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 = 4.0499990 4.0499990 4.0499990 Created orthogonal box = (0.0000000 -61.153644 0.0000000) to (43.242156 61.153644 5.7275635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8277089 5.9007902 5.7275635 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -61.153644 0.0000000) to (43.242156 61.153644 5.7275635) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8277089 5.9007902 5.7275635 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -61.153644 0.0000000) to (43.242156 61.153644 5.7275635) create_atoms CPU = 0.002 seconds 916 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 ghost atom cutoff = 8 binsize = 4, bins = 11 31 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_093637366498_001#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 ghost atom cutoff = 8 binsize = 4, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.569 | 5.569 | 5.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5765.8996 0 -5765.8996 27932.885 83 0 -6115.0135 0 -6115.0135 2498.3904 Loop time of 19.4409 on 1 procs for 83 steps with 1824 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5765.89964911346 -6115.00885351759 -6115.01347880941 Force two-norm initial, final = 361.28530 0.16302814 Force max component initial, final = 69.779232 0.019609949 Final line search alpha, max atom move = 1.0000000 0.019609949 Iterations, force evaluations = 83 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.375 | 19.375 | 19.375 | 0.0 | 99.66 Neigh | 0.030746 | 0.030746 | 0.030746 | 0.0 | 0.16 Comm | 0.01855 | 0.01855 | 0.01855 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01678 | | | 0.09 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8814.00 ave 8814 max 8814 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: 243552.0 ave 243552 max 243552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243552 Ave neighs/atom = 133.52632 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 ghost atom cutoff = 8 binsize = 4, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.569 | 5.569 | 5.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -6115.0135 0 -6115.0135 2498.3904 30292.115 91 0 -6115.3791 0 -6115.3791 5.6892602 30384.796 Loop time of 1.48213 on 1 procs for 8 steps with 1824 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 = -6115.01347880941 -6115.37912564671 -6115.37913015245 Force two-norm initial, final = 116.35138 0.33002637 Force max component initial, final = 114.54791 0.19252241 Final line search alpha, max atom move = 0.0025511084 0.00049114554 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4766 | 1.4766 | 1.4766 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084628 | 0.00084628 | 0.00084628 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004697 | | | 0.32 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8790.00 ave 8790 max 8790 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: 243688.0 ave 243688 max 243688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243688 Ave neighs/atom = 133.60088 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 ghost atom cutoff = 8 binsize = 4, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.707 | 5.707 | 5.707 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6115.3791 0 -6115.3791 5.6892602 Loop time of 2.331e-06 on 1 procs for 0 steps with 1824 atoms 214.5% 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 | | 2.331e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8769.00 ave 8769 max 8769 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: 243440.0 ave 243440 max 243440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243440 Ave neighs/atom = 133.46491 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 ghost atom cutoff = 8 binsize = 4, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.707 | 5.707 | 5.707 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 -6115.3791 -6115.3791 43.146788 123.14751 5.7185013 5.6892602 5.6892602 10.129231 5.3302214 1.6083287 2.631277 868.8249 Loop time of 2.499e-06 on 1 procs for 0 steps with 1824 atoms 280.1% 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 | | 2.499e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8769.00 ave 8769 max 8769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 121720.0 ave 121720 max 121720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 243440.0 ave 243440 max 243440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 243440 Ave neighs/atom = 133.46491 Neighbor list builds = 0 Dangerous builds = 0 1824 -6115.37913015245 eV 2.63127702491895 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21