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 = 3.52 3.52 3.52 Created orthogonal box = (0 -40.4452 0) to (28.5966 40.4452 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.06595 5.51478 4.97803 Created 532 atoms create_atoms CPU = 0.000420094 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.06595 5.51478 4.97803 Created 532 atoms create_atoms CPU = 0.000296116 secs 532 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 24 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4603.2594 0 -4603.2594 15982.497 63 0 -4649.7955 0 -4649.7955 -6799.3171 Loop time of 0.35267 on 1 procs for 63 steps with 1048 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4603.25943275 -4649.79157988 -4649.79552896 Force two-norm initial, final = 68.0754 0.219501 Force max component initial, final = 12.8744 0.0239457 Final line search alpha, max atom move = 1 0.0239457 Iterations, force evaluations = 63 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34033 | 0.34033 | 0.34033 | 0.0 | 96.50 Neigh | 0.0041082 | 0.0041082 | 0.0041082 | 0.0 | 1.16 Comm | 0.0046725 | 0.0046725 | 0.0046725 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003558 | | | 1.01 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5709 ave 5709 max 5709 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: 138104 ave 138104 max 138104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138104 Ave neighs/atom = 131.779 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -4649.7955 0 -4649.7955 -6799.3171 11515.151 67 0 -4649.9162 0 -4649.9162 -3962.5089 11496.378 Loop time of 0.0180941 on 1 procs for 4 steps with 1048 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 = -4649.79552896 -4649.91501087 -4649.91616031 Force two-norm initial, final = 67.8367 0.989371 Force max component initial, final = 65.1828 0.774456 Final line search alpha, max atom move = 0.000186528 0.000144458 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.017074 | 0.017074 | 0.017074 | 0.0 | 94.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020885 | 0.00020885 | 0.00020885 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008113 | | | 4.48 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5662 ave 5662 max 5662 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: 138128 ave 138128 max 138128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138128 Ave neighs/atom = 131.802 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.141 | 5.141 | 5.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4649.9162 0 -4649.9162 -3962.5089 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5655 ave 5655 max 5655 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: 138144 ave 138144 max 138144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138144 Ave neighs/atom = 131.817 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) = 5.141 | 5.141 | 5.141 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 -4649.9162 -4649.9162 28.641667 80.890478 4.9620982 -3962.5089 -3962.5089 -77.342413 -11702.599 -107.58547 2.3471829 708.27147 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5655 ave 5655 max 5655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69072 ave 69072 max 69072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138144 ave 138144 max 138144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138144 Ave neighs/atom = 131.817 Neighbor list builds = 0 Dangerous builds = 0 1048 -4649.91616031056 eV 2.34718291384326 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00