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 -71.573352 0.0000000) to (43.829548 71.573352 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0687232 5.1123823 5.9032705 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.573352 0.0000000) to (43.829548 71.573352 8.8549058) create_atoms CPU = 0.009 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0687232 5.1123823 5.9032705 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.573352 0.0000000) to (43.829548 71.573352 8.8549058) create_atoms CPU = 0.008 seconds 2358 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 = 12 38 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 30 atoms, new total = 4680 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 = 12 38 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) = 12.33 | 12.33 | 12.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16338.542 0 -16338.542 2627.1234 89 0 -16521.537 0 -16521.537 -2241.4547 Loop time of 11.4218 on 1 procs for 89 steps with 4680 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 = -16338.5419942587 -16521.5223340061 -16521.5368782455 Force two-norm initial, final = 77.425264 0.35947843 Force max component initial, final = 9.8816283 0.034606286 Final line search alpha, max atom move = 1.0000000 0.034606286 Iterations, force evaluations = 89 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.174 | 11.174 | 11.174 | 0.0 | 97.83 Neigh | 0.1101 | 0.1101 | 0.1101 | 0.0 | 0.96 Comm | 0.056516 | 0.056516 | 0.056516 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08086 | | | 0.71 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14584.0 ave 14584 max 14584 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: 796608.0 ave 796608 max 796608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 796608 Ave neighs/atom = 170.21538 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 38 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.32 | 12.32 | 12.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -16521.537 0 -16521.537 -2241.4547 55556.168 91 0 -16521.618 0 -16521.618 -2.9603347 55465.334 Loop time of 0.330292 on 1 procs for 2 steps with 4680 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 = -16521.5368782456 -16521.6084856552 -16521.6177052146 Force two-norm initial, final = 139.22135 5.4023847 Force max component initial, final = 100.92363 4.4136618 Final line search alpha, max atom move = 4.5661343e-05 0.00020153373 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32257 | 0.32257 | 0.32257 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006107 | | | 1.85 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14414.0 ave 14414 max 14414 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: 801156.0 ave 801156 max 801156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 801156 Ave neighs/atom = 171.18718 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 = 12 38 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) = 11.84 | 11.84 | 11.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16521.618 0 -16521.618 -2.9603347 Loop time of 6.906e-06 on 1 procs for 0 steps with 4680 atoms 202.7% 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 | | 6.906e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14434.0 ave 14434 max 14434 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: 803712.0 ave 803712 max 803712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 803712 Ave neighs/atom = 171.73333 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 = 12 38 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) = 11.84 | 11.84 | 11.84 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 -16521.618 -16521.618 43.799661 143.17488 8.8447191 -2.9603347 -2.9603347 -127.40649 37.467046 81.058439 2.2639924 1745.4105 Loop time of 6.816e-06 on 1 procs for 0 steps with 4680 atoms 293.4% 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 | | 6.816e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14434.0 ave 14434 max 14434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 401856.0 ave 401856 max 401856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 803712.0 ave 803712 max 803712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 803712 Ave neighs/atom = 171.73333 Neighbor list builds = 0 Dangerous builds = 0 4680 -16521.6177052146 eV 2.26399235462901 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13