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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -51.0377 0) to (10.4174 51.0377 7.69376) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.73518 4.63951 5.12917 Created 265 atoms create_atoms CPU = 0.000204086 secs 265 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.73518 4.63951 5.12917 Created 265 atoms create_atoms CPU = 8.89301e-05 secs 265 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 2 18 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 521 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 2 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3385.4612 0 -3385.4612 26688.552 140 0 -3500.7761 0 -3500.7761 -23217.8 Loop time of 1.37858 on 1 procs for 140 steps with 521 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3385.46123984 -3500.77269982 -3500.77612869 Force two-norm initial, final = 289.486 0.346791 Force max component initial, final = 142.587 0.0713824 Final line search alpha, max atom move = 0.608892 0.0434642 Iterations, force evaluations = 140 264 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3465 | 1.3465 | 1.3465 | 0.0 | 97.67 Neigh | 0.01511 | 0.01511 | 0.01511 | 0.0 | 1.10 Comm | 0.012663 | 0.012663 | 0.012663 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004314 | | | 0.31 Nlocal: 521 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7677 ave 7677 max 7677 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: 210394 ave 210394 max 210394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210394 Ave neighs/atom = 403.827 Neighbor list builds = 3 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 : 140 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 140 0 -3500.7761 0 -3500.7761 -23217.8 8181.2382 157 0 -3504.0754 0 -3504.0754 13181.939 8073.0396 Loop time of 0.097578 on 1 procs for 17 steps with 521 atoms 102.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3500.77612869 -3504.07458689 -3504.07536799 Force two-norm initial, final = 429.593 6.92197 Force max component initial, final = 425.824 5.78009 Final line search alpha, max atom move = 0.00108313 0.00626057 Iterations, force evaluations = 17 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09461 | 0.09461 | 0.09461 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080132 | 0.00080132 | 0.00080132 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002166 | | | 2.22 Nlocal: 521 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7675 ave 7675 max 7675 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: 210316 ave 210316 max 210316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210316 Ave neighs/atom = 403.678 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 2 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.576 | 5.576 | 5.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3504.0754 0 -3504.0754 13181.939 Loop time of 9.53674e-07 on 1 procs for 0 steps with 521 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: 521 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7762 ave 7762 max 7762 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: 213660 ave 213660 max 213660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213660 Ave neighs/atom = 410.096 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) = 5.576 | 5.576 | 5.576 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 -3504.0754 -3504.0754 10.442616 102.07549 7.5736686 13181.939 13181.939 564.38554 37852.219 1129.2133 2.5318988 1299.837 Loop time of 2.14577e-06 on 1 procs for 0 steps with 521 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 | | 2.146e-06 | | |100.00 Nlocal: 521 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7762 ave 7762 max 7762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106830 ave 106830 max 106830 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 213660 ave 213660 max 213660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213660 Ave neighs/atom = 410.096 Neighbor list builds = 0 Dangerous builds = 0 521 -3504.07536799382 eV 2.53189876358681 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01