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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -34.754466 0.0000000) to (28.376903 34.754466 7.0214624) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0538432 4.0192239 4.6809750 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -34.754466 0.0000000) to (28.376903 34.754466 7.0214624) create_atoms CPU = 0.003 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0538432 4.0192239 4.6809750 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.754466 0.0000000) to (28.376903 34.754466 7.0214624) create_atoms CPU = 0.002 seconds 590 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1168 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1197827.9 0 1197827.9 3.755879e+08 136 0 -4966.2761 0 -4966.2761 -1015.8078 Loop time of 4.87439 on 1 procs for 136 steps with 1168 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 = 1197827.85316974 -4966.27137379543 -4966.27612640468 Force two-norm initial, final = 6810786.2 0.30285832 Force max component initial, final = 2298716.1 0.055867561 Final line search alpha, max atom move = 1.0000000 0.055867561 Iterations, force evaluations = 136 249 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6933 | 4.6933 | 4.6933 | 0.0 | 96.28 Neigh | 0.1041 | 0.1041 | 0.1041 | 0.0 | 2.14 Comm | 0.040614 | 0.040614 | 0.040614 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03642 | | | 0.75 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5781.00 ave 5781 max 5781 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: 193556.0 ave 193556 max 193556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193556 Ave neighs/atom = 165.71575 Neighbor list builds = 4 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 136 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press Volume 136 0 -4966.2761 0 -4966.2761 -1015.8078 13849.471 139 0 -4966.3086 0 -4966.3086 -0.30143922 13841.323 Loop time of 0.133905 on 1 procs for 3 steps with 1168 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 = -4966.27612640468 -4966.3083539786 -4966.30858462875 Force two-norm initial, final = 31.690178 0.37539719 Force max component initial, final = 20.488534 0.068843373 Final line search alpha, max atom move = 0.00050424557 3.4713966e-05 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12998 | 0.12998 | 0.12998 | 0.0 | 97.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088743 | 0.00088743 | 0.00088743 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003039 | | | 2.27 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5787.00 ave 5787 max 5787 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: 193548.0 ave 193548 max 193548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193548 Ave neighs/atom = 165.70890 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.193 | 5.193 | 5.193 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4966.3086 0 -4966.3086 -0.30143922 Loop time of 6.405e-06 on 1 procs for 0 steps with 1168 atoms 203.0% 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 | | 6.405e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5778.00 ave 5778 max 5778 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: 193548.0 ave 193548 max 193548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193548 Ave neighs/atom = 165.70890 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.193 | 5.193 | 5.193 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 -4966.3086 -4966.3086 28.340558 69.616969 7.0154267 -0.30143922 -0.30143922 4.5504903 -0.68484837 -4.7699596 2.3216268 1026.3675 Loop time of 7.197e-06 on 1 procs for 0 steps with 1168 atoms 264.0% 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 | | 7.197e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5778.00 ave 5778 max 5778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96774.0 ave 96774 max 96774 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193548.0 ave 193548 max 193548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193548 Ave neighs/atom = 165.70890 Neighbor list builds = 0 Dangerous builds = 0 1168 -4966.30858462875 eV 2.32162682863834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05