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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -61.787846 0.0000000) to (25.224783 61.787846 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0539478 5.3549467 5.8254140 Created 1196 atoms using lattice units in orthogonal box = (0.0000000 -61.787846 0.0000000) to (25.224783 61.787846 8.7381210) create_atoms CPU = 0.002 seconds 1196 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0539478 5.3549467 5.8254140 Created 1204 atoms using lattice units in orthogonal box = (0.0000000 -61.787846 0.0000000) to (25.224783 61.787846 8.7381210) create_atoms CPU = 0.002 seconds 1204 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 45 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2382 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_196726067688_000#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 45 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.107 | 5.107 | 5.107 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9956.9533 0 -9956.9533 4201.7337 209 0 -10058.043 0 -10058.043 34150.385 Loop time of 23.7594 on 1 procs for 209 steps with 2382 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 = -9956.9532907638 -10058.0342195464 -10058.0433485446 Force two-norm initial, final = 105.47210 0.55121264 Force max component initial, final = 18.645515 0.10783781 Final line search alpha, max atom move = 0.63590059 0.068574128 Iterations, force evaluations = 209 393 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.638 | 23.638 | 23.638 | 0.0 | 99.49 Neigh | 0.047539 | 0.047539 | 0.047539 | 0.0 | 0.20 Comm | 0.028218 | 0.028218 | 0.028218 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04603 | | | 0.19 Nlocal: 2382.00 ave 2382 max 2382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6177.00 ave 6177 max 6177 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: 138958.0 ave 138958 max 138958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138958 Ave neighs/atom = 58.336692 Neighbor list builds = 4 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 45 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 209 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.108 | 5.108 | 5.108 Mbytes Step Temp E_pair E_mol TotEng Press Volume 209 0 -10058.043 0 -10058.043 34150.385 27238.209 217 0 -10061.411 0 -10061.411 -24.742023 27525.936 Loop time of 0.643954 on 1 procs for 8 steps with 2382 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 = -10058.0433485446 -10061.4105947623 -10061.4111569665 Force two-norm initial, final = 1018.5346 2.4505055 Force max component initial, final = 706.39764 0.75975801 Final line search alpha, max atom move = 8.9298624e-05 6.7845345e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63946 | 0.63946 | 0.63946 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057475 | 0.00057475 | 0.00057475 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003919 | | | 0.61 Nlocal: 2382.00 ave 2382 max 2382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6211.00 ave 6211 max 6211 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: 140028.0 ave 140028 max 140028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140028 Ave neighs/atom = 58.785894 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 45 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.246 | 5.246 | 5.246 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10061.411 0 -10061.411 -24.742023 Loop time of 2.099e-06 on 1 procs for 0 steps with 2382 atoms 190.6% 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 | | 2.099e-06 | | |100.00 Nlocal: 2382.00 ave 2382 max 2382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6190.00 ave 6190 max 6190 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: 136518.0 ave 136518 max 136518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136518 Ave neighs/atom = 57.312343 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 45 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.246 | 5.246 | 5.246 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 -10061.411 -10061.411 25.248568 124.40976 8.7629614 -24.742023 -24.742023 -44.264226 -43.798828 13.836985 2.3383658 2148.6355 Loop time of 2.522e-06 on 1 procs for 0 steps with 2382 atoms 198.3% 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 | | 2.522e-06 | | |100.00 Nlocal: 2382.00 ave 2382 max 2382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6190.00 ave 6190 max 6190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68259.0 ave 68259 max 68259 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136518.0 ave 136518 max 136518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136518 Ave neighs/atom = 57.312343 Neighbor list builds = 0 Dangerous builds = 0 2382 -10061.4111569665 eV 2.33836581784311 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24