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 -62.9872 0) to (31.4916 62.9872 4.03208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.67881 5.67881 4.03208 Created 490 atoms create_atoms CPU = 0.000219822 secs 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.67881 5.67881 4.03208 Created 490 atoms create_atoms CPU = 0.00010705 secs 490 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 = 9 34 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 972 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 = 9 34 2 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) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3235.5239 0 -3235.5239 6823.5756 68 0 -3260.8198 0 -3260.8198 -1555.6356 Loop time of 0.473289 on 1 procs for 68 steps with 972 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 = -3235.52392022 -3260.81735019 -3260.81983488 Force two-norm initial, final = 23.5575 0.140954 Force max component initial, final = 6.6945 0.0331299 Final line search alpha, max atom move = 1 0.0331299 Iterations, force evaluations = 68 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46197 | 0.46197 | 0.46197 | 0.0 | 97.61 Neigh | 0.0034461 | 0.0034461 | 0.0034461 | 0.0 | 0.73 Comm | 0.0048845 | 0.0048845 | 0.0048845 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002988 | | | 0.63 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6282 ave 6282 max 6282 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: 118824 ave 118824 max 118824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118824 Ave neighs/atom = 122.247 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -3260.8198 0 -3260.8198 -1555.6356 15995.799 71 0 -3260.8446 0 -3260.8446 -164.63829 15967.973 Loop time of 0.0180769 on 1 procs for 3 steps with 972 atoms 55.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3260.81983488 -3260.84300928 -3260.84460676 Force two-norm initial, final = 25.8648 0.148411 Force max component initial, final = 24.4539 0.032717 Final line search alpha, max atom move = 0.000159284 5.21129e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.017416 | 0.017416 | 0.017416 | 0.0 | 96.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017786 | 0.00017786 | 0.00017786 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004833 | | | 2.67 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6249 ave 6249 max 6249 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: 119828 ave 119828 max 119828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119828 Ave neighs/atom = 123.28 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 = 9 34 2 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3260.8446 0 -3260.8446 -164.63829 Loop time of 9.53674e-07 on 1 procs for 0 steps with 972 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254 ave 6254 max 6254 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: 120684 ave 120684 max 120684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120684 Ave neighs/atom = 124.16 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) = 5.126 | 5.126 | 5.126 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 -3260.8446 -3260.8446 31.423422 125.97436 4.0337981 -164.63829 -164.63829 1.6352611 -496.13802 0.58787738 2.5867865 197.95427 Loop time of 1.19209e-06 on 1 procs for 0 steps with 972 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254 ave 6254 max 6254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60342 ave 60342 max 60342 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120684 ave 120684 max 120684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120684 Ave neighs/atom = 124.16 Neighbor list builds = 0 Dangerous builds = 0 972 -3260.84460676325 eV 2.58678654463991 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00