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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -44.355317 0.0000000) to (36.215964 44.355317 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1737092 5.1295264 5.9740848 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.355317 0.0000000) to (36.215964 44.355317 8.9611272) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1737092 5.1295264 5.9740848 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.355317 0.0000000) to (36.215964 44.355317 8.9611272) create_atoms CPU = 0.001 seconds 1184 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.022 | 6.022 | 6.022 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8753.172 0 -8753.172 70156.317 774 0 -9509.9357 0 -9509.9357 -49333.389 Loop time of 25.6778 on 1 procs for 774 steps with 2352 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 = -8753.17199131094 -9509.92833321391 -9509.93570711271 Force two-norm initial, final = 1005.2937 0.26900851 Force max component initial, final = 172.59354 0.018308984 Final line search alpha, max atom move = 1.0000000 0.018308984 Iterations, force evaluations = 774 1535 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.13 | 25.13 | 25.13 | 0.0 | 97.86 Neigh | 0.28492 | 0.28492 | 0.28492 | 0.0 | 1.11 Comm | 0.11265 | 0.11265 | 0.11265 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1507 | | | 0.59 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8118.00 ave 8118 max 8118 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: 352816.0 ave 352816 max 352816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352816 Ave neighs/atom = 150.00680 Neighbor list builds = 12 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 774 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.019 | 6.019 | 6.019 Mbytes Step Temp E_pair E_mol TotEng Press Volume 774 0 -9509.9357 0 -9509.9357 -49333.389 28789.782 824 0 -9567.0922 0 -9567.0922 -20.27344 27943.082 Loop time of 0.944237 on 1 procs for 50 steps with 2352 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 = -9509.93570711272 -9567.08971303104 -9567.09221035478 Force two-norm initial, final = 2113.8169 7.7305561 Force max component initial, final = 1663.8830 4.3501256 Final line search alpha, max atom move = 0.00024151010 0.0010505993 Iterations, force evaluations = 50 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84661 | 0.84661 | 0.84661 | 0.0 | 89.66 Neigh | 0.071027 | 0.071027 | 0.071027 | 0.0 | 7.52 Comm | 0.0039885 | 0.0039885 | 0.0039885 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02261 | | | 2.39 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8111.00 ave 8111 max 8111 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: 376272.0 ave 376272 max 376272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376272 Ave neighs/atom = 159.97959 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.156 | 6.156 | 6.156 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9567.0922 0 -9567.0922 -20.27344 Loop time of 2.192e-06 on 1 procs for 0 steps with 2352 atoms 182.5% 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 | | 2.192e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8078.00 ave 8078 max 8078 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: 376556.0 ave 376556 max 376556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376556 Ave neighs/atom = 160.10034 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.156 | 6.156 | 6.156 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 -9567.0922 -9567.0922 35.323022 85.046845 9.3016128 -20.27344 -20.27344 17.394589 180.68593 -258.90084 2.2349848 4459.9697 Loop time of 2.287e-06 on 1 procs for 0 steps with 2352 atoms 218.6% 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 | | 2.287e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8078.00 ave 8078 max 8078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 188278.0 ave 188278 max 188278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 376556.0 ave 376556 max 376556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 376556 Ave neighs/atom = 160.10034 Neighbor list builds = 0 Dangerous builds = 0 2352 -9567.0922103548 eV 2.2349848292286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27