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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -58.824321 0.0000000) to (12.007464 58.824321 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4579383 5.3476656 5.9120667 Created 527 atoms using lattice units in orthogonal box = (0.0000000 -58.824321 0.0000000) to (12.007464 58.824321 8.8681001) create_atoms CPU = 0.001 seconds 527 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4579383 5.3476656 5.9120667 Created 529 atoms using lattice units in orthogonal box = (0.0000000 -58.824321 0.0000000) to (12.007464 58.824321 8.8681001) create_atoms CPU = 0.001 seconds 529 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 40 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1056 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_390178379548_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3600.5473 0 -3600.5473 34751.057 80 0 -3725.9845 0 -3725.9845 5436.128 Loop time of 2.84458 on 1 procs for 80 steps with 1056 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 = -3600.54731553731 -3725.9812528163 -3725.98453365856 Force two-norm initial, final = 189.26573 0.19876972 Force max component initial, final = 47.844505 0.068460593 Final line search alpha, max atom move = 1.0000000 0.068460593 Iterations, force evaluations = 80 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8211 | 2.8211 | 2.8211 | 0.0 | 99.18 Neigh | 0.0065879 | 0.0065879 | 0.0065879 | 0.0 | 0.23 Comm | 0.0076872 | 0.0076872 | 0.0076872 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009175 | | | 0.32 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 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: 81810.0 ave 81810 max 81810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81810 Ave neighs/atom = 77.471591 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -3725.9845 0 -3725.9845 5436.128 12527.627 86 0 -3726.1745 0 -3726.1745 -182.84388 12576.631 Loop time of 0.149164 on 1 procs for 6 steps with 1056 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3725.98453365856 -3726.17397803682 -3726.17445407652 Force two-norm initial, final = 85.960089 2.7688231 Force max component initial, final = 78.435842 2.3609854 Final line search alpha, max atom move = 0.00037761098 0.00089153400 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14694 | 0.14694 | 0.14694 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032526 | 0.00032526 | 0.00032526 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001894 | | | 1.27 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 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: 81786.0 ave 81786 max 81786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81786 Ave neighs/atom = 77.448864 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.705 | 4.705 | 4.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3726.1745 0 -3726.1745 -182.84388 Loop time of 1.988e-06 on 1 procs for 0 steps with 1056 atoms 201.2% 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 | | 1.988e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 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: 81748.0 ave 81748 max 81748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81748 Ave neighs/atom = 77.412879 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.705 | 4.705 | 4.705 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 -3726.1745 -3726.1745 11.989295 118.26149 8.8700749 -182.84388 -182.84388 -300.31824 -91.88274 -156.33065 2.2633926 438.60905 Loop time of 3.021e-06 on 1 procs for 0 steps with 1056 atoms 198.6% 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 | | 3.021e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40874.0 ave 40874 max 40874 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81748.0 ave 81748 max 81748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81748 Ave neighs/atom = 77.412879 Neighbor list builds = 0 Dangerous builds = 0 1056 -3726.17445407653 eV 2.2633925662946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03