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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -46.882140 0.0000000) to (33.150679 46.882140 5.7275650) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4322214 6.9973344 5.7275650 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -46.882140 0.0000000) to (33.150679 46.882140 5.7275650) create_atoms CPU = 0.006 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4322214 6.9973344 5.7275650 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.882140 0.0000000) to (33.150679 46.882140 5.7275650) create_atoms CPU = 0.005 seconds 538 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1068 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.000 | 5.000 | 5.000 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3493.3855 0 -3493.3855 12198.725 104 0 -3583.9772 0 -3583.9772 2260.9735 Loop time of 2.58205 on 1 procs for 104 steps with 1068 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 = -3493.38546156078 -3583.97393070289 -3583.97718067089 Force two-norm initial, final = 95.723876 0.12271387 Force max component initial, final = 25.671787 0.031239897 Final line search alpha, max atom move = 1.0000000 0.031239897 Iterations, force evaluations = 104 197 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5106 | 2.5106 | 2.5106 | 0.0 | 97.23 Neigh | 0.018684 | 0.018684 | 0.018684 | 0.0 | 0.72 Comm | 0.026573 | 0.026573 | 0.026573 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02617 | | | 1.01 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5573.00 ave 5573 max 5573 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: 137976.0 ave 137976 max 137976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137976 Ave neighs/atom = 129.19101 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -3583.9772 0 -3583.9772 2260.9735 17803.274 110 0 -3584.106 0 -3584.106 73.616355 17854.86 Loop time of 0.104759 on 1 procs for 6 steps with 1068 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 = -3583.97718067089 -3584.10545990682 -3584.10601447075 Force two-norm initial, final = 55.694866 1.4502247 Force max component initial, final = 53.500898 1.0058518 Final line search alpha, max atom move = 0.00049952211 0.00050244521 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10029 | 0.10029 | 0.10029 | 0.0 | 95.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095574 | 0.00095574 | 0.00095574 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003513 | | | 3.35 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5239.00 ave 5239 max 5239 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: 138664.0 ave 138664 max 138664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138664 Ave neighs/atom = 129.83521 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3584.106 0 -3584.106 73.616355 Loop time of 6.725e-06 on 1 procs for 0 steps with 1068 atoms 163.6% 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 | | 6.725e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5232.00 ave 5232 max 5232 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: 138208.0 ave 138208 max 138208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138208 Ave neighs/atom = 129.40824 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.137 | 5.137 | 5.137 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 -3584.106 -3584.106 33.111884 94.25905 5.7207042 73.616355 73.616355 60.731404 90.73473 69.382932 2.6063807 675.083 Loop time of 6.746e-06 on 1 procs for 0 steps with 1068 atoms 281.6% 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 | | 6.746e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5232.00 ave 5232 max 5232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69104.0 ave 69104 max 69104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138208.0 ave 138208 max 138208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138208 Ave neighs/atom = 129.40824 Neighbor list builds = 0 Dangerous builds = 0 1068 -3584.10601447075 eV 2.60638071139283 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03