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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -29.628450 0.0000000) to (20.950478 29.628450 4.0319213) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6556617 3.8407249 4.0319213 Created 215 atoms using lattice units in orthogonal box = (0.0000000 -29.628450 0.0000000) to (20.950478 29.628450 4.0319213) create_atoms CPU = 0.001 seconds 215 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6556617 3.8407249 4.0319213 Created 217 atoms using lattice units in orthogonal box = (0.0000000 -29.628450 0.0000000) to (20.950478 29.628450 4.0319213) create_atoms CPU = 0.000 seconds 217 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 17 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 428 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_262519520678_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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1376.0158 0 -1376.0158 111462.74 82 0 -1819.7022 0 -1819.7022 -2024.7501 Loop time of 3.69712 on 1 procs for 82 steps with 428 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1376.01577706439 -1819.7007428284 -1819.70220666035 Force two-norm initial, final = 452.23955 0.15772384 Force max component initial, final = 142.13175 0.045701971 Final line search alpha, max atom move = 1.0000000 0.045701971 Iterations, force evaluations = 82 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.684 | 3.684 | 3.684 | 0.0 | 99.64 Neigh | 0.0037598 | 0.0037598 | 0.0037598 | 0.0 | 0.10 Comm | 0.0050618 | 0.0050618 | 0.0050618 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004318 | | | 0.12 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3444.00 ave 3444 max 3444 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: 54964.0 ave 54964 max 54964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54964 Ave neighs/atom = 128.42056 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -1819.7022 0 -1819.7022 -2024.7501 5005.4704 85 0 -1819.725 0 -1819.725 -512.51574 5000.8541 Loop time of 0.122742 on 1 procs for 3 steps with 428 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 = -1819.70220666035 -1819.72317727163 -1819.7249818321 Force two-norm initial, final = 18.194036 2.9063140 Force max component initial, final = 18.061749 2.0768441 Final line search alpha, max atom move = 0.00025521865 0.00053004935 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12204 | 0.12204 | 0.12204 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013842 | 0.00013842 | 0.00013842 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005673 | | | 0.46 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3096.00 ave 3096 max 3096 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: 55432.0 ave 55432 max 55432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55432 Ave neighs/atom = 129.51402 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1819.725 0 -1819.725 -512.51574 Loop time of 1.975e-06 on 1 procs for 0 steps with 428 atoms 151.9% 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 | | 1.975e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3096.00 ave 3096 max 3096 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: 55484.0 ave 55484 max 55484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55484 Ave neighs/atom = 129.63551 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.592 | 4.592 | 4.592 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 -1819.725 -1819.725 20.947408 59.344658 4.0228353 -512.51574 -512.51574 -665.28301 -299.24743 -573.01676 2.3032771 431.73168 Loop time of 1.962e-06 on 1 procs for 0 steps with 428 atoms 152.9% 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 | | 1.962e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3096.00 ave 3096 max 3096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27742.0 ave 27742 max 27742 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55484.0 ave 55484 max 55484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55484 Ave neighs/atom = 129.63551 Neighbor list builds = 0 Dangerous builds = 0 428 -1819.7249818321 eV 2.30327712268865 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04