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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -46.244625 0.0000000) to (32.699888 46.244625 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5829077 6.2035472 5.1068645 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.244625 0.0000000) to (32.699888 46.244625 5.1068645) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5829077 6.2035472 5.1068645 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.244625 0.0000000) to (32.699888 46.244625 5.1068645) create_atoms CPU = 0.001 seconds 660 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1316 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5221.1245 0 -5221.1245 69037.72 790 0 -5622.8272 0 -5622.8272 4973.9886 Loop time of 150.435 on 1 procs for 790 steps with 1316 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 = -5221.12453500886 -5622.82205700408 -5622.82719381025 Force two-norm initial, final = 335.94929 0.21236920 Force max component initial, final = 57.811595 0.012970733 Final line search alpha, max atom move = 1.0000000 0.012970733 Iterations, force evaluations = 790 1504 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 149.97 | 149.97 | 149.97 | 0.0 | 99.69 Neigh | 0.22707 | 0.22707 | 0.22707 | 0.0 | 0.15 Comm | 0.12456 | 0.12456 | 0.12456 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1128 | | | 0.08 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6130.00 ave 6130 max 6130 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: 139786.0 ave 139786 max 139786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139786 Ave neighs/atom = 106.22036 Neighbor list builds = 25 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 790 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.050 | 5.050 | 5.050 Mbytes Step Temp E_pair E_mol TotEng Press Volume 790 0 -5622.8272 0 -5622.8272 4973.9886 15445.14 820 0 -5637.4611 0 -5637.4611 -1.3255063 15460.415 Loop time of 3.50284 on 1 procs for 30 steps with 1316 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 = -5622.82719381026 -5637.46071263679 -5637.46109932296 Force two-norm initial, final = 785.12371 0.20875548 Force max component initial, final = 586.97472 0.020559243 Final line search alpha, max atom move = 0.00031665977 6.5102850e-06 Iterations, force evaluations = 30 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4825 | 3.4825 | 3.4825 | 0.0 | 99.42 Neigh | 0.0087946 | 0.0087946 | 0.0087946 | 0.0 | 0.25 Comm | 0.0018636 | 0.0018636 | 0.0018636 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009733 | | | 0.28 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6128.00 ave 6128 max 6128 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: 137410.0 ave 137410 max 137410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137410 Ave neighs/atom = 104.41489 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.188 | 5.188 | 5.188 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5637.4611 0 -5637.4611 -1.3255063 Loop time of 2.43e-06 on 1 procs for 0 steps with 1316 atoms 205.8% 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 | | 2.43e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6184.00 ave 6184 max 6184 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: 136864.0 ave 136864 max 136864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136864 Ave neighs/atom = 104.00000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.188 | 5.188 | 5.188 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 -5637.4611 -5637.4611 33.05188 94.309628 4.9598545 -1.3255063 -1.3255063 -1.1692608 -0.73801791 -2.0692403 2.462777 0.095807655 Loop time of 2.226e-06 on 1 procs for 0 steps with 1316 atoms 224.6% 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 | | 2.226e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6184.00 ave 6184 max 6184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68432.0 ave 68432 max 68432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136864.0 ave 136864 max 136864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136864 Ave neighs/atom = 104.00000 Neighbor list builds = 0 Dangerous builds = 0 1316 -5637.46109932296 eV 2.4627770337282 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:34