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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -29.173891 0.0000000) to (20.629056 29.173891 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6404217 4.5762967 4.0851619 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -29.173891 0.0000000) to (20.629056 29.173891 4.0851619) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6404217 4.5762967 4.0851619 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -29.173891 0.0000000) to (20.629056 29.173891 4.0851619) create_atoms CPU = 0.000 seconds 206 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 410 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.810 | 4.810 | 4.810 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1534.8956 0 -1534.8956 103907.61 53 0 -1698.3001 0 -1698.3001 16588.94 Loop time of 4.00985 on 1 procs for 53 steps with 410 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 = -1534.89563334954 -1698.29863802695 -1698.30010747189 Force two-norm initial, final = 299.19902 0.17065916 Force max component initial, final = 75.659291 0.042797098 Final line search alpha, max atom move = 1.0000000 0.042797098 Iterations, force evaluations = 53 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9827 | 3.9827 | 3.9827 | 0.0 | 99.32 Neigh | 0.020388 | 0.020388 | 0.020388 | 0.0 | 0.51 Comm | 0.0033188 | 0.0033188 | 0.0033188 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003406 | | | 0.08 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2171.00 ave 2171 max 2171 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: 23608.0 ave 23608 max 23608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23608 Ave neighs/atom = 57.580488 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.810 | 4.810 | 4.810 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1698.3001 0 -1698.3001 16588.94 4917.1447 62 0 -1698.7136 0 -1698.7136 -110.31189 4959.4313 Loop time of 0.644096 on 1 procs for 9 steps with 410 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 = -1698.3001074719 -1698.71347836075 -1698.71359892723 Force two-norm initial, final = 105.40144 1.0639407 Force max component initial, final = 90.741433 0.65724226 Final line search alpha, max atom move = 0.00077121870 0.00050687752 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64166 | 0.64166 | 0.64166 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040198 | 0.00040198 | 0.00040198 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002033 | | | 0.32 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2167.00 ave 2167 max 2167 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: 23616.0 ave 23616 max 23616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23616 Ave neighs/atom = 57.600000 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1698.7136 0 -1698.7136 -110.31189 Loop time of 2.908e-06 on 1 procs for 0 steps with 410 atoms 137.6% 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 | | 2.908e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2163.00 ave 2163 max 2163 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: 23572.0 ave 23572 max 23572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23572 Ave neighs/atom = 57.492683 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.948 | 4.948 | 4.948 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 -1698.7136 -1698.7136 20.697281 58.787009 4.0760285 -110.31189 -110.31189 -16.140151 -213.92472 -100.87079 2.2613629 372.22254 Loop time of 3.019e-06 on 1 procs for 0 steps with 410 atoms 132.5% 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 | | 3.019e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2163.00 ave 2163 max 2163 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11786.0 ave 11786 max 11786 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23572.0 ave 23572 max 23572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23572 Ave neighs/atom = 57.492683 Neighbor list builds = 0 Dangerous builds = 0 410 -1698.71359892723 eV 2.26136288635166 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05