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 = 3.99462 3.99462 3.99462 Created orthogonal box = (0 -76.4255 0) to (44.122 76.4255 6.91888) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5098 5.84645 6.91888 Created 1465 atoms create_atoms CPU = 0.000831127 secs 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5098 5.84645 6.91888 Created 1465 atoms create_atoms CPU = 0.000701904 secs 1465 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 41 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2908 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 6.2 | 6.2 | 6.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9503.0931 0 -9503.0931 1700.1151 70 0 -9535.0724 0 -9535.0724 -2225.2428 Loop time of 2.29991 on 1 procs for 70 steps with 2908 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 = -9503.09314166 -9535.06392366 -9535.07240575 Force two-norm initial, final = 23.8058 0.203407 Force max component initial, final = 4.67187 0.0327699 Final line search alpha, max atom move = 1 0.0327699 Iterations, force evaluations = 70 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2417 | 2.2417 | 2.2417 | 0.0 | 97.47 Neigh | 0.041474 | 0.041474 | 0.041474 | 0.0 | 1.80 Comm | 0.0090647 | 0.0090647 | 0.0090647 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007645 | | | 0.33 Nlocal: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11397 ave 11397 max 11397 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: 383156 ave 383156 max 383156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383156 Ave neighs/atom = 131.759 Neighbor list builds = 4 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 : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.2 | 6.2 | 6.2 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -9535.0724 0 -9535.0724 -2225.2428 46661.543 72 0 -9535.1046 0 -9535.1046 -1399.9387 46563.947 Loop time of 0.0842359 on 1 procs for 2 steps with 2908 atoms 106.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9535.07240575 -9535.10322693 -9535.10457448 Force two-norm initial, final = 41.5064 1.46126 Force max component initial, final = 33.3237 1.42006 Final line search alpha, max atom move = 0.000138582 0.000196794 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083015 | 0.083015 | 0.083015 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026917 | 0.00026917 | 0.00026917 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000952 | | | 1.13 Nlocal: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11392 ave 11392 max 11392 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: 383352 ave 383352 max 383352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383352 Ave neighs/atom = 131.827 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 6.338 | 6.338 | 6.338 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9535.1046 0 -9535.1046 -1399.9387 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2908 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: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11392 ave 11392 max 11392 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: 383464 ave 383464 max 383464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383464 Ave neighs/atom = 131.865 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) = 6.338 | 6.338 | 6.338 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 -9535.1046 -9535.1046 44.064871 152.85102 6.9133563 -1399.9387 -1399.9387 -9.4058292 -4239.2326 48.822452 2.552129 1456.561 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2908 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: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11392 ave 11392 max 11392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 191732 ave 191732 max 191732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 383464 ave 383464 max 383464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383464 Ave neighs/atom = 131.865 Neighbor list builds = 0 Dangerous builds = 0 2908 -9535.10457448386 eV 2.55212898237066 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02