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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -46.051694 0.0000000) to (21.707317 46.051694 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5699614 5.6550387 4.9800000 Created 459 atoms using lattice units in orthogonal box = (0.0000000 -46.051694 0.0000000) to (21.707317 46.051694 4.9800000) create_atoms CPU = 0.001 seconds 459 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5699614 5.6550387 4.9800000 Created 459 atoms using lattice units in orthogonal box = (0.0000000 -46.051694 0.0000000) to (21.707317 46.051694 4.9800000) create_atoms CPU = 0.001 seconds 459 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 30 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 904 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3984.2445 0 -3984.2445 6614.5671 56 0 -4007.0564 0 -4007.0564 -3614.7436 Loop time of 3.0162 on 1 procs for 56 steps with 904 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3984.24454688709 -4007.05243115111 -4007.05640519069 Force two-norm initial, final = 31.917792 0.20984751 Force max component initial, final = 5.3587588 0.026052518 Final line search alpha, max atom move = 1.0000000 0.026052518 Iterations, force evaluations = 56 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.994 | 2.994 | 2.994 | 0.0 | 99.27 Neigh | 0.012298 | 0.012298 | 0.012298 | 0.0 | 0.41 Comm | 0.0050808 | 0.0050808 | 0.0050808 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004773 | | | 0.16 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5163.00 ave 5163 max 5163 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: 77528.0 ave 77528 max 77528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77528 Ave neighs/atom = 85.761062 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -4007.0564 0 -4007.0564 -3614.7436 9956.6006 58 0 -4007.066 0 -4007.066 -1624.4543 9945.8685 Loop time of 0.14897 on 1 procs for 2 steps with 904 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 = -4007.05640519069 -4007.06575831025 -4007.06599237192 Force two-norm initial, final = 22.690418 0.21356059 Force max component initial, final = 19.546133 0.026866191 Final line search alpha, max atom move = 0.00057315097 1.5398384e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14799 | 0.14799 | 0.14799 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020098 | 0.00020098 | 0.00020098 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007827 | | | 0.53 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 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: 77544.0 ave 77544 max 77544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77544 Ave neighs/atom = 85.778761 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.729 | 4.729 | 4.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4007.066 0 -4007.066 -1624.4543 Loop time of 1.57e-06 on 1 procs for 0 steps with 904 atoms 127.4% 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 | | 1.57e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 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: 77544.0 ave 77544 max 77544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77544 Ave neighs/atom = 85.778761 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.729 | 4.729 | 4.729 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 -4007.066 -4007.066 21.702054 92.103387 4.9758385 -1624.4543 -1624.4543 -4.3106494 -4867.8459 -1.2062295 2.3792764 537.39114 Loop time of 1.569e-06 on 1 procs for 0 steps with 904 atoms 127.5% 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 | | 1.569e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5156.00 ave 5156 max 5156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38772.0 ave 38772 max 38772 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77544.0 ave 77544 max 77544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77544 Ave neighs/atom = 85.778761 Neighbor list builds = 0 Dangerous builds = 0 904 -4007.06599237192 eV 2.37927638732654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03