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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -42.773259 0.0000000) to (52.386329 42.773259 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9870091 5.4994190 5.9032705 Created 1665 atoms using lattice units in orthogonal box = (0.0000000 -42.773259 0.0000000) to (52.386329 42.773259 8.8549058) create_atoms CPU = 0.007 seconds 1665 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9870091 5.4994190 5.9032705 Created 1689 atoms using lattice units in orthogonal box = (0.0000000 -42.773259 0.0000000) to (52.386329 42.773259 8.8549058) create_atoms CPU = 0.007 seconds 1689 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3354 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.968 | 6.968 | 6.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11401.022 0 -11401.022 14574.316 91 0 -11828.996 0 -11828.996 2963.6812 Loop time of 7.27176 on 1 procs for 91 steps with 3354 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 = -11401.0216509934 -11828.9847162264 -11828.9956545787 Force two-norm initial, final = 104.84490 0.32250069 Force max component initial, final = 11.876718 0.060430694 Final line search alpha, max atom move = 1.0000000 0.060430694 Iterations, force evaluations = 91 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7841 | 6.7841 | 6.7841 | 0.0 | 93.29 Neigh | 0.39409 | 0.39409 | 0.39409 | 0.0 | 5.42 Comm | 0.038199 | 0.038199 | 0.038199 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0554 | | | 0.76 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10723.0 ave 10723 max 10723 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: 562470.0 ave 562470 max 562470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562470 Ave neighs/atom = 167.70125 Neighbor list builds = 5 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.968 | 6.968 | 6.968 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -11828.996 0 -11828.996 2963.6812 39682.977 95 0 -11829.22 0 -11829.22 -68.435467 39770.776 Loop time of 0.295833 on 1 procs for 4 steps with 3354 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 = -11828.9956545787 -11829.2171329667 -11829.2202628183 Force two-norm initial, final = 155.70592 4.9225339 Force max component initial, final = 146.40869 4.2189494 Final line search alpha, max atom move = 4.4009376e-05 0.00018567333 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28851 | 0.28851 | 0.28851 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001388 | 0.001388 | 0.001388 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005938 | | | 2.01 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10723.0 ave 10723 max 10723 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: 563098.0 ave 563098 max 563098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 563098 Ave neighs/atom = 167.88849 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.106 | 7.106 | 7.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11829.22 0 -11829.22 -68.435467 Loop time of 6.705e-06 on 1 procs for 0 steps with 3354 atoms 179.0% 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 | | 6.705e-06 | | |100.00 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10723.0 ave 10723 max 10723 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: 559842.0 ave 559842 max 559842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559842 Ave neighs/atom = 166.91771 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 7.106 | 7.106 | 7.106 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 -11829.22 -11829.22 52.37315 85.826413 8.8477817 -68.435467 -68.435467 -86.927063 51.445443 -169.82478 2.2958233 1848.7284 Loop time of 7.126e-06 on 1 procs for 0 steps with 3354 atoms 280.7% 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 | | 7.126e-06 | | |100.00 Nlocal: 3354.00 ave 3354 max 3354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10723.0 ave 10723 max 10723 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 279921.0 ave 279921 max 279921 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 559842.0 ave 559842 max 559842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559842 Ave neighs/atom = 166.91771 Neighbor list builds = 0 Dangerous builds = 0 3354 -11829.2202628183 eV 2.29582333873981 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08