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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -37.822774 0.0000000) to (13.372370 37.822774 4.0319213) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8626801 4.2980425 4.0319213 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -37.822774 0.0000000) to (13.372370 37.822774 4.0319213) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8626801 4.2980425 4.0319213 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.822774 0.0000000) to (13.372370 37.822774 4.0319213) create_atoms CPU = 0.000 seconds 178 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 ghost atom cutoff = 7 binsize = 3.5, bins = 4 22 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 350 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1235.1979 0 -1235.1979 152119.7 90 0 -1491.5073 0 -1491.5073 -201.48658 Loop time of 3.47271 on 1 procs for 90 steps with 350 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 = -1235.19791940961 -1491.50599262676 -1491.50731488172 Force two-norm initial, final = 600.98209 0.15716955 Force max component initial, final = 208.58500 0.047473423 Final line search alpha, max atom move = 1.0000000 0.047473423 Iterations, force evaluations = 90 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4573 | 3.4573 | 3.4573 | 0.0 | 99.56 Neigh | 0.0058007 | 0.0058007 | 0.0058007 | 0.0 | 0.17 Comm | 0.0055221 | 0.0055221 | 0.0055221 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004122 | | | 0.12 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3469.00 ave 3469 max 3469 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: 45392.0 ave 45392 max 45392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45392 Ave neighs/atom = 129.69143 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -1491.5073 0 -1491.5073 -201.48658 4078.5314 95 0 -1491.5717 0 -1491.5717 -3.1306017 4077.6594 Loop time of 0.150746 on 1 procs for 5 steps with 350 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 = -1491.50731488172 -1491.5714874875 -1491.57174468199 Force two-norm initial, final = 23.413872 0.28192395 Force max component initial, final = 17.581644 0.089060442 Final line search alpha, max atom move = 0.00087069384 7.7544378e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14962 | 0.14962 | 0.14962 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020058 | 0.00020058 | 0.00020058 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009291 | | | 0.62 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471.00 ave 3471 max 3471 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: 46160.0 ave 46160 max 46160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46160 Ave neighs/atom = 131.88571 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 ghost atom cutoff = 7 binsize = 3.5, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1491.5717 0 -1491.5717 -3.1306017 Loop time of 2.204e-06 on 1 procs for 0 steps with 350 atoms 181.5% 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 | | 2.204e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471.00 ave 3471 max 3471 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: 46060.0 ave 46060 max 46060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46060 Ave neighs/atom = 131.60000 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 ghost atom cutoff = 7 binsize = 3.5, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.590 | 4.590 | 4.590 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 -1491.5717 -1491.5717 13.356603 75.969759 4.0185943 -3.1306017 -3.1306017 17.5084 -21.812956 -5.0872488 2.2979745 271.13504 Loop time of 1.888e-06 on 1 procs for 0 steps with 350 atoms 158.9% 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 | | 1.888e-06 | | |100.00 Nlocal: 350.000 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471.00 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23030.0 ave 23030 max 23030 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46060.0 ave 46060 max 46060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46060 Ave neighs/atom = 131.60000 Neighbor list builds = 0 Dangerous builds = 0 350 -1491.57174468199 eV 2.29797453311425 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04