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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -42.924378 0.0000000) to (24.782401 42.924378 5.7360113) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3105145 5.1100450 5.7360113 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -42.924378 0.0000000) to (24.782401 42.924378 5.7360113) create_atoms CPU = 0.004 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3105145 5.1100450 5.7360113 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -42.924378 0.0000000) to (24.782401 42.924378 5.7360113) create_atoms CPU = 0.004 seconds 676 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 23 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1340 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4781.7368 0 -4781.7368 122711.7 149 0 -5193.4061 0 -5193.4061 121414.13 Loop time of 9.17831 on 1 procs for 149 steps with 1340 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 = -4781.73675577245 -5193.40109614996 -5193.40605336363 Force two-norm initial, final = 494.46985 0.39916267 Force max component initial, final = 82.172864 0.023108639 Final line search alpha, max atom move = 0.64520519 0.014909814 Iterations, force evaluations = 149 293 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0411 | 9.0411 | 9.0411 | 0.0 | 98.51 Neigh | 0.035637 | 0.035637 | 0.035637 | 0.0 | 0.39 Comm | 0.054679 | 0.054679 | 0.054679 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04688 | | | 0.51 Nlocal: 1340.00 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7610.00 ave 7610 max 7610 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: 261512.0 ave 261512 max 261512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261512 Ave neighs/atom = 195.15821 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 149 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.509 | 5.509 | 5.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 149 0 -5193.4061 0 -5193.4061 121414.13 12203.584 172 0 -5210.9559 0 -5210.9559 -261.23844 12666.304 Loop time of 0.838168 on 1 procs for 23 steps with 1340 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 = -5193.40605336366 -5210.95345573286 -5210.95593175322 Force two-norm initial, final = 1692.8934 7.9377130 Force max component initial, final = 1366.6301 5.5617164 Final line search alpha, max atom move = 0.00012011332 0.00066803621 Iterations, force evaluations = 23 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78065 | 0.78065 | 0.78065 | 0.0 | 93.14 Neigh | 0.035603 | 0.035603 | 0.035603 | 0.0 | 4.25 Comm | 0.0049353 | 0.0049353 | 0.0049353 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01698 | | | 2.03 Nlocal: 1340.00 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7800.00 ave 7800 max 7800 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: 259360.0 ave 259360 max 259360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259360 Ave neighs/atom = 193.55224 Neighbor list builds = 1 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.647 | 5.647 | 5.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5210.9559 0 -5210.9559 -261.23844 Loop time of 6.746e-06 on 1 procs for 0 steps with 1340 atoms 192.7% 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 | | 6.746e-06 | | |100.00 Nlocal: 1340.00 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7791.00 ave 7791 max 7791 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: 258088.0 ave 258088 max 258088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258088 Ave neighs/atom = 192.60299 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.647 | 5.647 | 5.647 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 -5210.9559 -5210.9559 25.004819 87.709405 5.7753727 -261.23844 -261.23844 -151.97886 -718.75597 87.019508 2.24371 1197.9431 Loop time of 6.465e-06 on 1 procs for 0 steps with 1340 atoms 293.9% 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 | | 6.465e-06 | | |100.00 Nlocal: 1340.00 ave 1340 max 1340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7791.00 ave 7791 max 7791 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129044.0 ave 129044 max 129044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258088.0 ave 258088 max 258088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258088 Ave neighs/atom = 192.60299 Neighbor list builds = 0 Dangerous builds = 0 1340 -5210.95593175322 eV 2.24371001642109 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12