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 -59.653887 0.0000000) to (48.707195 59.653887 9.8739816) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0049966 5.7202357 6.5826544 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -59.653887 0.0000000) to (48.707195 59.653887 9.8739816) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0049966 5.7202357 6.5826544 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -59.653887 0.0000000) to (48.707195 59.653887 9.8739816) create_atoms CPU = 0.002 seconds 1759 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 = 13 32 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3510 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 = 13 32 3 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) = 6.538 | 6.538 | 6.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11470.04 0 -11470.04 12031.946 79 0 -11761.518 0 -11761.518 4616.2743 Loop time of 2.71353 on 1 procs for 79 steps with 3510 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 = -11470.039899682 -11761.5075855038 -11761.5182517642 Force two-norm initial, final = 83.015483 0.29821614 Force max component initial, final = 6.8798024 0.089516090 Final line search alpha, max atom move = 1.0000000 0.089516090 Iterations, force evaluations = 79 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6148 | 2.6148 | 2.6148 | 0.0 | 96.36 Neigh | 0.059948 | 0.059948 | 0.059948 | 0.0 | 2.21 Comm | 0.015334 | 0.015334 | 0.015334 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02344 | | | 0.86 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9920.00 ave 9920 max 9920 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: 461278.0 ave 461278 max 461278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461278 Ave neighs/atom = 131.41823 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 32 3 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.538 | 6.538 | 6.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -11761.518 0 -11761.518 4616.2743 57379.158 89 0 -11762.807 0 -11762.807 31.186736 57727.856 Loop time of 0.260024 on 1 procs for 10 steps with 3510 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11761.5182517641 -11762.8072092349 -11762.8073242926 Force two-norm initial, final = 340.50744 2.2163224 Force max component initial, final = 315.12824 1.5659219 Final line search alpha, max atom move = 0.00041529704 0.00065032272 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22123 | 0.22123 | 0.22123 | 0.0 | 85.08 Neigh | 0.0299 | 0.0299 | 0.0299 | 0.0 | 11.50 Comm | 0.0013683 | 0.0013683 | 0.0013683 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007527 | | | 2.89 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9915.00 ave 9915 max 9915 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: 461610.0 ave 461610 max 461610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461610 Ave neighs/atom = 131.51282 Neighbor list builds = 1 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 = 13 32 3 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) = 6.676 | 6.676 | 6.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11762.807 0 -11762.807 31.186736 Loop time of 2.51e-06 on 1 procs for 0 steps with 3510 atoms 159.4% 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 | | 2.51e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9915.00 ave 9915 max 9915 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: 461612.0 ave 461612 max 461612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461612 Ave neighs/atom = 131.51339 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 = 13 32 3 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) = 6.676 | 6.676 | 6.676 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 -11762.807 -11762.807 48.647706 120.38423 9.8571973 31.186736 31.186736 15.220877 43.852655 34.486675 2.5794796 2339.3726 Loop time of 2.623e-06 on 1 procs for 0 steps with 3510 atoms 305.0% 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 | | 2.623e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9915.00 ave 9915 max 9915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230806.0 ave 230806 max 230806 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 461612.0 ave 461612 max 461612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461612 Ave neighs/atom = 131.51339 Neighbor list builds = 0 Dangerous builds = 0 3510 -11762.8073242926 eV 2.57947958621231 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03