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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -32.919740 0.0000000) to (19.004441 32.919740 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0011686 4.6198817 5.3397869 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.919740 0.0000000) to (19.004441 32.919740 5.3397869) create_atoms CPU = 0.001 seconds 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0011686 4.6198817 5.3397869 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.919740 0.0000000) to (19.004441 32.919740 5.3397869) create_atoms CPU = 0.000 seconds 230 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 456 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.843 | 4.843 | 4.843 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2748.7806 0 -2748.7806 118643.88 135 0 -2955.929 0 -2955.929 7764.9804 Loop time of 30.4307 on 1 procs for 135 steps with 456 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2748.78055176517 -2955.92616095279 -2955.92901046367 Force two-norm initial, final = 344.16898 0.25957218 Force max component initial, final = 81.199755 0.055691799 Final line search alpha, max atom move = 1.0000000 0.055691799 Iterations, force evaluations = 135 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.387 | 30.387 | 30.387 | 0.0 | 99.86 Neigh | 0.031787 | 0.031787 | 0.031787 | 0.0 | 0.10 Comm | 0.0064629 | 0.0064629 | 0.0064629 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00587 | | | 0.02 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2813.00 ave 2813 max 2813 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: 34592.0 ave 34592 max 34592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34592 Ave neighs/atom = 75.859649 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.843 | 4.843 | 4.843 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -2955.929 0 -2955.929 7764.9804 6681.3682 142 0 -2956.2401 0 -2956.2401 3890.5985 6692.5734 Loop time of 1.17332 on 1 procs for 7 steps with 456 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 = -2955.92901046367 -2956.23928714345 -2956.24008561512 Force two-norm initial, final = 93.787499 5.7237613 Force max component initial, final = 88.259737 4.2784033 Final line search alpha, max atom move = 0.014255811 0.060992107 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1722 | 1.1722 | 1.1722 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021927 | 0.00021927 | 0.00021927 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000935 | | | 0.08 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2813.00 ave 2813 max 2813 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: 34322.0 ave 34322 max 34322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34322 Ave neighs/atom = 75.267544 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.981 | 4.981 | 4.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2956.2401 0 -2956.2401 3890.5985 Loop time of 1.739e-06 on 1 procs for 0 steps with 456 atoms 115.0% 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 | | 1.739e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2809.00 ave 2809 max 2809 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: 34444.0 ave 34444 max 34444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34444 Ave neighs/atom = 75.535088 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.981 | 4.981 | 4.981 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 -2956.2401 -2956.2401 18.93048 65.83948 5.3696395 3890.5985 3890.5985 890.02146 9751.8147 1029.9595 2.5351514 1030.0668 Loop time of 1.586e-06 on 1 procs for 0 steps with 456 atoms 126.1% 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 | | 1.586e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2809.00 ave 2809 max 2809 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17222.0 ave 17222 max 17222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34444.0 ave 34444 max 34444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34444 Ave neighs/atom = 75.535088 Neighbor list builds = 0 Dangerous builds = 0 456 -2956.24008561512 eV 2.53515135216964 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32