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 = 3.6390299 3.6390299 3.6390299 Created orthogonal box = (0.0000000 -53.852724 0.0000000) to (43.970565 53.852724 8.9137664) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4210286 5.1639599 5.9425109 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -53.852724 0.0000000) to (43.970565 53.852724 8.9137664) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4210286 5.1639599 5.9425109 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -53.852724 0.0000000) to (43.970565 53.852724 8.9137664) create_atoms CPU = 0.002 seconds 1759 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3504 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_748636486270_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9172.5933 0 -9172.5933 166545.15 55 0 -11945.763 0 -11945.763 4801.2945 Loop time of 2.88671 on 1 procs for 55 steps with 3504 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 = -9172.59333110799 -11945.7525019688 -11945.7628929869 Force two-norm initial, final = 3181.7413 0.26004673 Force max component initial, final = 440.75525 0.033881520 Final line search alpha, max atom move = 1.0000000 0.033881520 Iterations, force evaluations = 55 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7771 | 2.7771 | 2.7771 | 0.0 | 96.20 Neigh | 0.080815 | 0.080815 | 0.080815 | 0.0 | 2.80 Comm | 0.011912 | 0.011912 | 0.011912 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01686 | | | 0.58 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12070.0 ave 12070 max 12070 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: 615736.0 ave 615736 max 615736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 615736 Ave neighs/atom = 175.72374 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.439 | 7.439 | 7.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -11945.763 0 -11945.763 4801.2945 42214.434 60 0 -11946.279 0 -11946.279 -396.97854 42366.697 Loop time of 0.215652 on 1 procs for 5 steps with 3504 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 = -11945.7628929868 -11946.2685021246 -11946.278525481 Force two-norm initial, final = 259.98405 19.413775 Force max component initial, final = 236.87269 15.686357 Final line search alpha, max atom move = 3.9705995e-05 0.00062284240 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2106 | 0.2106 | 0.2106 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069166 | 0.00069166 | 0.00069166 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004365 | | | 2.02 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12046.0 ave 12046 max 12046 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: 615014.0 ave 615014 max 615014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 615014 Ave neighs/atom = 175.51769 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.578 | 7.578 | 7.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11946.279 0 -11946.279 -396.97854 Loop time of 2.489e-06 on 1 procs for 0 steps with 3504 atoms 160.7% 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 | | 2.489e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12046.0 ave 12046 max 12046 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: 614312.0 ave 614312 max 614312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614312 Ave neighs/atom = 175.31735 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.578 | 7.578 | 7.578 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 -11946.279 -11946.279 43.962738 108.2127 8.9055687 -396.97854 -396.97854 -593.10355 -234.00456 -363.8275 2.2236464 1507.996 Loop time of 2.605e-06 on 1 procs for 0 steps with 3504 atoms 307.1% 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 | | 2.605e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12046.0 ave 12046 max 12046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307156.0 ave 307156 max 307156 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 614312.0 ave 614312 max 614312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 614312 Ave neighs/atom = 175.31735 Neighbor list builds = 0 Dangerous builds = 0 3504 -11946.278525481 eV 2.223646414661 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03