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 = 4.0501807 4.0501807 4.0501807 Created orthogonal box = (0.0000000 -47.232818 0.0000000) to (16.699323 47.232818 5.7278205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8761918 6.9460027 5.7278205 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.232818 0.0000000) to (16.699323 47.232818 5.7278205) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8761918 6.9460027 5.7278205 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.232818 0.0000000) to (16.699323 47.232818 5.7278205) create_atoms CPU = 0.001 seconds 274 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 4 23 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 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_131650261510_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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1924.6293 0 -1924.6293 11954.094 47 0 -1951.5287 0 -1951.5287 8535.9925 Loop time of 0.413364 on 1 procs for 47 steps with 546 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1924.62933531457 -1951.52690750004 -1951.52872529025 Force two-norm initial, final = 33.067020 0.085811768 Force max component initial, final = 9.6090047 0.0086808771 Final line search alpha, max atom move = 1.0000000 0.0086808771 Iterations, force evaluations = 47 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40702 | 0.40702 | 0.40702 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003569 | 0.003569 | 0.003569 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002773 | | | 0.67 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4606.00 ave 4606 max 4606 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: 77116.0 ave 77116 max 77116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77116 Ave neighs/atom = 141.23810 Neighbor list builds = 0 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.525 | 4.525 | 4.525 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1951.5287 0 -1951.5287 8535.9925 9035.7066 61 0 -1952.0341 0 -1952.0341 24.649968 9135.798 Loop time of 0.0811559 on 1 procs for 14 steps with 546 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 = -1951.52872529024 -1952.032383757 -1952.03407283834 Force two-norm initial, final = 93.583143 0.34566141 Force max component initial, final = 82.832233 0.19521274 Final line search alpha, max atom move = 0.00036404028 7.1065301e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07199 | 0.07199 | 0.07199 | 0.0 | 88.71 Neigh | 0.0055637 | 0.0055637 | 0.0055637 | 0.0 | 6.86 Comm | 0.00075302 | 0.00075302 | 0.00075302 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002849 | | | 3.51 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4622.00 ave 4622 max 4622 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: 76320.0 ave 76320 max 76320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76320 Ave neighs/atom = 139.78022 Neighbor list builds = 1 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 4.663 | 4.663 | 4.663 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1952.0341 0 -1952.0341 24.649968 Loop time of 1.69e-06 on 1 procs for 0 steps with 546 atoms 118.3% 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 | | 1.69e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4622.00 ave 4622 max 4622 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: 76276.0 ave 76276 max 76276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76276 Ave neighs/atom = 139.69963 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 4.663 | 4.663 | 4.663 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 -1952.0341 -1952.0341 16.677595 95.784513 5.7189693 24.649968 24.649968 34.19059 21.66932 18.089994 2.69132 386.63173 Loop time of 1.626e-06 on 1 procs for 0 steps with 546 atoms 123.0% 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 | | 1.626e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4622.00 ave 4622 max 4622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38138.0 ave 38138 max 38138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76276.0 ave 76276 max 76276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76276 Ave neighs/atom = 139.69963 Neighbor list builds = 0 Dangerous builds = 0 546 -1952.03355213216 eV 2.69131997128301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00