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 -80.189488 0.0000000) to (49.105832 80.189488 9.9208762) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6789057 5.7278205 6.6139175 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -80.189488 0.0000000) to (49.105832 80.189488 9.9208762) create_atoms CPU = 0.004 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6789057 5.7278205 6.6139175 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.189488 0.0000000) to (49.105832 80.189488 9.9208762) create_atoms CPU = 0.003 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 12 39 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 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 4704 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 = 12 39 3 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) = 11.51 | 11.51 | 11.51 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16623.877 0 -16623.877 6968.2471 74 0 -16820.02 0 -16820.02 4213.3679 Loop time of 4.75536 on 1 procs for 74 steps with 4704 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 = -16623.8767282271 -16820.0038740449 -16820.0201388946 Force two-norm initial, final = 142.84893 0.28364426 Force max component initial, final = 21.401069 0.028238926 Final line search alpha, max atom move = 1.0000000 0.028238926 Iterations, force evaluations = 74 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6115 | 4.6115 | 4.6115 | 0.0 | 96.98 Neigh | 0.092279 | 0.092279 | 0.092279 | 0.0 | 1.94 Comm | 0.021127 | 0.021127 | 0.021127 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03042 | | | 0.64 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14274.0 ave 14274 max 14274 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: 657756.0 ave 657756 max 657756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657756 Ave neighs/atom = 139.82908 Neighbor list builds = 2 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 = 12 39 3 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.51 | 11.51 | 11.51 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -16820.02 0 -16820.02 4213.3679 78132.287 82 0 -16821.132 0 -16821.132 114.21756 78551.162 Loop time of 0.381268 on 1 procs for 8 steps with 4704 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 = -16820.0201388946 -16821.1270073609 -16821.1320074588 Force two-norm initial, final = 395.78460 11.409090 Force max component initial, final = 345.03657 10.498755 Final line search alpha, max atom move = 0.00010584095 0.0011111982 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3282 | 0.3282 | 0.3282 | 0.0 | 86.08 Neigh | 0.044038 | 0.044038 | 0.044038 | 0.0 | 11.55 Comm | 0.0014815 | 0.0014815 | 0.0014815 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007554 | | | 1.98 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13900.0 ave 13900 max 13900 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: 657732.0 ave 657732 max 657732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657732 Ave neighs/atom = 139.82398 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 = 12 39 3 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) = 11.02 | 11.02 | 11.02 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16821.132 0 -16821.132 114.21756 Loop time of 4.286e-06 on 1 procs for 0 steps with 4704 atoms 186.7% 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 | | 4.286e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13900.0 ave 13900 max 13900 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: 657756.0 ave 657756 max 657756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657756 Ave neighs/atom = 139.82908 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 = 12 39 3 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) = 11.02 | 11.02 | 11.02 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 -16821.132 -16821.132 49.092056 161.51997 9.906384 114.21756 114.21756 54.665424 215.66235 72.324892 2.5309464 2292.4988 Loop time of 2.322e-06 on 1 procs for 0 steps with 4704 atoms 301.5% 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 | | 2.322e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13900.0 ave 13900 max 13900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 328878.0 ave 328878 max 328878 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 657756.0 ave 657756 max 657756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 657756 Ave neighs/atom = 139.82908 Neighbor list builds = 0 Dangerous builds = 0 4704 -16821.1275213748 eV 2.53094642319489 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05