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 = 3.9946083 3.9946083 3.9946083 Created orthogonal box = (0.0000000 -49.410576 0.0000000) to (16.470192 49.410576 3.9946083) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8441742 4.8441742 3.9946083 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -49.410576 0.0000000) to (16.470192 49.410576 3.9946083) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8441742 4.8441742 3.9946083 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -49.410576 0.0000000) to (16.470192 49.410576 3.9946083) create_atoms CPU = 0.000 seconds 206 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 5 27 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 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_623376124862_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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1308.4048 0 -1308.4048 9281.8017 59 0 -1336.1956 0 -1336.1956 1721.3956 Loop time of 0.556442 on 1 procs for 59 steps with 408 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1308.40479373996 -1336.19489393854 -1336.19558809119 Force two-norm initial, final = 58.703853 0.047188397 Force max component initial, final = 20.224874 0.0074354113 Final line search alpha, max atom move = 1.0000000 0.0074354113 Iterations, force evaluations = 59 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54699 | 0.54699 | 0.54699 | 0.0 | 98.30 Neigh | 0.0031654 | 0.0031654 | 0.0031654 | 0.0 | 0.57 Comm | 0.0036099 | 0.0036099 | 0.0036099 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002674 | | | 0.48 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3651.00 ave 3651 max 3651 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: 53568.0 ave 53568 max 53568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53568 Ave neighs/atom = 131.29412 Neighbor list builds = 1 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -1336.1956 0 -1336.1956 1721.3956 6501.638 63 0 -1336.2149 0 -1336.2149 61.5555 6528.9764 Loop time of 0.0311982 on 1 procs for 4 steps with 408 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 = -1336.19558809119 -1336.21467321965 -1336.21492666028 Force two-norm initial, final = 12.554613 0.59613857 Force max component initial, final = 9.3824556 0.54903016 Final line search alpha, max atom move = 0.00085534282 0.00046960900 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030109 | 0.030109 | 0.030109 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019096 | 0.00019096 | 0.00019096 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008982 | | | 2.88 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3638.00 ave 3638 max 3638 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: 53704.0 ave 53704 max 53704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53704 Ave neighs/atom = 131.62745 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1336.2149 0 -1336.2149 61.5555 Loop time of 1.884e-06 on 1 procs for 0 steps with 408 atoms 159.2% 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 | | 1.884e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3638.00 ave 3638 max 3638 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: 53696.0 ave 53696 max 53696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53696 Ave neighs/atom = 131.60784 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 = 7.6000971 ghost atom cutoff = 7.6000971 binsize = 3.8000485, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600097095572612 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) = 4.600 | 4.600 | 4.600 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 -1336.2149 -1336.2149 16.466564 99.123026 4.0000697 61.5555 61.5555 -5.315871 135.14068 54.841693 2.5541127 231.33208 Loop time of 2.319e-06 on 1 procs for 0 steps with 408 atoms 215.6% 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 | | 2.319e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3638.00 ave 3638 max 3638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26848.0 ave 26848 max 26848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53696.0 ave 53696 max 53696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53696 Ave neighs/atom = 131.60784 Neighbor list builds = 0 Dangerous builds = 0 408 -1336.21492666028 eV 2.55411274485374 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00