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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -50.294727 0.0000000) to (13.688491 50.294727 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8664960 5.5883029 5.9741471 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -50.294727 0.0000000) to (13.688491 50.294727 8.9612207) create_atoms CPU = 0.001 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8664960 5.5883029 5.9741471 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -50.294727 0.0000000) to (13.688491 50.294727 8.9612207) create_atoms CPU = 0.001 seconds 508 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 24 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1008 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.499 | 5.499 | 5.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3499.4655 0 -3499.4655 102416.1 212 0 -3935.6788 0 -3935.6788 -84674.974 Loop time of 4.49765 on 1 procs for 212 steps with 1008 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 = -3499.46548245533 -3935.67500564721 -3935.67879612764 Force two-norm initial, final = 866.57639 0.20455606 Force max component initial, final = 161.73117 0.015339606 Final line search alpha, max atom move = 1.0000000 0.015339606 Iterations, force evaluations = 212 406 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4189 | 4.4189 | 4.4189 | 0.0 | 98.25 Neigh | 0.037322 | 0.037322 | 0.037322 | 0.0 | 0.83 Comm | 0.021925 | 0.021925 | 0.021925 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01953 | | | 0.43 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6672.00 ave 6672 max 6672 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: 208368.0 ave 208368 max 208368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208368 Ave neighs/atom = 206.71429 Neighbor list builds = 3 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 212 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.499 | 5.499 | 5.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 212 0 -3935.6788 0 -3935.6788 -84674.974 12338.864 245 0 -3957.1435 0 -3957.1435 268.31681 11622.823 Loop time of 0.404796 on 1 procs for 33 steps with 1008 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 = -3935.67879612766 -3957.1402323258 -3957.14351810097 Force two-norm initial, final = 1138.9651 8.4811441 Force max component initial, final = 742.52009 6.3146543 Final line search alpha, max atom move = 0.00065759669 0.0041524958 Iterations, force evaluations = 33 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38264 | 0.38264 | 0.38264 | 0.0 | 94.53 Neigh | 0.011613 | 0.011613 | 0.011613 | 0.0 | 2.87 Comm | 0.0018876 | 0.0018876 | 0.0018876 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008653 | | | 2.14 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6833.00 ave 6833 max 6833 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: 215128.0 ave 215128 max 215128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 215128 Ave neighs/atom = 213.42063 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.639 | 5.639 | 5.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3957.1435 0 -3957.1435 268.31681 Loop time of 1.593e-06 on 1 procs for 0 steps with 1008 atoms 188.3% 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 | | 1.593e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939.00 ave 6939 max 6939 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: 218484.0 ave 218484 max 218484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218484 Ave neighs/atom = 216.75000 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.639 | 5.639 | 5.639 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 -3957.1435 -3957.1435 13.462164 99.551268 8.6726127 268.31681 268.31681 856.06674 -427.29355 376.17725 2.2949212 4059.507 Loop time of 2.012e-06 on 1 procs for 0 steps with 1008 atoms 198.8% 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 | | 2.012e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6939.00 ave 6939 max 6939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109242.0 ave 109242 max 109242 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218484.0 ave 218484 max 218484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218484 Ave neighs/atom = 216.75000 Neighbor list builds = 0 Dangerous builds = 0 1008 -3957.14351810097 eV 2.29492116924245 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05