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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -51.622450 0.0000000) to (36.502584 51.622450 5.7007459) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2321486 6.9249628 5.7007459 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.622450 0.0000000) to (36.502584 51.622450 5.7007459) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2321486 6.9249628 5.7007459 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.622450 0.0000000) to (36.502584 51.622450 5.7007459) create_atoms CPU = 0.005 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.060 | 5.060 | 5.060 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4316.8838 0 -4316.8838 6820.0278 68 0 -4399.2212 0 -4399.2212 1990.4679 Loop time of 2.1136 on 1 procs for 68 steps with 1312 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 = -4316.88381114921 -4399.21775172296 -4399.2212369221 Force two-norm initial, final = 39.099378 0.13587956 Force max component initial, final = 6.0554867 0.0098476830 Final line search alpha, max atom move = 1.0000000 0.0098476830 Iterations, force evaluations = 68 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0496 | 2.0496 | 2.0496 | 0.0 | 96.97 Neigh | 0.02363 | 0.02363 | 0.02363 | 0.0 | 1.12 Comm | 0.020629 | 0.020629 | 0.020629 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0197 | | | 0.93 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6700.00 ave 6700 max 6700 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: 171416.0 ave 171416 max 171416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171416 Ave neighs/atom = 130.65244 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.060 | 5.060 | 5.060 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4399.2212 0 -4399.2212 1990.4679 21484.434 76 0 -4399.5375 0 -4399.5375 21.174762 21540.245 Loop time of 0.169015 on 1 procs for 8 steps with 1312 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 = -4399.22123692208 -4399.53730942093 -4399.53749923679 Force two-norm initial, final = 83.510696 0.55406455 Force max component initial, final = 80.890809 0.35625559 Final line search alpha, max atom move = 0.00069358274 0.00024709273 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16208 | 0.16208 | 0.16208 | 0.0 | 95.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014315 | 0.0014315 | 0.0014315 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005503 | | | 3.26 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6696.00 ave 6696 max 6696 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: 172744.0 ave 172744 max 172744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172744 Ave neighs/atom = 131.66463 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.198 | 5.198 | 5.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4399.5375 0 -4399.5375 21.174762 Loop time of 6.685e-06 on 1 procs for 0 steps with 1312 atoms 194.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6682.00 ave 6682 max 6682 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: 172608.0 ave 172608 max 172608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172608 Ave neighs/atom = 131.56098 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.198 | 5.198 | 5.198 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 -4399.5375 -4399.5375 36.34803 103.97998 5.6992807 21.174762 21.174762 18.17075 18.861839 26.491696 2.6762891 781.27088 Loop time of 7.137e-06 on 1 procs for 0 steps with 1312 atoms 224.2% 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 | | 7.137e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6682.00 ave 6682 max 6682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86304.0 ave 86304 max 86304 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 172608.0 ave 172608 max 172608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172608 Ave neighs/atom = 131.56098 Neighbor list builds = 0 Dangerous builds = 0 1312 -4399.53749923681 eV 2.67628911194018 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02