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 = 3.58787 3.58787 3.58787 Created orthogonal box = (0 -35.8823 0) to (17.9393 35.8823 3.58787) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.02302 5.02302 3.58787 Created 201 atoms create_atoms CPU = 0.000217199 secs 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.02302 5.02302 3.58787 Created 201 atoms create_atoms CPU = 8.82149e-05 secs 201 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 = 8.29999 ghost atom cutoff = 8.29999 binsize = 4.14999, bins = 5 18 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 8.29999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 398 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 = 8.29999 ghost atom cutoff = 8.29999 binsize = 4.14999, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.29999 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) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1369.3417 0 -1369.3417 27921.211 61 0 -1395.9771 0 -1395.9771 716.04787 Loop time of 0.59159 on 1 procs for 61 steps with 398 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1369.34171765 -1395.97574952 -1395.97705594 Force two-norm initial, final = 37.9663 0.11244 Force max component initial, final = 13.6209 0.0306777 Final line search alpha, max atom move = 1 0.0306777 Iterations, force evaluations = 61 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58429 | 0.58429 | 0.58429 | 0.0 | 98.77 Neigh | 0.002048 | 0.002048 | 0.002048 | 0.0 | 0.35 Comm | 0.0037344 | 0.0037344 | 0.0037344 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001516 | | | 0.26 Nlocal: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5296 ave 5296 max 5296 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: 79430 ave 79430 max 79430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79430 Ave neighs/atom = 199.573 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -1395.9771 0 -1395.9771 716.04787 4619.0581 65 0 -1395.9943 0 -1395.9943 90.505525 4621.0609 Loop time of 0.034966 on 1 procs for 4 steps with 398 atoms 114.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1395.97705594 -1395.99412801 -1395.99428127 Force two-norm initial, final = 8.45119 0.143923 Force max component initial, final = 6.00795 0.0344803 Final line search alpha, max atom move = 0.000568692 1.96087e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0343 | 0.0343 | 0.0343 | 0.0 | 98.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018191 | 0.00018191 | 0.00018191 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004842 | | | 1.38 Nlocal: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5224 ave 5224 max 5224 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: 79530 ave 79530 max 79530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79530 Ave neighs/atom = 199.824 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 = 8.29999 ghost atom cutoff = 8.29999 binsize = 4.14999, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.29999 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1395.9943 0 -1395.9943 90.505525 Loop time of 9.53674e-07 on 1 procs for 0 steps with 398 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: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5230 ave 5230 max 5230 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: 79522 ave 79522 max 79522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79522 Ave neighs/atom = 199.804 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) = 4.629 | 4.629 | 4.629 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 -1395.9943 -1395.9943 17.892052 71.76457 3.5989138 90.505525 90.505525 -11.923213 286.27838 -2.8385911 2.2932202 154.09041 Loop time of 9.53674e-07 on 1 procs for 0 steps with 398 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: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5230 ave 5230 max 5230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39761 ave 39761 max 39761 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79522 ave 79522 max 79522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79522 Ave neighs/atom = 199.804 Neighbor list builds = 0 Dangerous builds = 0 398 -1395.9942812688 eV 2.29322022632168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00