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 = 4.1288715 4.1288715 4.1288715 Created orthogonal box = (0.0000000 -74.319686 0.0000000) to (52.551954 74.319686 5.8391060) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.1366851 6.8814524 5.8391060 Created 1296 atoms using lattice units in orthogonal box = (0.0000000 -74.319686 0.0000000) to (52.551954 74.319686 5.8391060) create_atoms CPU = 0.011 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.1366851 6.8814524 5.8391060 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -74.319686 0.0000000) to (52.551954 74.319686 5.8391060) create_atoms CPU = 0.010 seconds 1300 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 33 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 2584 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_122703700223_003#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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 6.544 | 6.544 | 6.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9277.2766 0 -9277.2766 10776.204 76 0 -9584.8029 0 -9584.8029 -1518.9196 Loop time of 11.3614 on 1 procs for 76 steps with 2584 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9277.27658929295 -9584.79467771426 -9584.80292587381 Force two-norm initial, final = 340.25992 0.20869184 Force max component initial, final = 73.924939 0.026421060 Final line search alpha, max atom move = 1.0000000 0.026421060 Iterations, force evaluations = 76 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.214 | 11.214 | 11.214 | 0.0 | 98.70 Neigh | 0.062561 | 0.062561 | 0.062561 | 0.0 | 0.55 Comm | 0.046791 | 0.046791 | 0.046791 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03794 | | | 0.33 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13488.0 ave 13488 max 13488 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: 461672.0 ave 461672 max 461672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461672 Ave neighs/atom = 178.66563 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -9584.8029 0 -9584.8029 -1518.9196 45610.947 78 0 -9584.8366 0 -9584.8366 -2.8235955 45542.31 Loop time of 0.400358 on 1 procs for 2 steps with 2584 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 = -9584.80292587377 -9584.83593297025 -9584.83662664424 Force two-norm initial, final = 75.117097 0.30215557 Force max component initial, final = 47.837122 0.21133299 Final line search alpha, max atom move = 0.00027702203 5.8543893e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39381 | 0.39381 | 0.39381 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016684 | 0.0016684 | 0.0016684 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004876 | | | 1.22 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14082.0 ave 14082 max 14082 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: 459640.0 ave 459640 max 459640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459640 Ave neighs/atom = 177.87926 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 9.824 | 9.824 | 9.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9584.8366 0 -9584.8366 -2.8235955 Loop time of 6.394e-06 on 1 procs for 0 steps with 2584 atoms 203.3% 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 | | 6.394e-06 | | |100.00 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14082.0 ave 14082 max 14082 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: 460512.0 ave 460512 max 460512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460512 Ave neighs/atom = 178.21672 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 12 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 9.824 | 9.824 | 9.824 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 -9584.8366 -9584.8366 52.52988 148.52155 5.837396 -2.8235955 -2.8235955 -7.4315626 -1.4987189 0.45949497 2.7561592 1705.3514 Loop time of 6.515e-06 on 1 procs for 0 steps with 2584 atoms 260.9% 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 | | 6.515e-06 | | |100.00 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14082.0 ave 14082 max 14082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230256.0 ave 230256 max 230256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 460512.0 ave 460512 max 460512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460512 Ave neighs/atom = 178.21672 Neighbor list builds = 0 Dangerous builds = 0 2584 -9584.83662664424 eV 2.75615923171915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13