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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -37.477796 0.0000000) to (26.500804 37.477796 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8890675 4.8582328 5.1000820 Created 431 atoms using lattice units in orthogonal box = (0.0000000 -37.477796 0.0000000) to (26.500804 37.477796 5.1000820) create_atoms CPU = 0.001 seconds 431 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8890675 4.8582328 5.1000820 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -37.477796 0.0000000) to (26.500804 37.477796 5.1000820) create_atoms CPU = 0.001 seconds 439 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 864 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.635 | 6.635 | 6.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3467.458 0 -3467.458 38716.616 88 0 -3607.8579 0 -3607.8579 8183.6698 Loop time of 4.48733 on 1 procs for 88 steps with 864 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 = -3467.45802988359 -3607.85450859003 -3607.85791343611 Force two-norm initial, final = 174.60007 0.26030152 Force max component initial, final = 27.602242 0.039410951 Final line search alpha, max atom move = 1.0000000 0.039410951 Iterations, force evaluations = 88 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3976 | 4.3976 | 4.3976 | 0.0 | 98.00 Neigh | 0.053025 | 0.053025 | 0.053025 | 0.0 | 1.18 Comm | 0.024849 | 0.024849 | 0.024849 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01184 | | | 0.26 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11223.0 ave 11223 max 11223 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: 531856.0 ave 531856 max 531856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 531856 Ave neighs/atom = 615.57407 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.631 | 6.631 | 6.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -3607.8579 0 -3607.8579 8183.6698 10130.718 91 0 -3607.9828 0 -3607.9828 -2.0137814 10178.866 Loop time of 0.174309 on 1 procs for 3 steps with 864 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 = -3607.85791343611 -3607.98172173484 -3607.98283791872 Force two-norm initial, final = 89.847654 0.63811889 Force max component initial, final = 56.727309 0.44916068 Final line search alpha, max atom move = 0.00030468621 0.00013685306 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17141 | 0.17141 | 0.17141 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058483 | 0.00058483 | 0.00058483 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002313 | | | 1.33 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11126.0 ave 11126 max 11126 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: 533684.0 ave 533684 max 533684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533684 Ave neighs/atom = 617.68981 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.769 | 6.769 | 6.769 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3607.9828 0 -3607.9828 -2.0137814 Loop time of 2.222e-06 on 1 procs for 0 steps with 864 atoms 180.0% 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 | | 2.222e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11126.0 ave 11126 max 11126 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: 529612.0 ave 529612 max 529612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 529612 Ave neighs/atom = 612.97685 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.769 | 6.769 | 6.769 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 -3607.9828 -3607.9828 26.536627 75.123501 5.1059655 -2.0137814 -2.0137814 -70.794473 7.471731 57.281398 2.3679712 605.86201 Loop time of 2.585e-06 on 1 procs for 0 steps with 864 atoms 270.8% 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 | | 2.585e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11126.0 ave 11126 max 11126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 264806.0 ave 264806 max 264806 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 529612.0 ave 529612 max 529612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 529612 Ave neighs/atom = 612.97685 Neighbor list builds = 0 Dangerous builds = 0 864 -3607.98283791872 eV 2.3679712073726 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05