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 -39.0231 0) to (13.0065 39.0231 3.60735) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0025 5.0025 3.60735 Created 158 atoms create_atoms CPU = 0.000159979 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0025 5.0025 3.60735 Created 158 atoms create_atoms CPU = 4.91142e-05 secs 158 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 = 3 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 4 atoms, new total = 312 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 = 3 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) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1067.8872 0 -1067.8872 27262.157 27 0 -1095.0313 0 -1095.0313 6458.1033 Loop time of 0.231713 on 1 procs for 27 steps with 312 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1067.88722299 -1095.03022719 -1095.03126317 Force two-norm initial, final = 41.3081 0.131969 Force max component initial, final = 13.5455 0.0161318 Final line search alpha, max atom move = 1 0.0161318 Iterations, force evaluations = 27 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22868 | 0.22868 | 0.22868 | 0.0 | 98.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023642 | 0.0023642 | 0.0023642 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006659 | | | 0.29 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8440 ave 8440 max 8440 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: 195892 ave 195892 max 195892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195892 Ave neighs/atom = 627.859 Neighbor list builds = 0 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -1095.0313 0 -1095.0313 6458.1033 3661.8502 36 0 -1095.1317 0 -1095.1317 614.12497 3677.0311 Loop time of 0.0642109 on 1 procs for 9 steps with 312 atoms 109.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1095.03126317 -1095.13111773 -1095.1316922 Force two-norm initial, final = 22.4525 0.346156 Force max component initial, final = 22.39 0.0593684 Final line search alpha, max atom move = 0.000840764 4.99148e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062227 | 0.062227 | 0.062227 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005331 | 0.0005331 | 0.0005331 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001451 | | | 2.26 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8464 ave 8464 max 8464 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: 196220 ave 196220 max 196220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196220 Ave neighs/atom = 628.91 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 = 3 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) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1095.1317 0 -1095.1317 614.12497 Loop time of 9.53674e-07 on 1 procs for 0 steps with 312 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 | | 9.537e-07 | | |100.00 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8502 ave 8502 max 8502 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: 196396 ave 196396 max 196396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196396 Ave neighs/atom = 629.474 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) = 5.083 | 5.083 | 5.083 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 -1095.1317 -1095.1317 12.948968 78.046186 3.6384003 614.12497 614.12497 23.425204 1840.1515 -21.201823 2.2589588 125.07547 Loop time of 9.53674e-07 on 1 procs for 0 steps with 312 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 | | 9.537e-07 | | |100.00 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8502 ave 8502 max 8502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98198 ave 98198 max 98198 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 196396 ave 196396 max 196396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196396 Ave neighs/atom = 629.474 Neighbor list builds = 0 Dangerous builds = 0 312 -1095.13169220101 eV 2.25895883498014 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00