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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -37.514823 0.0000000) to (17.684657 37.514823 4.0571386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7230857 4.6070836 4.0571386 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -37.514823 0.0000000) to (17.684657 37.514823 4.0571386) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7230857 4.6070836 4.0571386 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -37.514823 0.0000000) to (17.684657 37.514823 4.0571386) create_atoms CPU = 0.001 seconds 230 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 456 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 4.940 | 4.940 | 4.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1621.6603 0 -1621.6603 79648.548 60 0 -1869.0065 0 -1869.0065 8470.7612 Loop time of 0.793014 on 1 procs for 60 steps with 456 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 = -1621.66025832923 -1869.00499729329 -1869.00648597394 Force two-norm initial, final = 496.13623 0.15586180 Force max component initial, final = 170.70580 0.019879446 Final line search alpha, max atom move = 1.0000000 0.019879446 Iterations, force evaluations = 60 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7727 | 0.7727 | 0.7727 | 0.0 | 97.44 Neigh | 0.0095438 | 0.0095438 | 0.0095438 | 0.0 | 1.20 Comm | 0.0070885 | 0.0070885 | 0.0070885 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003685 | | | 0.46 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7705.00 ave 7705 max 7705 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: 177120.0 ave 177120 max 177120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177120 Ave neighs/atom = 388.42105 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.942 | 4.942 | 4.942 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1869.0065 0 -1869.0065 8470.7612 5383.3101 68 0 -1869.2341 0 -1869.2341 -530.35463 5411.7478 Loop time of 0.0706819 on 1 procs for 8 steps with 456 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 = -1869.00648597394 -1869.23293320425 -1869.23412738102 Force two-norm initial, final = 68.427681 3.9782448 Force max component initial, final = 52.714215 2.8915725 Final line search alpha, max atom move = 0.00023045271 0.00066637071 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067817 | 0.067817 | 0.067817 | 0.0 | 95.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056232 | 0.00056232 | 0.00056232 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002303 | | | 3.26 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7744.00 ave 7744 max 7744 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: 176520.0 ave 176520 max 176520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176520 Ave neighs/atom = 387.10526 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.080 | 5.080 | 5.080 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1869.2341 0 -1869.2341 -530.35463 Loop time of 1.617e-06 on 1 procs for 0 steps with 456 atoms 185.5% 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 | | 1.617e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7702.00 ave 7702 max 7702 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: 175760.0 ave 175760 max 175760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175760 Ave neighs/atom = 385.43860 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.080 | 5.080 | 5.080 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 -1869.2341 -1869.2341 17.812387 75.182701 4.0410804 -530.35463 -530.35463 60.335 -798.72192 -852.67697 2.3092327 477.05264 Loop time of 1.953e-06 on 1 procs for 0 steps with 456 atoms 256.0% 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 | | 1.953e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7702.00 ave 7702 max 7702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87880.0 ave 87880 max 87880 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175760.0 ave 175760 max 175760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175760 Ave neighs/atom = 385.43860 Neighbor list builds = 0 Dangerous builds = 0 456 -1869.23412738102 eV 2.30923267714604 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01