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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -36.047039 0.0000000) to (18.021718 36.047039 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0460809 5.0460809 3.6043435 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.047039 0.0000000) to (18.021718 36.047039 3.6043435) create_atoms CPU = 0.001 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0460809 5.0460809 3.6043435 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.047039 0.0000000) to (18.021718 36.047039 3.6043435) create_atoms CPU = 0.000 seconds 201 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 = 7 25 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 399 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_492310898779_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 = 7 25 2 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) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1665.2923 0 -1665.2923 17031.477 36 0 -1688.2981 0 -1688.2981 278.39022 Loop time of 0.880637 on 1 procs for 36 steps with 399 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 = -1665.29226601393 -1688.29644035531 -1688.29812125964 Force two-norm initial, final = 27.551991 0.14014874 Force max component initial, final = 9.4420779 0.039149895 Final line search alpha, max atom move = 1.0000000 0.039149895 Iterations, force evaluations = 36 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87545 | 0.87545 | 0.87545 | 0.0 | 99.41 Neigh | 0.0020027 | 0.0020027 | 0.0020027 | 0.0 | 0.23 Comm | 0.0016397 | 0.0016397 | 0.0016397 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001545 | | | 0.18 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2701.00 ave 2701 max 2701 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: 30828.0 ave 30828 max 30828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30828 Ave neighs/atom = 77.263158 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 = 7 25 2 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1688.2981 0 -1688.2981 278.39022 4682.9762 49 0 -1688.5514 0 -1688.5514 -3570.3889 4693.8343 Loop time of 0.23542 on 1 procs for 13 steps with 399 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 = -1688.29812125964 -1688.54992010148 -1688.55139181658 Force two-norm initial, final = 29.262778 0.48604268 Force max component initial, final = 22.471163 0.087988753 Final line search alpha, max atom move = 0.00055298677 4.8656617e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23324 | 0.23324 | 0.23324 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036377 | 0.00036377 | 0.00036377 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001821 | | | 0.77 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2701.00 ave 2701 max 2701 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: 30840.0 ave 30840 max 30840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30840 Ave neighs/atom = 77.293233 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 = 6 25 2 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) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1688.5514 0 -1688.5514 -3570.3889 Loop time of 1.832e-06 on 1 procs for 0 steps with 399 atoms 163.8% 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 | | 1.832e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2713.00 ave 2713 max 2713 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: 30870.0 ave 30870 max 30870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30870 Ave neighs/atom = 77.368421 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 = 6 25 2 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) = 4.576 | 4.576 | 4.576 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 -1688.5514 -1688.5514 17.832274 72.094079 3.6510807 -3570.3889 -3570.3889 18.933787 -10704.937 -25.163199 2.2833229 153.98099 Loop time of 1.665e-06 on 1 procs for 0 steps with 399 atoms 180.2% 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 | | 1.665e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2713.00 ave 2713 max 2713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15435.0 ave 15435 max 15435 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30870.0 ave 30870 max 30870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30870 Ave neighs/atom = 77.368421 Neighbor list builds = 0 Dangerous builds = 0 399 -1688.55139181658 eV 2.28332288117356 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01