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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -56.546207 0.0000000) to (28.273104 56.546207 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0984285 5.0984285 3.6200000 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.546207 0.0000000) to (28.273104 56.546207 3.6200000) create_atoms CPU = 0.004 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0984285 5.0984285 3.6200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.546207 0.0000000) to (28.273104 56.546207 3.6200000) create_atoms CPU = 0.003 seconds 490 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_313717476091_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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3159.6703 0 -3159.6703 94433.796 24 0 -3453.1981 0 -3453.1981 4739.1725 Loop time of 2.27671 on 1 procs for 24 steps with 978 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 = -3159.67029220209 -3453.19692671207 -3453.19808905609 Force two-norm initial, final = 949.21445 1.4772490 Force max component initial, final = 413.28353 0.62430808 Final line search alpha, max atom move = 0.51648535 0.32244598 Iterations, force evaluations = 24 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2641 | 2.2641 | 2.2641 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064073 | 0.0064073 | 0.0064073 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006198 | | | 0.27 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5182.00 ave 5182 max 5182 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: 76276.0 ave 76276 max 76276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76276 Ave neighs/atom = 77.991820 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -3453.1981 0 -3453.1981 4739.1725 11574.854 29 0 -3453.3317 0 -3453.3317 -333.13651 11617.425 Loop time of 0.302677 on 1 procs for 5 steps with 978 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 = -3453.19808905609 -3453.33066408925 -3453.33171154915 Force two-norm initial, final = 71.779721 5.0788678 Force max component initial, final = 65.612279 4.3569580 Final line search alpha, max atom move = 0.00029769917 0.0012970628 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29893 | 0.29893 | 0.29893 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082311 | 0.00082311 | 0.00082311 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002919 | | | 0.96 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 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: 76008.0 ave 76008 max 76008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76008 Ave neighs/atom = 77.717791 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3453.3317 0 -3453.3317 -333.13651 Loop time of 6.515e-06 on 1 procs for 0 steps with 978 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 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: 75948.0 ave 75948 max 75948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75948 Ave neighs/atom = 77.656442 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.722 | 4.722 | 4.722 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 -3453.3317 -3453.3317 28.254682 113.57738 3.6201585 -333.13651 -333.13651 -124.14321 -274.36536 -600.90095 2.1758531 162.67753 Loop time of 7.297e-06 on 1 procs for 0 steps with 978 atoms 246.7% 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 | | 7.297e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5206.00 ave 5206 max 5206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37974.0 ave 37974 max 37974 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75948.0 ave 75948 max 75948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75948 Ave neighs/atom = 77.656442 Neighbor list builds = 0 Dangerous builds = 0 978 -3453.33171154915 eV 2.17585311623934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03