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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -40.398439 0.0000000) to (28.566010 40.398439 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3281834 5.5088781 4.9727041 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.398439 0.0000000) to (28.566010 40.398439 4.9727041) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3281834 5.5088781 4.9727041 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.398439 0.0000000) to (28.566010 40.398439 4.9727041) create_atoms CPU = 0.001 seconds 532 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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_047308317761_000#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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4673.2626 0 -4673.2626 92016.475 38 0 -5087.5341 0 -5087.5341 -2481.2656 Loop time of 1.02599 on 1 procs for 38 steps with 1048 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4673.2625971655 -5087.52963073595 -5087.53413455246 Force two-norm initial, final = 717.28235 0.22333496 Force max component initial, final = 174.17982 0.016175073 Final line search alpha, max atom move = 1.0000000 0.016175073 Iterations, force evaluations = 38 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98481 | 0.98481 | 0.98481 | 0.0 | 95.99 Neigh | 0.030571 | 0.030571 | 0.030571 | 0.0 | 2.98 Comm | 0.0059054 | 0.0059054 | 0.0059054 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004705 | | | 0.46 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8795.00 ave 8795 max 8795 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: 263256.0 ave 263256 max 263256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263256 Ave neighs/atom = 251.19847 Neighbor list builds = 2 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -5087.5341 0 -5087.5341 -2481.2656 11477.222 40 0 -5087.5477 0 -5087.5477 -12.758143 11461.193 Loop time of 0.0778747 on 1 procs for 2 steps with 1048 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 = -5087.53413455246 -5087.54718585327 -5087.54765679629 Force two-norm initial, final = 31.202439 1.4580751 Force max component initial, final = 21.902711 1.2176502 Final line search alpha, max atom move = 0.00038339928 0.00046684620 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076238 | 0.076238 | 0.076238 | 0.0 | 97.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032995 | 0.00032995 | 0.00032995 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001307 | | | 1.68 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8804.00 ave 8804 max 8804 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: 263064.0 ave 263064 max 263064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263064 Ave neighs/atom = 251.01527 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.591 | 5.591 | 5.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5087.5477 0 -5087.5477 -12.758143 Loop time of 1.753e-06 on 1 procs for 0 steps with 1048 atoms 171.1% 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 | | 1.753e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8804.00 ave 8804 max 8804 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: 263184.0 ave 263184 max 263184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263184 Ave neighs/atom = 251.12977 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.591 | 5.591 | 5.591 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 -5087.5477 -5087.5477 28.558991 80.732871 4.9709175 -12.758143 -12.758143 103.69831 28.183165 -170.1559 2.241907 466.15493 Loop time of 2.142e-06 on 1 procs for 0 steps with 1048 atoms 186.7% 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 | | 2.142e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8804.00 ave 8804 max 8804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 131592.0 ave 131592 max 131592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 263184.0 ave 263184 max 263184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 263184 Ave neighs/atom = 251.12977 Neighbor list builds = 0 Dangerous builds = 0 1048 -5087.54765679629 eV 2.24190702340685 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01