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 = 4.0499989 4.0499989 4.0499989 Created orthogonal box = (0.0000000 -77.485091 0.0000000) to (44.733700 77.485091 7.0148038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6000541 5.9275113 7.0148038 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.485091 0.0000000) to (44.733700 77.485091 7.0148038) create_atoms CPU = 0.009 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6000541 5.9275113 7.0148038 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.485091 0.0000000) to (44.733700 77.485091 7.0148038) create_atoms CPU = 0.008 seconds 1465 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2904 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_315820974149_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.786 | 5.786 | 5.786 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9679.2765 0 -9679.2765 3933.1071 63 0 -9731.0745 0 -9731.0745 -2306.8642 Loop time of 20.7399 on 1 procs for 63 steps with 2904 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 = -9679.27646027343 -9731.06580470603 -9731.07452073876 Force two-norm initial, final = 59.826299 0.37065154 Force max component initial, final = 10.334804 0.068076426 Final line search alpha, max atom move = 0.57333256 0.039030432 Iterations, force evaluations = 63 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.632 | 20.632 | 20.632 | 0.0 | 99.48 Neigh | 0.043137 | 0.043137 | 0.043137 | 0.0 | 0.21 Comm | 0.028363 | 0.028363 | 0.028363 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0366 | | | 0.18 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9558.00 ave 9558 max 9558 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: 226564.0 ave 226564 max 226564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226564 Ave neighs/atom = 78.017906 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.786 | 5.786 | 5.786 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -9731.0745 0 -9731.0745 -2306.8642 48629.353 65 0 -9731.1252 0 -9731.1252 -808.55843 48534.212 Loop time of 0.662449 on 1 procs for 2 steps with 2904 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9731.07452073875 -9731.12471594082 -9731.12524687753 Force two-norm initial, final = 73.730751 2.1884125 Force max component initial, final = 56.743030 2.0839001 Final line search alpha, max atom move = 0.00017691739 0.00036867817 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65842 | 0.65842 | 0.65842 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087869 | 0.00087869 | 0.00087869 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003154 | | | 0.48 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9546.00 ave 9546 max 9546 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: 227260.0 ave 227260 max 227260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227260 Ave neighs/atom = 78.257576 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.924 | 5.924 | 5.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9731.1252 0 -9731.1252 -808.55843 Loop time of 6.505e-06 on 1 procs for 0 steps with 2904 atoms 199.8% 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 | | 6.505e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9546.00 ave 9546 max 9546 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: 227502.0 ave 227502 max 227502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227502 Ave neighs/atom = 78.340909 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.924 | 5.924 | 5.924 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 -9731.1252 -9731.1252 44.681187 154.97018 7.0093079 -808.55843 -808.55843 18.16322 -2512.5768 68.738315 2.5368877 1411.9921 Loop time of 7.377e-06 on 1 procs for 0 steps with 2904 atoms 311.8% 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 | | 7.377e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9546.00 ave 9546 max 9546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113751.0 ave 113751 max 113751 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227502.0 ave 227502 max 227502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227502 Ave neighs/atom = 78.340909 Neighbor list builds = 0 Dangerous builds = 0 2904 -9731.12524687753 eV 2.53688766855917 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22