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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -57.7039 0) to (40.8 57.7039 5.71314) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.39999 5.09116 5.71314 Created 822 atoms create_atoms CPU = 0.000488043 secs 822 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.39999 5.09116 5.71314 Created 822 atoms create_atoms CPU = 0.000357866 secs 822 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 7 20 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1626 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 7 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 7.576 | 7.576 | 7.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4595.6179 0 -4595.6179 9193.3791 52 0 -4673.4638 0 -4673.4638 -326.93994 Loop time of 1.29386 on 1 procs for 52 steps with 1626 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4595.61785552 -4673.45966226 -4673.46380509 Force two-norm initial, final = 55.5296 0.213956 Force max component initial, final = 7.87542 0.0222718 Final line search alpha, max atom move = 1 0.0222718 Iterations, force evaluations = 52 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2645 | 1.2645 | 1.2645 | 0.0 | 97.73 Neigh | 0.01678 | 0.01678 | 0.01678 | 0.0 | 1.30 Comm | 0.0088477 | 0.0088477 | 0.0088477 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003704 | | | 0.29 Nlocal: 1626 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14536 ave 14536 max 14536 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: 668264 ave 668264 max 668264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 668264 Ave neighs/atom = 410.986 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.576 | 7.576 | 7.576 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4673.4638 0 -4673.4638 -326.93994 26901.077 54 0 -4673.4828 0 -4673.4828 -905.61359 26921.628 Loop time of 0.067647 on 1 procs for 2 steps with 1626 atoms 103.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4673.46380509 -4673.48198897 -4673.48275529 Force two-norm initial, final = 29.9455 0.263104 Force max component initial, final = 28.9659 0.099289 Final line search alpha, max atom move = 0.000226437 2.24826e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066303 | 0.066303 | 0.066303 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039911 | 0.00039911 | 0.00039911 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009451 | | | 1.40 Nlocal: 1626 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14545 ave 14545 max 14545 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: 652900 ave 652900 max 652900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 652900 Ave neighs/atom = 401.538 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 7 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 7.332 | 7.332 | 7.332 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4673.4828 0 -4673.4828 -905.61359 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1626 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: 1626 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14534 ave 14534 max 14534 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: 652256 ave 652256 max 652256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 652256 Ave neighs/atom = 401.141 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) = 7.332 | 7.332 | 7.332 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 -4673.4828 -4673.4828 40.848859 115.40781 5.7106586 -905.61359 -905.61359 -5.9160279 -2705.5026 -5.4221746 2.6140261 622.90748 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1626 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: 1626 ave 1626 max 1626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14534 ave 14534 max 14534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 326128 ave 326128 max 326128 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 652256 ave 652256 max 652256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 652256 Ave neighs/atom = 401.141 Neighbor list builds = 0 Dangerous builds = 0 1626 -4673.4827552948 eV 2.61402611715362 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01