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 = 3.62844 3.62844 3.62844 Created orthogonal box = (0 -42.0059 0) to (29.7001 42.0059 5.13139) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7627 6.26899 5.13139 Created 538 atoms create_atoms CPU = 0.000463963 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7627 6.26899 5.13139 Created 538 atoms create_atoms CPU = 0.000340939 secs 538 atoms in group lower Displacing atoms ... 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 = 7.54989 ghost atom cutoff = 7.54989 binsize = 3.77495, bins = 8 23 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 7.54989 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1064 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 = 7.54989 ghost atom cutoff = 7.54989 binsize = 3.77495, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.54989 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) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4415.6275 0 -4415.6275 9825.3819 358 0 -4518.2297 0 -4518.2297 -24920.025 Loop time of 2.28229 on 1 procs for 358 steps with 1064 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4415.62747451 -4518.22555867 -4518.22967373 Force two-norm initial, final = 58.989 0.196589 Force max component initial, final = 15.3215 0.0240904 Final line search alpha, max atom move = 1 0.0240904 Iterations, force evaluations = 358 647 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1872 | 2.1872 | 2.1872 | 0.0 | 95.83 Neigh | 0.051213 | 0.051213 | 0.051213 | 0.0 | 2.24 Comm | 0.02658 | 0.02658 | 0.02658 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01728 | | | 0.76 Nlocal: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6347 ave 6347 max 6347 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: 164652 ave 164652 max 164652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164652 Ave neighs/atom = 154.748 Neighbor list builds = 11 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 : 358 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.019 | 5.019 | 5.019 Mbytes Step Temp E_pair E_mol TotEng Press Volume 358 0 -4518.2297 0 -4518.2297 -24920.025 12803.624 396 0 -4534.2507 0 -4534.2507 -5623.8351 12597.467 Loop time of 0.108192 on 1 procs for 38 steps with 1064 atoms 101.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4518.22967373 -4534.25023095 -4534.25068249 Force two-norm initial, final = 712.979 2.74726 Force max component initial, final = 666.473 1.84466 Final line search alpha, max atom move = 0.000430973 0.000794997 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10278 | 0.10278 | 0.10278 | 0.0 | 95.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012143 | 0.0012143 | 0.0012143 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004197 | | | 3.88 Nlocal: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6356 ave 6356 max 6356 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: 164720 ave 164720 max 164720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164720 Ave neighs/atom = 154.812 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 = 7.54989 ghost atom cutoff = 7.54989 binsize = 3.77495, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.54989 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) = 5.159 | 5.159 | 5.159 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4534.2507 0 -4534.2507 -5623.8351 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1064 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: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6463 ave 6463 max 6463 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: 170200 ave 170200 max 170200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170200 Ave neighs/atom = 159.962 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) = 5.159 | 5.159 | 5.159 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 -4534.2507 -4534.2507 30.335341 84.011766 4.9430412 -5623.8351 -5623.8351 -239.62598 -16606.054 -25.82578 2.4287115 2994.7901 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1064 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: 1064 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6463 ave 6463 max 6463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85100 ave 85100 max 85100 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170200 ave 170200 max 170200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170200 Ave neighs/atom = 159.962 Neighbor list builds = 0 Dangerous builds = 0 1064 -4534.25068249064 eV 2.42871154756631 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02