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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -38.034547 0.0000000) to (23.289553 38.034547 7.0220643) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2344641 4.3217818 4.6813762 Created 534 atoms using lattice units in orthogonal box = (0.0000000 -38.034547 0.0000000) to (23.289553 38.034547 7.0220643) create_atoms CPU = 0.003 seconds 534 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2344641 4.3217818 4.6813762 Created 534 atoms using lattice units in orthogonal box = (0.0000000 -38.034547 0.0000000) to (23.289553 38.034547 7.0220643) create_atoms CPU = 0.002 seconds 534 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 20 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1044 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.042 | 5.042 | 5.042 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4394.4829 0 -4394.4829 13730.35 33 0 -4437.2363 0 -4437.2363 -10191.856 Loop time of 0.987302 on 1 procs for 33 steps with 1044 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 = -4394.48288365249 -4437.23226351209 -4437.23627600594 Force two-norm initial, final = 54.789962 0.25260928 Force max component initial, final = 8.1789435 0.021265679 Final line search alpha, max atom move = 1.0000000 0.021265679 Iterations, force evaluations = 33 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97122 | 0.97122 | 0.97122 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0081782 | 0.0081782 | 0.0081782 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007901 | | | 0.80 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5538.00 ave 5538 max 5538 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: 172872.0 ave 172872 max 172872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172872 Ave neighs/atom = 165.58621 Neighbor list builds = 0 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -4437.2363 0 -4437.2363 -10191.856 12440.396 37 0 -4437.4322 0 -4437.4322 -554.31018 12386.559 Loop time of 0.115585 on 1 procs for 4 steps with 1044 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 = -4437.23627600594 -4437.43191930452 -4437.43216895397 Force two-norm initial, final = 125.98434 0.37415825 Force max component initial, final = 97.702319 0.034874659 Final line search alpha, max atom move = 0.00036113845 1.2594581e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11183 | 0.11183 | 0.11183 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082247 | 0.00082247 | 0.00082247 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002934 | | | 2.54 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5478.00 ave 5478 max 5478 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: 173280.0 ave 173280 max 173280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173280 Ave neighs/atom = 165.97701 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4437.4322 0 -4437.4322 -554.31018 Loop time of 6.365e-06 on 1 procs for 0 steps with 1044 atoms 172.8% 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 | | 6.365e-06 | | |100.00 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5478.00 ave 5478 max 5478 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: 173340.0 ave 173340 max 173340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173340 Ave neighs/atom = 166.03448 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.179 | 5.179 | 5.179 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 -4437.4322 -4437.4322 23.228722 76.069094 7.0099856 -554.31018 -554.31018 4.2607117 -1662.688 -4.5032077 2.3186281 845.0424 Loop time of 7.137e-06 on 1 procs for 0 steps with 1044 atoms 238.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5478.00 ave 5478 max 5478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86670.0 ave 86670 max 86670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 173340.0 ave 173340 max 173340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173340 Ave neighs/atom = 166.03448 Neighbor list builds = 0 Dangerous builds = 0 1044 -4437.43216895397 eV 2.3186280847956 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01