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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -56.549827 0.0000000) to (28.273104 56.549827 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0984285 5.0984285 3.6200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.549827 0.0000000) to (28.273104 56.549827 3.6200000) create_atoms CPU = 0.003 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0984285 5.0984285 3.6200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.549827 0.0000000) to (28.273104 56.549827 3.6200000) create_atoms CPU = 0.002 seconds 490 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 968 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_313717476091_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3397.7986 0 -3397.7986 1333.5079 20 0 -3415.6527 0 -3415.6527 -6159.1918 Loop time of 1.5452 on 1 procs for 20 steps with 968 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 = -3397.79861152138 -3415.65262013687 -3415.6526512272 Force two-norm initial, final = 30.592789 1.4040656 Force max component initial, final = 9.5342876 0.53447963 Final line search alpha, max atom move = 0.45776344 0.24466524 Iterations, force evaluations = 20 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5352 | 1.5352 | 1.5352 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004919 | 0.004919 | 0.004919 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005051 | | | 0.33 Nlocal: 968.000 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5112.00 ave 5112 max 5112 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: 74796.0 ave 74796 max 74796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74796 Ave neighs/atom = 77.268595 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -3415.6527 0 -3415.6527 -6159.1918 11575.595 25 0 -3415.7609 0 -3415.7609 -421.79962 11526.654 Loop time of 0.270004 on 1 procs for 5 steps with 968 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 = -3415.6526512272 -3415.75904187929 -3415.76087280059 Force two-norm initial, final = 61.492991 3.5899126 Force max component initial, final = 51.241886 3.3351215 Final line search alpha, max atom move = 0.00013600393 0.00045358964 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26633 | 0.26633 | 0.26633 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077232 | 0.00077232 | 0.00077232 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002897 | | | 1.07 Nlocal: 968.000 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5124.00 ave 5124 max 5124 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: 74884.0 ave 74884 max 74884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74884 Ave neighs/atom = 77.359504 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3415.7609 0 -3415.7609 -421.79962 Loop time of 6.235e-06 on 1 procs for 0 steps with 968 atoms 192.5% 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 | | 6.235e-06 | | |100.00 Nlocal: 968.000 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5124.00 ave 5124 max 5124 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: 74892.0 ave 74892 max 74892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74892 Ave neighs/atom = 77.367769 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.722 | 4.722 | 4.722 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 -3415.7609 -3415.7609 28.272391 113.09965 3.6047857 -421.79962 -421.79962 463.56197 -1777.5732 48.612419 2.3718493 228.66902 Loop time of 6.785e-06 on 1 procs for 0 steps with 968 atoms 309.5% 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 | | 6.785e-06 | | |100.00 Nlocal: 968.000 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5124.00 ave 5124 max 5124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37446.0 ave 37446 max 37446 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74892.0 ave 74892 max 74892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74892 Ave neighs/atom = 77.367769 Neighbor list builds = 0 Dangerous builds = 0 968 -3415.76087280059 eV 2.37184930383995 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02