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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -30.428231 0.0000000) to (14.344006 30.428231 3.4789324) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2188252 4.1764239 3.4789324 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -30.428231 0.0000000) to (14.344006 30.428231 3.4789324) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2188252 4.1764239 3.4789324 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -30.428231 0.0000000) to (14.344006 30.428231 3.4789324) create_atoms CPU = 0.001 seconds 206 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 17 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_677328661525_000#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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.892 | 4.892 | 4.892 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1745.4282 0 1745.4282 5991542.1 59 0 -5145.7756 0 -5145.7756 63211.131 Loop time of 3.13229 on 1 procs for 59 steps with 408 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 1745.4281992369 -5145.77076916657 -5145.77555302943 Force two-norm initial, final = 36989.866 0.53862695 Force max component initial, final = 12403.870 0.066496677 Final line search alpha, max atom move = 0.72502268 0.048211600 Iterations, force evaluations = 59 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1093 | 3.1093 | 3.1093 | 0.0 | 99.27 Neigh | 0.013178 | 0.013178 | 0.013178 | 0.0 | 0.42 Comm | 0.0062698 | 0.0062698 | 0.0062698 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003493 | | | 0.11 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 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: 103844.0 ave 103844 max 103844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103844 Ave neighs/atom = 254.51961 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.892 | 4.892 | 4.892 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -5145.7756 0 -5145.7756 63211.131 3036.8486 68 0 -5147.0305 0 -5147.0305 580.31265 3063.0942 Loop time of 0.305592 on 1 procs for 9 steps with 408 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 = -5145.77555302937 -5147.02632919899 -5147.03049982173 Force two-norm initial, final = 271.95507 2.3026737 Force max component initial, final = 236.12771 1.3586132 Final line search alpha, max atom move = 9.0675121e-05 0.00012319242 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30333 | 0.30333 | 0.30333 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004395 | 0.0004395 | 0.0004395 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001825 | | | 0.60 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 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: 103800.0 ave 103800 max 103800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103800 Ave neighs/atom = 254.41176 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.030 | 5.030 | 5.030 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5147.0305 0 -5147.0305 580.31265 Loop time of 1.77e-06 on 1 procs for 0 steps with 408 atoms 169.5% 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 | | 1.77e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 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: 103488.0 ave 103488 max 103488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103488 Ave neighs/atom = 253.64706 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 4 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.030 | 5.030 | 5.030 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 -5147.0305 -5147.0305 14.404329 61.355569 3.4658784 580.31265 580.31265 713.62235 508.32974 518.98586 2.0182138 243.74274 Loop time of 1.586e-06 on 1 procs for 0 steps with 408 atoms 126.1% 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 | | 1.586e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51744.0 ave 51744 max 51744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103488.0 ave 103488 max 103488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103488 Ave neighs/atom = 253.64706 Neighbor list builds = 0 Dangerous builds = 0 408 -5147.03049982173 eV 2.01821383561205 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03