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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -58.022827 0.0000000) to (29.009840 58.022827 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4367991 4.4367991 3.1465590 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.022827 0.0000000) to (29.009840 58.022827 3.1465590) create_atoms CPU = 0.002 seconds 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4367991 4.4367991 3.1465590 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.022827 0.0000000) to (29.009840 58.022827 3.1465590) create_atoms CPU = 0.001 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 36 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 678 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_356501945107_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 = 9 36 1 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4402.5972 0 -4402.5972 79835.547 36 0 -4604.621 0 -4604.621 -4187.9782 Loop time of 3.5891 on 1 procs for 36 steps with 678 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 = -4402.59724654351 -4604.61727792936 -4604.62100251422 Force two-norm initial, final = 309.98063 0.35508256 Force max component initial, final = 86.971999 0.073276651 Final line search alpha, max atom move = 0.86018959 0.063031812 Iterations, force evaluations = 36 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.574 | 3.574 | 3.574 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0079765 | 0.0079765 | 0.0079765 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007166 | | | 0.20 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4792.00 ave 4792 max 4792 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: 43636.0 ave 43636 max 43636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43636 Ave neighs/atom = 64.359882 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 = 9 36 1 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -4604.621 0 -4604.621 -4187.9782 10592.783 38 0 -4604.642 0 -4604.642 -506.0147 10577.949 Loop time of 0.283208 on 1 procs for 2 steps with 678 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4604.62100251422 -4604.64183515938 -4604.64200735577 Force two-norm initial, final = 40.788489 0.36275913 Force max component initial, final = 33.298962 0.073974175 Final line search alpha, max atom move = 0.00051104449 3.7804094e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28028 | 0.28028 | 0.28028 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058106 | 0.00058106 | 0.00058106 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002345 | | | 0.83 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4815.00 ave 4815 max 4815 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: 43486.0 ave 43486 max 43486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43486 Ave neighs/atom = 64.138643 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 = 9 36 1 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4604.642 0 -4604.642 -506.0147 Loop time of 6.264e-06 on 1 procs for 0 steps with 678 atoms 175.6% 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 | | 6.264e-06 | | |100.00 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4817.00 ave 4817 max 4817 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: 43486.0 ave 43486 max 43486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43486 Ave neighs/atom = 64.138643 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 = 9 36 1 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) = 4.666 | 4.666 | 4.666 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 -4604.642 -4604.642 28.995814 116.04565 3.1436725 -506.0147 -506.0147 -9.3257633 -1511.1251 2.4067346 2.5240338 163.95277 Loop time of 7.177e-06 on 1 procs for 0 steps with 678 atoms 250.8% 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 | | 7.177e-06 | | |100.00 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4817.00 ave 4817 max 4817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21743.0 ave 21743 max 21743 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43486.0 ave 43486 max 43486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43486 Ave neighs/atom = 64.138643 Neighbor list builds = 0 Dangerous builds = 0 678 -4604.64200735577 eV 2.52403380068283 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04