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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -43.942695 0.0000000) to (31.072178 43.942695 4.8825217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7541070 5.9675265 4.8825217 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -43.942695 0.0000000) to (31.072178 43.942695 4.8825217) create_atoms CPU = 0.006 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7541070 5.9675265 4.8825217 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -43.942695 0.0000000) to (31.072178 43.942695 4.8825217) create_atoms CPU = 0.006 seconds 650 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 23 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.487 | 5.487 | 5.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5699.6792 0 -5699.6792 47338.369 42 0 -5828.4081 0 -5828.4081 22567.183 Loop time of 2.2914 on 1 procs for 42 steps with 1298 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5699.67924019132 -5828.40255767398 -5828.40814938939 Force two-norm initial, final = 172.89467 0.25040221 Force max component initial, final = 43.842013 0.035266248 Final line search alpha, max atom move = 1.0000000 0.035266248 Iterations, force evaluations = 42 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2621 | 2.2621 | 2.2621 | 0.0 | 98.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.016324 | 0.016324 | 0.016324 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01299 | | | 0.57 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8545.00 ave 8545 max 8545 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: 260492.0 ave 260492 max 260492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260492 Ave neighs/atom = 200.68721 Neighbor list builds = 0 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.497 | 5.497 | 5.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -5828.4081 0 -5828.4081 22567.183 13333.144 48 0 -5829.16 0 -5829.16 -556.25873 13409.497 Loop time of 0.228975 on 1 procs for 6 steps with 1298 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5828.40814938937 -5829.15597008486 -5829.16001489486 Force two-norm initial, final = 340.14940 12.549114 Force max component initial, final = 267.61473 9.3816851 Final line search alpha, max atom move = 4.3459613e-05 0.00040772440 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22234 | 0.22234 | 0.22234 | 0.0 | 97.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015965 | 0.0015965 | 0.0015965 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005042 | | | 2.20 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9133.00 ave 9133 max 9133 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: 259416.0 ave 259416 max 259416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259416 Ave neighs/atom = 199.85824 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.635 | 5.635 | 5.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5829.16 0 -5829.16 -556.25873 Loop time of 6.605e-06 on 1 procs for 0 steps with 1298 atoms 227.1% 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 | | 6.605e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9133.00 ave 9133 max 9133 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: 259072.0 ave 259072 max 259072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259072 Ave neighs/atom = 199.59322 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.635 | 5.635 | 5.635 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 -5829.16 -5829.16 31.095582 88.354263 4.8807469 -556.25873 -556.25873 -922.80401 374.55096 -1120.5232 2.2773986 458.83615 Loop time of 6.415e-06 on 1 procs for 0 steps with 1298 atoms 265.0% 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 | | 6.415e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9133.00 ave 9133 max 9133 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129536.0 ave 129536 max 129536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 259072.0 ave 259072 max 259072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259072 Ave neighs/atom = 199.59322 Neighbor list builds = 0 Dangerous builds = 0 1298 -5829.16001489807 eV 2.27739859895392 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03