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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -47.920302 0.0000000) to (58.690144 47.920302 9.9204450) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074450 6.1611817 6.6136300 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -47.920302 0.0000000) to (58.690144 47.920302 9.9204450) create_atoms CPU = 0.008 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074450 6.1611817 6.6136300 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -47.920302 0.0000000) to (58.690144 47.920302 9.9204450) create_atoms CPU = 0.007 seconds 1685 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3346 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_651801486679_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.548 | 6.548 | 6.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11108.523 0 -11108.523 1673.8742 123 0 -11207.269 0 -11207.269 718.76375 Loop time of 10.9448 on 1 procs for 123 steps with 3346 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 = -11108.5232839779 -11207.2589244364 -11207.2686732171 Force two-norm initial, final = 33.888602 0.29165616 Force max component initial, final = 3.2207355 0.10002041 Final line search alpha, max atom move = 1.0000000 0.10002041 Iterations, force evaluations = 123 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.466 | 10.466 | 10.466 | 0.0 | 95.62 Neigh | 0.349 | 0.349 | 0.349 | 0.0 | 3.19 Comm | 0.054791 | 0.054791 | 0.054791 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07525 | | | 0.69 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9982.00 ave 9982 max 9982 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: 466678.0 ave 466678 max 466678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466678 Ave neighs/atom = 139.47340 Neighbor list builds = 5 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 123 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.547 | 6.547 | 6.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 123 0 -11207.269 0 -11207.269 718.76375 55801.499 127 0 -11207.446 0 -11207.446 -123.17293 55861.858 Loop time of 0.282009 on 1 procs for 4 steps with 3346 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11207.2686732171 -11207.444130042 -11207.4463045721 Force two-norm initial, final = 93.463032 7.9661703 Force max component initial, final = 88.787537 5.9199907 Final line search alpha, max atom move = 9.6760296e-05 0.00057282005 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27486 | 0.27486 | 0.27486 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013035 | 0.0013035 | 0.0013035 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005843 | | | 2.07 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9990.00 ave 9990 max 9990 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: 466760.0 ave 466760 max 466760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466760 Ave neighs/atom = 139.49791 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.685 | 6.685 | 6.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11207.446 0 -11207.446 -123.17293 Loop time of 6.444e-06 on 1 procs for 0 steps with 3346 atoms 201.7% 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 | | 6.444e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 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: 466678.0 ave 466678 max 466678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466678 Ave neighs/atom = 139.47340 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.685 | 6.685 | 6.685 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 -11207.446 -11207.446 58.675802 96.163481 9.9002501 -123.17293 -123.17293 -140.41601 -59.656906 -169.44588 2.574775 2315.9144 Loop time of 6.626e-06 on 1 procs for 0 steps with 3346 atoms 286.7% 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 | | 6.626e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233339.0 ave 233339 max 233339 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 466678.0 ave 466678 max 466678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466678 Ave neighs/atom = 139.47340 Neighbor list builds = 0 Dangerous builds = 0 3346 -11207.4463049208 eV 2.57477497262991 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12