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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -46.532031 0.0000000) to (9.4983110 46.532031 7.0149676) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3174141 4.2301846 4.6766450 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -46.532031 0.0000000) to (9.4983110 46.532031 7.0149676) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3174141 4.2301846 4.6766450 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -46.532031 0.0000000) to (9.4983110 46.532031 7.0149676) create_atoms CPU = 0.001 seconds 266 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.882 | 5.882 | 5.882 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1860.8505 0 -1860.8505 86744.629 80 0 -2194.4939 0 -2194.4939 6613.454 Loop time of 2.27991 on 1 procs for 80 steps with 528 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 = -1860.85046731634 -2194.49203054445 -2194.49386319563 Force two-norm initial, final = 628.78351 0.18217289 Force max component initial, final = 167.95553 0.030087618 Final line search alpha, max atom move = 1.0000000 0.030087618 Iterations, force evaluations = 80 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2419 | 2.2419 | 2.2419 | 0.0 | 98.33 Neigh | 0.017654 | 0.017654 | 0.017654 | 0.0 | 0.77 Comm | 0.013643 | 0.013643 | 0.013643 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006743 | | | 0.30 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9703.00 ave 9703 max 9703 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: 320124.0 ave 320124 max 320124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320124 Ave neighs/atom = 606.29545 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.879 | 5.879 | 5.879 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -2194.4939 0 -2194.4939 6613.454 6200.8904 87 0 -2194.721 0 -2194.721 -2.4798212 6224.5956 Loop time of 0.139938 on 1 procs for 7 steps with 528 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 = -2194.49386319561 -2194.71996962721 -2194.72101226382 Force two-norm initial, final = 72.595969 0.47102683 Force max component initial, final = 68.397120 0.11303095 Final line search alpha, max atom move = 0.00037435913 4.2314168e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13645 | 0.13645 | 0.13645 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069697 | 0.00069697 | 0.00069697 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002789 | | | 1.99 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9625.00 ave 9625 max 9625 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: 320048.0 ave 320048 max 320048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320048 Ave neighs/atom = 606.15152 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.017 | 6.017 | 6.017 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2194.721 0 -2194.721 -2.4798212 Loop time of 1.805e-06 on 1 procs for 0 steps with 528 atoms 166.2% 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 | | 1.805e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9625.00 ave 9625 max 9625 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: 319312.0 ave 319312 max 319312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319312 Ave neighs/atom = 604.75758 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.017 | 6.017 | 6.017 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 -2194.721 -2194.721 9.4954534 93.657309 6.9992863 -2.4798212 -2.4798212 -5.1844644 -29.279001 27.024002 2.334409 486.66505 Loop time of 2.579e-06 on 1 procs for 0 steps with 528 atoms 232.6% 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 | | 2.579e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9625.00 ave 9625 max 9625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159656.0 ave 159656 max 159656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 319312.0 ave 319312 max 319312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319312 Ave neighs/atom = 604.75758 Neighbor list builds = 0 Dangerous builds = 0 528 -2194.72101226382 eV 2.33440902335614 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02