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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -41.388898 0.0000000) to (6.3363551 41.388898 8.9609594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3363551 5.1736123 5.9739729 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -41.388898 0.0000000) to (6.3363551 41.388898 8.9609594) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3363551 5.1736123 5.9739729 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -41.388898 0.0000000) to (6.3363551 41.388898 8.9609594) create_atoms CPU = 0.000 seconds 198 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 = 2 21 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 390 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_942420706858_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 ghost atom cutoff = 8 binsize = 4, bins = 2 21 3 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -975.44552 0 -975.44552 344577.98 127 0 -1569.1827 0 -1569.1827 -10574.636 Loop time of 1.09356 on 1 procs for 127 steps with 390 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -975.445520641987 -1569.18150242853 -1569.18268072286 Force two-norm initial, final = 516.91885 0.095180604 Force max component initial, final = 102.35827 0.011710953 Final line search alpha, max atom move = 1.0000000 0.011710953 Iterations, force evaluations = 127 245 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0657 | 1.0657 | 1.0657 | 0.0 | 97.46 Neigh | 0.0096212 | 0.0096212 | 0.0096212 | 0.0 | 0.88 Comm | 0.01038 | 0.01038 | 0.01038 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007817 | | | 0.71 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4079.00 ave 4079 max 4079 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: 69132.0 ave 69132 max 69132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69132 Ave neighs/atom = 177.26154 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 = 2 21 3 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 : 127 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 127 0 -1569.1827 0 -1569.1827 -10574.636 4700.1085 174 0 -1573.0325 0 -1573.0325 -308.62995 4678.2758 Loop time of 0.231943 on 1 procs for 47 steps with 390 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 = -1569.18268072286 -1573.0321608747 -1573.03248493106 Force two-norm initial, final = 163.51041 1.9714136 Force max component initial, final = 138.34712 1.1045883 Final line search alpha, max atom move = 0.0011560819 0.0012769945 Iterations, force evaluations = 47 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21161 | 0.21161 | 0.21161 | 0.0 | 91.23 Neigh | 0.0098933 | 0.0098933 | 0.0098933 | 0.0 | 4.27 Comm | 0.0020676 | 0.0020676 | 0.0020676 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00837 | | | 3.61 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4213.00 ave 4213 max 4213 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: 68964.0 ave 68964 max 68964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68964 Ave neighs/atom = 176.83077 Neighbor list builds = 2 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 = 2 21 3 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) = 4.687 | 4.687 | 4.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1573.0325 0 -1573.0325 -308.62995 Loop time of 2.176e-06 on 1 procs for 0 steps with 390 atoms 183.8% 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 | | 2.176e-06 | | |100.00 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4192.00 ave 4192 max 4192 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: 68894.0 ave 68894 max 68894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68894 Ave neighs/atom = 176.65128 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 = 2 21 3 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) = 4.687 | 4.687 | 4.687 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 -1573.0325 -1573.0325 6.299259 80.172774 9.2633792 -308.62995 -308.62995 -320.6492 -366.38529 -238.85536 2.3447147 73.033209 Loop time of 2.515e-06 on 1 procs for 0 steps with 390 atoms 278.3% 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 | | 2.515e-06 | | |100.00 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4192.00 ave 4192 max 4192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34447.0 ave 34447 max 34447 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68894.0 ave 68894 max 68894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68894 Ave neighs/atom = 176.65128 Neighbor list builds = 0 Dangerous builds = 0 390 -1573.03248493106 eV 2.34471465692784 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01