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 = 2.6534432 2.6534432 2.6534432 Created orthogonal box = (0.0000000 -48.927075 0.0000000) to (24.463538 48.927075 2.6534432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7414822 3.7414822 2.6534432 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -48.927075 0.0000000) to (24.463538 48.927075 2.6534432) create_atoms CPU = 0.001 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7414822 3.7414822 2.6534432 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -48.927075 0.0000000) to (24.463538 48.927075 2.6534432) create_atoms CPU = 0.000 seconds 341 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 = 7 26 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 1 atoms, new total = 680 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_201919462778_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 26 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) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2793.8417 0 -2793.8417 1275332.9 57 0 -5675.2706 0 -5675.2706 39044.142 Loop time of 2.80865 on 1 procs for 57 steps with 680 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2793.84173179321 -5675.26677993278 -5675.27062166765 Force two-norm initial, final = 13792.095 0.40607989 Force max component initial, final = 6026.9194 0.045632231 Final line search alpha, max atom move = 1.0000000 0.045632231 Iterations, force evaluations = 57 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7884 | 2.7884 | 2.7884 | 0.0 | 99.28 Neigh | 0.00785 | 0.00785 | 0.00785 | 0.0 | 0.28 Comm | 0.0075454 | 0.0075454 | 0.0075454 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004885 | | | 0.17 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7880.00 ave 7880 max 7880 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: 120820.0 ave 120820 max 120820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120820 Ave neighs/atom = 177.67647 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 26 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -5675.2706 0 -5675.2706 39044.142 6351.9681 66 0 -5676.4417 0 -5676.4417 57.068471 6388.4499 Loop time of 0.335077 on 1 procs for 9 steps with 680 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 = -5675.27062166765 -5676.44148881287 -5676.44169137555 Force two-norm initial, final = 345.40467 1.2609506 Force max component initial, final = 332.49743 0.73835643 Final line search alpha, max atom move = 0.00023325490 0.00017222526 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33053 | 0.33053 | 0.33053 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080354 | 0.00080354 | 0.00080354 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003738 | | | 1.12 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8182.00 ave 8182 max 8182 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: 120944.0 ave 120944 max 120944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120944 Ave neighs/atom = 177.85882 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 = 7 27 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) = 5.094 | 5.094 | 5.094 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5676.4417 0 -5676.4417 57.068471 Loop time of 1.969e-06 on 1 procs for 0 steps with 680 atoms 203.1% 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 | | 1.969e-06 | | |100.00 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8182.00 ave 8182 max 8182 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: 120380.0 ave 120380 max 120380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120380 Ave neighs/atom = 177.02941 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 = 7 27 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) = 5.094 | 5.094 | 5.094 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 -5676.4417 -5676.4417 24.486476 98.58624 2.6463842 57.068471 57.068471 -80.336991 186.55976 64.982641 2.2039113 177.77415 Loop time of 2.84e-06 on 1 procs for 0 steps with 680 atoms 316.9% 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 | | 2.84e-06 | | |100.00 Nlocal: 680.000 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8182.00 ave 8182 max 8182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60190.0 ave 60190 max 60190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120380.0 ave 120380 max 120380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120380 Ave neighs/atom = 177.02941 Neighbor list builds = 0 Dangerous builds = 0 680 -5676.44169137556 eV 2.20391126941529 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03