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 = 4.04093 4.04093 4.04093 Created orthogonal box = (0 -49.8239 0) to (17.614 49.8239 5.71473) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.48936 5.2442 5.71473 Created 306 atoms create_atoms CPU = 0.000267982 secs 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.48936 5.2442 5.71473 Created 306 atoms create_atoms CPU = 0.000137091 secs 306 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 20 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 604 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 4.964 | 4.964 | 4.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2340.3921 0 -2340.3921 5499.3291 19 0 -2352.212 0 -2352.212 -9.6244089 Loop time of 0.109537 on 1 procs for 19 steps with 604 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2340.39208633 -2352.21018293 -2352.2120133 Force two-norm initial, final = 19.1548 0.112251 Force max component initial, final = 5.46958 0.020479 Final line search alpha, max atom move = 1 0.020479 Iterations, force evaluations = 19 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10771 | 0.10771 | 0.10771 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001178 | 0.001178 | 0.001178 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006516 | | | 0.59 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254 ave 6254 max 6254 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: 148928 ave 148928 max 148928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148928 Ave neighs/atom = 246.57 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.964 | 4.964 | 4.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -2352.212 0 -2352.212 -9.6244089 10030.479 20 0 -2352.2138 0 -2352.2138 -521.20194 10036.716 Loop time of 0.00969791 on 1 procs for 1 steps with 604 atoms 103.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2352.2120133 -2352.2120133 -2352.21383515 Force two-norm initial, final = 5.33935 2.17453 Force max component initial, final = 5.31747 2.16198 Final line search alpha, max atom move = 0.000188059 0.000406581 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.009378 | 0.009378 | 0.009378 | 0.0 | 96.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.6308e-05 | 8.6308e-05 | 8.6308e-05 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002337 | | | 2.41 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254 ave 6254 max 6254 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: 148912 ave 148912 max 148912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148912 Ave neighs/atom = 246.543 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.102 | 5.102 | 5.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2352.2138 0 -2352.2138 -521.20194 Loop time of 9.53674e-07 on 1 procs for 0 steps with 604 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: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254 ave 6254 max 6254 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: 148872 ave 148872 max 148872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148872 Ave neighs/atom = 246.477 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) = 5.102 | 5.102 | 5.102 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 -2352.2138 -2352.2138 17.626004 99.647857 5.7143887 -521.20194 -521.20194 -32.674787 -1185.8312 -345.09984 2.702496 282.81839 Loop time of 2.14577e-06 on 1 procs for 0 steps with 604 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 | | 2.146e-06 | | |100.00 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254 ave 6254 max 6254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74436 ave 74436 max 74436 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 148872 ave 148872 max 148872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148872 Ave neighs/atom = 246.477 Neighbor list builds = 0 Dangerous builds = 0 604 -2352.21383515004 eV 2.70249598406376 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00