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 = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -79.8352 0) to (48.8864 79.8352 9.87655) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.65353 5.70223 6.58436 Created 2357 atoms create_atoms CPU = 0.000908136 secs 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.65353 5.70223 6.58436 Created 2357 atoms create_atoms CPU = 0.000787973 secs 2357 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 13 43 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 4667 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 11.42 | 11.42 | 11.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15619.161 0 -15619.161 -303.99542 30 0 -15653.004 0 -15653.004 -3576.7898 Loop time of 0.694789 on 1 procs for 30 steps with 4667 atoms 100.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15619.1609854 -15652.9914301 -15653.0041548 Force two-norm initial, final = 33.5816 0.31697 Force max component initial, final = 6.55398 0.0607183 Final line search alpha, max atom move = 1 0.0607183 Iterations, force evaluations = 30 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68628 | 0.68628 | 0.68628 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003659 | 0.003659 | 0.003659 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004855 | | | 0.70 Nlocal: 4667 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12534 ave 12534 max 12534 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: 615934 ave 615934 max 615934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 615934 Ave neighs/atom = 131.976 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.42 | 11.42 | 11.42 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -15653.004 0 -15653.004 -3576.7898 77093.463 33 0 -15653.261 0 -15653.261 -853.49054 76832.45 Loop time of 0.0984452 on 1 procs for 3 steps with 4667 atoms 101.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15653.0041548 -15653.2602459 -15653.2609172 Force two-norm initial, final = 211.245 0.334921 Force max component initial, final = 161.304 0.0514064 Final line search alpha, max atom move = 0.000201676 1.03674e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095965 | 0.095965 | 0.095965 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050545 | 0.00050545 | 0.00050545 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001975 | | | 2.01 Nlocal: 4667 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12516 ave 12516 max 12516 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: 560086 ave 560086 max 560086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560086 Ave neighs/atom = 120.01 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 10.55 | 10.55 | 10.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15653.261 0 -15653.261 -853.49054 Loop time of 1.19209e-06 on 1 procs for 0 steps with 4667 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: 4667 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12522 ave 12522 max 12522 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: 579512 ave 579512 max 579512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579512 Ave neighs/atom = 124.172 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) = 10.55 | 10.55 | 10.55 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 -15653.261 -15653.261 48.81936 159.67039 9.8566242 -853.49054 -853.49054 -0.6420832 -2559.7013 -0.12829247 2.5715478 2373.3959 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4667 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: 4667 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12522 ave 12522 max 12522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 289756 ave 289756 max 289756 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 579512 ave 579512 max 579512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 579512 Ave neighs/atom = 124.172 Neighbor list builds = 0 Dangerous builds = 0 4667 -15653.2609172157 eV 2.57154779895555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01