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 = 2.85531 2.85531 2.85531 Created orthogonal box = (0 -37.4499 0) to (26.4791 37.4499 4.03802) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.92634 4.78974 4.03802 Created 345 atoms create_atoms CPU = 0.000191927 secs 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.92634 4.78974 4.03802 Created 345 atoms create_atoms CPU = 0.000161886 secs 345 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 687 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2689.6347 0 -2689.6347 31331.794 27 0 -2744.2636 0 -2744.2636 1009.7564 Loop time of 0.0961039 on 1 procs for 27 steps with 687 atoms 93.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2689.63465412 -2744.26133147 -2744.26362478 Force two-norm initial, final = 104.531 0.155517 Force max component initial, final = 26.0592 0.0284038 Final line search alpha, max atom move = 1 0.0284038 Iterations, force evaluations = 27 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.093837 | 0.093837 | 0.093837 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013754 | 0.0013754 | 0.0013754 | 0.0 | 1.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008917 | | | 0.93 Nlocal: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5029 ave 5029 max 5029 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: 93534 ave 93534 max 93534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93534 Ave neighs/atom = 136.148 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -2744.2636 0 -2744.2636 1009.7564 8008.5245 29 0 -2744.2699 0 -2744.2699 281.05559 8011.877 Loop time of 0.00905013 on 1 procs for 2 steps with 687 atoms 110.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2744.26362478 -2744.26927543 -2744.26988999 Force two-norm initial, final = 12.5378 0.161324 Force max component initial, final = 12.2222 0.0269287 Final line search alpha, max atom move = 0.000215755 5.81e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0086029 | 0.0086029 | 0.0086029 | 0.0 | 95.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011611 | 0.00011611 | 0.00011611 | 0.0 | 1.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003312 | | | 3.66 Nlocal: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039 ave 5039 max 5039 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: 94622 ave 94622 max 94622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94622 Ave neighs/atom = 137.732 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.671 | 4.671 | 4.671 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2744.2699 0 -2744.2699 281.05559 Loop time of 9.53674e-07 on 1 procs for 0 steps with 687 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: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039 ave 5039 max 5039 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: 94592 ave 94592 max 94592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94592 Ave neighs/atom = 137.689 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) = 4.671 | 4.671 | 4.671 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 -2744.2699 -2744.2699 26.503263 74.899856 4.0360259 281.05559 281.05559 -1.5862764 845.0218 -0.26874931 2.2423307 414.77747 Loop time of 2.14577e-06 on 1 procs for 0 steps with 687 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: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5039 ave 5039 max 5039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47296 ave 47296 max 47296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94592 ave 94592 max 94592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94592 Ave neighs/atom = 137.689 Neighbor list builds = 0 Dangerous builds = 0 687 -2744.26988998717 eV 2.24233071375061 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00