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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -36.584048 0.0000000) to (3.6584048 36.584048 3.6584048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6584048 3.6584048 3.6584048 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -36.584048 0.0000000) to (3.6584048 36.584048 3.6584048) create_atoms CPU = 0.000 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6584048 3.6584048 3.6584048 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -36.584048 0.0000000) to (3.6584048 36.584048 3.6584048) create_atoms CPU = 0.000 seconds 42 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 82 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.393 | 4.393 | 4.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 13.799904 0 13.799904 826327.6 56 0 -318.90463 0 -318.90463 19313.593 Loop time of 0.108927 on 1 procs for 56 steps with 82 atoms 63.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 13.7999038306395 -318.904339748668 -318.904634537296 Force two-norm initial, final = 1423.0617 0.066526744 Force max component initial, final = 711.47698 0.020322368 Final line search alpha, max atom move = 1.0000000 0.020322368 Iterations, force evaluations = 56 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10659 | 0.10659 | 0.10659 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015442 | 0.0015442 | 0.0015442 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007889 | | | 0.72 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2078.00 ave 2078 max 2078 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: 11220.0 ave 11220 max 11220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11220 Ave neighs/atom = 136.82927 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.394 | 4.394 | 4.394 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -318.90463 0 -318.90463 19313.593 979.27638 355 0 -328.38543 0 -328.38543 121.74092 955.26937 Loop time of 0.291801 on 1 procs for 299 steps with 82 atoms 90.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -318.904634537296 -328.385206419846 -328.385430599268 Force two-norm initial, final = 21.212296 0.72034381 Force max component initial, final = 15.118941 0.46415139 Final line search alpha, max atom move = 0.0017170646 0.00079697793 Iterations, force evaluations = 299 319 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25696 | 0.25696 | 0.25696 | 0.0 | 88.06 Neigh | 0.0094098 | 0.0094098 | 0.0094098 | 0.0 | 3.22 Comm | 0.0062481 | 0.0062481 | 0.0062481 | 0.0 | 2.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01919 | | | 6.58 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2096.00 ave 2096 max 2096 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: 11360.0 ave 11360 max 11360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11360 Ave neighs/atom = 138.53659 Neighbor list builds = 14 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.531 | 4.531 | 4.531 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -328.38543 0 -328.38543 121.74092 Loop time of 1.521e-06 on 1 procs for 0 steps with 82 atoms 131.5% 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 | | 1.521e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2086.00 ave 2086 max 2086 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: 11388.0 ave 11388 max 11388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11388 Ave neighs/atom = 138.87805 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.531 | 4.531 | 4.531 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 -328.38543 -328.38543 4.0422752 58.536629 4.0371257 121.74092 121.74092 431.4983 -622.80216 556.52661 2.4249424 211.86205 Loop time of 1.489e-06 on 1 procs for 0 steps with 82 atoms 201.5% 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 | | 1.489e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2086.00 ave 2086 max 2086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5694.00 ave 5694 max 5694 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11388.0 ave 11388 max 11388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11388 Ave neighs/atom = 138.87805 Neighbor list builds = 0 Dangerous builds = 0 82 -328.385430599267 eV 2.4249424240518 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00