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 = 0.002 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 = 0.001 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 6 24 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 6.1 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.437 | 4.437 | 4.437 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1665.3332 0 -1665.3332 16739.55 35 0 -1688.3041 0 -1688.3041 352.84475 Loop time of 2.18249 on 1 procs for 35 steps with 399 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 = -1665.33319917445 -1688.302437844 -1688.30410832148 Force two-norm initial, final = 27.563818 0.13502175 Force max component initial, final = 9.4417285 0.051580916 Final line search alpha, max atom move = 1.0000000 0.051580916 Iterations, force evaluations = 35 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1688 | 2.1688 | 2.1688 | 0.0 | 99.37 Neigh | 0.005115 | 0.005115 | 0.005115 | 0.0 | 0.23 Comm | 0.0043548 | 0.0043548 | 0.0043548 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004201 | | | 0.19 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2729.00 ave 2729 max 2729 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: 31028.0 ave 31028 max 31028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31028 Ave neighs/atom = 77.764411 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1688.3041 0 -1688.3041 352.84475 4682.9762 48 0 -1688.5572 0 -1688.5572 -3573.9172 4694.0232 Loop time of 0.554749 on 1 procs for 13 steps with 399 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1688.30410832148 -1688.55565036094 -1688.55716800869 Force two-norm initial, final = 29.242592 0.47968953 Force max component initial, final = 22.684537 0.093303264 Final line search alpha, max atom move = 0.00054367535 5.0726685e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55037 | 0.55037 | 0.55037 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091107 | 0.00091107 | 0.00091107 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003468 | | | 0.63 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2721.00 ave 2721 max 2721 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: 31040.0 ave 31040 max 31040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31040 Ave neighs/atom = 77.794486 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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 -1688.5572 0 -1688.5572 -3573.9172 Loop time of 6.616e-06 on 1 procs for 0 steps with 399 atoms 151.1% 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 | | 6.616e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2749.00 ave 2749 max 2749 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: 31028.0 ave 31028 max 31028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31028 Ave neighs/atom = 77.764411 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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 -1688.5572 -1688.5572 17.832731 72.094079 3.6511341 -3573.9172 -3573.9172 19.040383 -10717.324 -23.468329 2.2777152 155.16944 Loop time of 6.816e-06 on 1 procs for 0 steps with 399 atoms 264.1% 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 | | 6.816e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2749.00 ave 2749 max 2749 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15514.0 ave 15514 max 15514 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31028.0 ave 31028 max 31028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31028 Ave neighs/atom = 77.764411 Neighbor list builds = 0 Dangerous builds = 0 399 -1688.55716800869 eV 2.27771524471242 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03