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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -37.378067 0.0000000) to (37.378067 37.378067 3.5162328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9616903 4.9616903 3.5162328 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -37.378067 0.0000000) to (37.378067 37.378067 3.5162328) create_atoms CPU = 0.002 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9616903 4.9616903 3.5162328 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.378067 0.0000000) to (37.378067 37.378067 3.5162328) create_atoms CPU = 0.002 seconds 454 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 17 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.403 | 5.403 | 5.403 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3940.8915 0 -3940.8915 168930.13 77 0 -4406.4686 0 -4406.4686 8906.8966 Loop time of 4.81554 on 1 procs for 77 steps with 906 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 = -3940.89148672864 -4406.4648992789 -4406.46864933164 Force two-norm initial, final = 553.63340 0.20264143 Force max component initial, final = 91.392412 0.014409746 Final line search alpha, max atom move = 1.0000000 0.014409746 Iterations, force evaluations = 77 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7069 | 4.7069 | 4.7069 | 0.0 | 97.74 Neigh | 0.059732 | 0.059732 | 0.059732 | 0.0 | 1.24 Comm | 0.030007 | 0.030007 | 0.030007 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01895 | | | 0.39 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9018.00 ave 9018 max 9018 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: 239748.0 ave 239748 max 239748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239748 Ave neighs/atom = 264.62252 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.403 | 5.403 | 5.403 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -4406.4686 0 -4406.4686 8906.8966 9825.1977 83 0 -4406.7608 0 -4406.7608 -186.11989 9873.2418 Loop time of 0.364257 on 1 procs for 6 steps with 906 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4406.46864933164 -4406.75885688705 -4406.76084408623 Force two-norm initial, final = 116.37261 4.4455691 Force max component initial, final = 96.262593 4.3822388 Final line search alpha, max atom move = 0.00010462530 0.00045849307 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35611 | 0.35611 | 0.35611 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019686 | 0.0019686 | 0.0019686 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006182 | | | 1.70 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9018.00 ave 9018 max 9018 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: 238652.0 ave 238652 max 238652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238652 Ave neighs/atom = 263.41280 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.541 | 5.541 | 5.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4406.7608 0 -4406.7608 -186.11989 Loop time of 6.736e-06 on 1 procs for 0 steps with 906 atoms 178.1% 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 | | 6.736e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9000.00 ave 9000 max 9000 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: 236576.0 ave 236576 max 236576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236576 Ave neighs/atom = 261.12141 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.541 | 5.541 | 5.541 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 -4406.7608 -4406.7608 37.283772 75.057626 3.5281343 -186.11989 -186.11989 55.278372 -713.99408 100.35602 2.2400502 137.53279 Loop time of 8.57e-06 on 1 procs for 0 steps with 906 atoms 256.7% 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 | | 8.57e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9000.00 ave 9000 max 9000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118288.0 ave 118288 max 118288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 236576.0 ave 236576 max 236576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236576 Ave neighs/atom = 261.12141 Neighbor list builds = 0 Dangerous builds = 0 906 -4406.76084408623 eV 2.2400502080954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06