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 = 3.6800447 3.6800447 3.6800447 Created orthogonal box = (0.0000000 -73.784667 0.0000000) to (42.599597 73.784667 6.3740244) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7223340 5.8734063 6.3740244 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -73.784667 0.0000000) to (42.599597 73.784667 6.3740244) create_atoms CPU = 0.010 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7223340 5.8734063 6.3740244 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -73.784667 0.0000000) to (42.599597 73.784667 6.3740244) create_atoms CPU = 0.009 seconds 1610 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 15 52 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3210 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.362 | 5.362 | 5.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13399.286 0 -13399.286 8515.3735 106 0 -13641.471 0 -13641.471 -7178.8763 Loop time of 3.35217 on 1 procs for 106 steps with 3210 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 = -13399.2862760988 -13641.4584745006 -13641.4714746378 Force two-norm initial, final = 161.11739 0.42614030 Force max component initial, final = 30.233158 0.11968328 Final line search alpha, max atom move = 0.92991539 0.11129533 Iterations, force evaluations = 106 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1148 | 3.1148 | 3.1148 | 0.0 | 92.92 Neigh | 0.13893 | 0.13893 | 0.13893 | 0.0 | 4.14 Comm | 0.038912 | 0.038912 | 0.038912 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05953 | | | 1.78 Nlocal: 3210.00 ave 3210 max 3210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8538.00 ave 8538 max 8538 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: 178340.0 ave 178340 max 178340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178340 Ave neighs/atom = 55.557632 Neighbor list builds = 4 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -13641.471 0 -13641.471 -7178.8763 40069.63 112 0 -13642.345 0 -13642.345 -12.881911 39872.565 Loop time of 0.141261 on 1 procs for 6 steps with 3210 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13641.4714746378 -13642.3403915992 -13642.3450276609 Force two-norm initial, final = 361.31838 1.0561198 Force max component initial, final = 327.47179 0.74923958 Final line search alpha, max atom move = 7.3368842e-05 5.4970840e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13239 | 0.13239 | 0.13239 | 0.0 | 93.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001485 | 0.001485 | 0.001485 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007387 | | | 5.23 Nlocal: 3210.00 ave 3210 max 3210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8545.00 ave 8545 max 8545 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: 178340.0 ave 178340 max 178340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178340 Ave neighs/atom = 55.557632 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.507 | 5.507 | 5.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13642.345 0 -13642.345 -12.881911 Loop time of 6.966e-06 on 1 procs for 0 steps with 3210 atoms 186.6% 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 | | 6.966e-06 | | |100.00 Nlocal: 3210.00 ave 3210 max 3210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8545.00 ave 8545 max 8545 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: 178664.0 ave 178664 max 178664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178664 Ave neighs/atom = 55.658567 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.507 | 5.507 | 5.507 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 -13642.345 -13642.345 42.64298 146.77902 6.3703406 -12.881911 -12.881911 -3.9084674 -4.6484002 -30.088866 2.2803694 1610.3543 Loop time of 6.926e-06 on 1 procs for 0 steps with 3210 atoms 288.8% 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 | | 6.926e-06 | | |100.00 Nlocal: 3210.00 ave 3210 max 3210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8545.00 ave 8545 max 8545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89332.0 ave 89332 max 89332 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 178664.0 ave 178664 max 178664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178664 Ave neighs/atom = 55.658567 Neighbor list builds = 0 Dangerous builds = 0 3210 -13642.3450276609 eV 2.28036940233973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04