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 -43.633069 0.0000000) to (53.439378 43.633069 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1243239 5.3794195 5.8968992 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -43.633069 0.0000000) to (53.439378 43.633069 8.8453488) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1243239 5.3794195 5.8968992 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -43.633069 0.0000000) to (53.439378 43.633069 8.8453488) create_atoms CPU = 0.002 seconds 1755 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 = 17 27 3 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 3 atoms, new total = 3501 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_179420363944_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 = 17 27 3 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) = 6.067 | 6.067 | 6.067 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13818.037 0 -13818.037 58016.335 71 0 -14819.559 0 -14819.559 3844.0648 Loop time of 21.4548 on 1 procs for 71 steps with 3501 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13818.0374936767 -14819.5450833567 -14819.5593085812 Force two-norm initial, final = 855.64248 0.40469614 Force max component initial, final = 112.13708 0.076641408 Final line search alpha, max atom move = 1.0000000 0.076641408 Iterations, force evaluations = 71 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.363 | 21.363 | 21.363 | 0.0 | 99.57 Neigh | 0.053331 | 0.053331 | 0.053331 | 0.0 | 0.25 Comm | 0.014655 | 0.014655 | 0.014655 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02343 | | | 0.11 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8669.00 ave 8669 max 8669 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: 304728.0 ave 304728 max 304728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304728 Ave neighs/atom = 87.040274 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 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 : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -14819.559 0 -14819.559 3844.0648 41249.825 76 0 -14819.982 0 -14819.982 97.877303 41339.256 Loop time of 1.26652 on 1 procs for 5 steps with 3501 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 = -14819.5593085811 -14819.9799998853 -14819.9817278727 Force two-norm initial, final = 221.14320 7.7855835 Force max component initial, final = 205.40138 7.5273148 Final line search alpha, max atom move = 5.4546871e-05 0.00041059147 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2621 | 1.2621 | 1.2621 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056104 | 0.00056104 | 0.00056104 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003852 | | | 0.30 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8652.00 ave 8652 max 8652 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: 305612.0 ave 305612 max 305612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305612 Ave neighs/atom = 87.292773 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 = 17 27 3 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) = 6.205 | 6.205 | 6.205 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14819.982 0 -14819.982 97.877303 Loop time of 2.583e-06 on 1 procs for 0 steps with 3501 atoms 193.6% 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 | | 2.583e-06 | | |100.00 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8669.00 ave 8669 max 8669 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: 305450.0 ave 305450 max 305450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305450 Ave neighs/atom = 87.246501 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 = 17 27 3 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) = 6.205 | 6.205 | 6.205 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 -14819.982 -14819.982 53.47298 87.058017 8.8801336 97.877303 97.877303 291.91793 -51.702784 53.416763 2.33084 1687.0246 Loop time of 2.647e-06 on 1 procs for 0 steps with 3501 atoms 302.2% 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 | | 2.647e-06 | | |100.00 Nlocal: 3501.00 ave 3501 max 3501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8669.00 ave 8669 max 8669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152725.0 ave 152725 max 152725 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 305450.0 ave 305450 max 305450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305450 Ave neighs/atom = 87.246501 Neighbor list builds = 0 Dangerous builds = 0 3501 -14819.9817278727 eV 2.33084001454357 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23