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 = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -41.9161 0) to (29.6363 41.9161 5.70351) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.58584 5.43304 5.70351 Created 440 atoms create_atoms CPU = 0.000331163 secs 440 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.58584 5.43304 5.70351 Created 440 atoms create_atoms CPU = 0.00019002 secs 440 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 13 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 864 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 6.65 | 6.65 | 6.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2451.8967 0 -2451.8967 15077.241 40 0 -2509.6266 0 -2509.6266 3121.6344 Loop time of 1.15017 on 1 procs for 40 steps with 864 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2451.89665314 -2509.62454609 -2509.62655055 Force two-norm initial, final = 51.6152 0.132703 Force max component initial, final = 7.55017 0.0107462 Final line search alpha, max atom move = 1 0.0107462 Iterations, force evaluations = 40 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1422 | 1.1422 | 1.1422 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059135 | 0.0059135 | 0.0059135 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002059 | | | 0.18 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11864 ave 11864 max 11864 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: 581120 ave 581120 max 581120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581120 Ave neighs/atom = 672.593 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.65 | 6.65 | 6.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -2509.6266 0 -2509.6266 3121.6344 14170.217 44 0 -2509.6867 0 -2509.6867 278.91965 14224.523 Loop time of 0.0792038 on 1 procs for 4 steps with 864 atoms 101.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2509.62655055 -2509.6866698 -2509.6866892 Force two-norm initial, final = 41.5456 0.167326 Force max component initial, final = 36.7674 0.0409584 Final line search alpha, max atom move = 0.00175118 7.17256e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077904 | 0.077904 | 0.077904 | 0.0 | 98.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003922 | 0.0003922 | 0.0003922 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009074 | | | 1.15 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11858 ave 11858 max 11858 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: 578288 ave 578288 max 578288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 578288 Ave neighs/atom = 669.315 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 6.788 | 6.788 | 6.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2509.6867 0 -2509.6867 278.91965 Loop time of 9.53674e-07 on 1 procs for 0 steps with 864 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: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11810 ave 11810 max 11810 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: 577696 ave 577696 max 577696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577696 Ave neighs/atom = 668.63 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) = 6.788 | 6.788 | 6.788 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 -2509.6867 -2509.6867 29.714278 83.832158 5.7103388 278.91965 278.91965 -1.7979604 833.93804 4.6188702 2.6423988 574.11748 Loop time of 1.90735e-06 on 1 procs for 0 steps with 864 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 | | 1.907e-06 | | |100.00 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11810 ave 11810 max 11810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288848 ave 288848 max 288848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 577696 ave 577696 max 577696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577696 Ave neighs/atom = 668.63 Neighbor list builds = 0 Dangerous builds = 0 864 -2509.6866892037 eV 2.64239884887247 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01