builds = 0 677 -4530.51748603471 eV 2.61569997061423 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03