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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -56.365463 0.0000000) to (28.182732 56.365463 3.6084290) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0821319 5.0821319 3.6084290 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.365463 0.0000000) to (28.182732 56.365463 3.6084290) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0821319 5.0821319 3.6084290 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.365463 0.0000000) to (28.182732 56.365463 3.6084290) create_atoms CPU = 0.001 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_549900287421_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 -4094.6719 0 -4094.6719 21054.933 69 0 -4153.4663 0 -4153.4663 6041.5835 Loop time of 3.86651 on 1 procs for 69 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 = -4094.6719015203 -4153.46241449097 -4153.46625230314 Force two-norm initial, final = 61.543719 0.17725405 Force max component initial, final = 16.096815 0.040946300 Final line search alpha, max atom move = 1.0000000 0.040946300 Iterations, force evaluations = 69 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8491 | 3.8491 | 3.8491 | 0.0 | 99.55 Neigh | 0.0052486 | 0.0052486 | 0.0052486 | 0.0 | 0.14 Comm | 0.0063501 | 0.0063501 | 0.0063501 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005828 | | | 0.15 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5226.00 ave 5226 max 5226 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: 75744.0 ave 75744 max 75744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75744 Ave neighs/atom = 77.447853 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 = 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 : 69 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 69 0 -4153.4663 0 -4153.4663 6041.5835 11464.215 76 0 -4153.7218 0 -4153.7218 -108.0631 11505.467 Loop time of 0.298339 on 1 procs for 7 steps with 978 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4153.46625230314 -4153.72024938191 -4153.72180481656 Force two-norm initial, final = 93.227889 1.6642553 Force max component initial, final = 68.487625 1.2249019 Final line search alpha, max atom move = 8.5002661e-05 0.00010411992 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29609 | 0.29609 | 0.29609 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038326 | 0.00038326 | 0.00038326 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001862 | | | 0.62 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5202.00 ave 5202 max 5202 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: 75952.0 ave 75952 max 75952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75952 Ave neighs/atom = 77.660532 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 -4153.7218 0 -4153.7218 -108.0631 Loop time of 1.65e-06 on 1 procs for 0 steps with 978 atoms 181.8% 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 | | 1.65e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5214.00 ave 5214 max 5214 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: 75936.0 ave 75936 max 75936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75936 Ave neighs/atom = 77.644172 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 -4153.7218 -4153.7218 28.066888 112.95593 3.6291172 -108.0631 -108.0631 -151.93782 -170.91231 -1.3391749 2.2862382 155.52123 Loop time of 1.692e-06 on 1 procs for 0 steps with 978 atoms 177.3% 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 | | 1.692e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5214.00 ave 5214 max 5214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37968.0 ave 37968 max 37968 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75936.0 ave 75936 max 75936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75936 Ave neighs/atom = 77.644172 Neighbor list builds = 0 Dangerous builds = 0 978 -4153.72180481656 eV 2.28623819596431 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04