LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -38.5196 0) to (27.2349 38.5196 5.10157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.25586 6.08147 5.10157 Created 458 atoms create_atoms CPU = 0.000350952 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.25586 6.08147 5.10157 Created 458 atoms create_atoms CPU = 0.000244141 secs 458 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 13 1 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 896 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.651 | 6.651 | 6.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3103.2611 0 -3103.2611 2292.4674 46 0 -3142.0599 0 -3142.0599 -16557.831 Loop time of 1.20599 on 1 procs for 46 steps with 896 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3103.26108905 -3142.0569607 -3142.05989158 Force two-norm initial, final = 31.5487 0.222692 Force max component initial, final = 9.81636 0.0360849 Final line search alpha, max atom move = 1 0.0360849 Iterations, force evaluations = 46 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1838 | 1.1838 | 1.1838 | 0.0 | 98.16 Neigh | 0.012993 | 0.012993 | 0.012993 | 0.0 | 1.08 Comm | 0.0068204 | 0.0068204 | 0.0068204 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002423 | | | 0.20 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11948 ave 11948 max 11948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 557656 ave 557656 max 557656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557656 Ave neighs/atom = 622.384 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.652 | 6.652 | 6.652 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3142.0599 0 -3142.0599 -16557.831 10703.883 61 0 -3143.2331 0 -3143.2331 -2181.0974 10587.734 Loop time of 0.270307 on 1 procs for 15 steps with 896 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 = -3142.05989158 -3143.23304443 -3143.23311664 Force two-norm initial, final = 180.652 1.67474 Force max component initial, final = 176.507 1.12442 Final line search alpha, max atom move = 0.00469454 0.00527862 Iterations, force evaluations = 15 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26525 | 0.26525 | 0.26525 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013547 | 0.0013547 | 0.0013547 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003699 | | | 1.37 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11882 ave 11882 max 11882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 557512 ave 557512 max 557512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 557512 Ave neighs/atom = 622.223 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.79 | 6.79 | 6.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3143.2331 0 -3143.2331 -2181.0974 Loop time of 1.19209e-06 on 1 procs for 0 steps with 896 atoms 0.0% 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 | | 1.192e-06 | | |100.00 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11982 ave 11982 max 11982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 564764 ave 564764 max 564764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 564764 Ave neighs/atom = 630.317 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.79 | 6.79 | 6.79 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 -3143.2331 -3143.2331 26.856893 77.039189 5.1172371 -2181.0974 -2181.0974 155.97869 -6869.9444 170.67346 2.3306391 764.995 Loop time of 1.90735e-06 on 1 procs for 0 steps with 896 atoms 0.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11982 ave 11982 max 11982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 282382 ave 282382 max 282382 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 564764 ave 564764 max 564764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 564764 Ave neighs/atom = 630.317 Neighbor list builds = 0 Dangerous builds = 0 896 -3143.2331166439 eV 2.33063914009419 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01