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 = 4.2107 4.2107 4.2107 Created orthogonal box = (0 -44.1664 0) to (54.0874 44.1664 10.3141) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.88385 6.42359 6.87604 Created 1323 atoms create_atoms CPU = 0.000413895 secs 1323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.88385 6.42359 6.87604 Created 1323 atoms create_atoms CPU = 0.000301838 secs 1323 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 43 atoms, new total = 2603 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.474 | 6.474 | 6.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9651.779 0 -9651.779 1456.8257 68 0 -9686.2317 0 -9686.2317 -3144.6287 Loop time of 1.82716 on 1 procs for 68 steps with 2603 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9651.77898754 -9686.22245673 -9686.23173542 Force two-norm initial, final = 36.0555 0.170473 Force max component initial, final = 5.28406 0.0337139 Final line search alpha, max atom move = 1 0.0337139 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7919 | 1.7919 | 1.7919 | 0.0 | 98.07 Neigh | 0.020906 | 0.020906 | 0.020906 | 0.0 | 1.14 Comm | 0.0070326 | 0.0070326 | 0.0070326 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007327 | | | 0.40 Nlocal: 2603 ave 2603 max 2603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8868 ave 8868 max 8868 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: 438902 ave 438902 max 438902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438902 Ave neighs/atom = 168.614 Neighbor list builds = 2 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.474 | 6.474 | 6.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -9686.2317 0 -9686.2317 -3144.6287 49277.463 72 0 -9686.4752 0 -9686.4752 -783.18148 48977.692 Loop time of 0.063976 on 1 procs for 4 steps with 2603 atoms 93.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9686.23173542 -9686.47416001 -9686.47522429 Force two-norm initial, final = 112.553 1.47752 Force max component initial, final = 82.6492 1.2684 Final line search alpha, max atom move = 0.000156549 0.000198567 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062775 | 0.062775 | 0.062775 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025725 | 0.00025725 | 0.00025725 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009439 | | | 1.48 Nlocal: 2603 ave 2603 max 2603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8872 ave 8872 max 8872 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: 440356 ave 440356 max 440356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440356 Ave neighs/atom = 169.172 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.612 | 6.612 | 6.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9686.4752 0 -9686.4752 -783.18148 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2603 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: 2603 ave 2603 max 2603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8881 ave 8881 max 8881 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: 442914 ave 442914 max 442914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442914 Ave neighs/atom = 170.155 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) = 6.612 | 6.612 | 6.612 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 -9686.4752 -9686.4752 53.911485 88.332816 10.284779 -783.18148 -783.18148 -23.78327 -2367.1356 41.374461 2.7008906 2681.8342 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2603 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: 2603 ave 2603 max 2603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8881 ave 8881 max 8881 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 221457 ave 221457 max 221457 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 442914 ave 442914 max 442914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442914 Ave neighs/atom = 170.155 Neighbor list builds = 0 Dangerous builds = 0 2603 -9686.47522428703 eV 2.70089064794626 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02