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 = 3.5181211 3.5181211 3.5181211 Created orthogonal box = (0.0000000 -40.420134 0.0000000) to (28.581351 40.420134 4.9753746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0627108 5.5118365 4.9753746 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.420134 0.0000000) to (28.581351 40.420134 4.9753746) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0627108 5.5118365 4.9753746 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.420134 0.0000000) to (28.581351 40.420134 4.9753746) create_atoms CPU = 0.002 seconds 532 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 17 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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_149104665840_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.848 | 5.848 | 5.848 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4172.2545 0 -4172.2545 91864.103 75 0 -4579.7075 0 -4579.7075 -4980.7757 Loop time of 2.73212 on 1 procs for 75 steps with 1048 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 = -4172.25451379491 -4579.70376722745 -4579.70750176201 Force two-norm initial, final = 721.00131 0.18924315 Force max component initial, final = 175.25844 0.019030826 Final line search alpha, max atom move = 1.0000000 0.019030826 Iterations, force evaluations = 75 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6722 | 2.6722 | 2.6722 | 0.0 | 97.81 Neigh | 0.039953 | 0.039953 | 0.039953 | 0.0 | 1.46 Comm | 0.01159 | 0.01159 | 0.01159 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008359 | | | 0.31 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9267.00 ave 9267 max 9267 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: 341152.0 ave 341152 max 341152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341152 Ave neighs/atom = 325.52672 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.848 | 5.848 | 5.848 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4579.7075 0 -4579.7075 -4980.7757 11495.723 79 0 -4579.8467 0 -4579.8467 30.448678 11460.259 Loop time of 0.150922 on 1 procs for 4 steps with 1048 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4579.70750176195 -4579.84645593452 -4579.84673539624 Force two-norm initial, final = 81.714116 1.1029759 Force max component initial, final = 59.666891 0.99934544 Final line search alpha, max atom move = 0.00026017732 0.00026000702 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14734 | 0.14734 | 0.14734 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053466 | 0.00053466 | 0.00053466 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003043 | | | 2.02 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9275.00 ave 9275 max 9275 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: 341264.0 ave 341264 max 341264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341264 Ave neighs/atom = 325.63359 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.986 | 5.986 | 5.986 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4579.8467 0 -4579.8467 30.448678 Loop time of 2.154e-06 on 1 procs for 0 steps with 1048 atoms 139.3% 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 | | 2.154e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9275.00 ave 9275 max 9275 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: 343000.0 ave 343000 max 343000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343000 Ave neighs/atom = 327.29008 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.986 | 5.986 | 5.986 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 -4579.8467 -4579.8467 28.625893 80.647965 4.9641165 30.448678 30.448678 9.0157313 -57.064872 139.39518 2.2798852 508.80341 Loop time of 2.056e-06 on 1 procs for 0 steps with 1048 atoms 194.6% 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 | | 2.056e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9275.00 ave 9275 max 9275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171500.0 ave 171500 max 171500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 343000.0 ave 343000 max 343000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343000 Ave neighs/atom = 327.29008 Neighbor list builds = 0 Dangerous builds = 0 1048 -4579.84673539624 eV 2.27988523887038 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03