LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.16926 3.16926 3.16926 Created orthogonal box = (0 -39.2047 0) to (18.4798 39.2047 4.48201) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.43523 5.38061 4.48201 Created 206 atoms create_atoms CPU = 0.000441074 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.43523 5.38061 4.48201 Created 206 atoms create_atoms CPU = 0.000301123 secs 206 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 408 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4361.3645 0 -4361.3645 22664.08 35 0 -4409.6792 0 -4409.6792 10390.6 Loop time of 5.91196 on 1 procs for 35 steps with 408 atoms 79.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4361.36446173 -4409.67616814 -4409.67915735 Force two-norm initial, final = 83.2121 0.181208 Force max component initial, final = 25.6253 0.035573 Final line search alpha, max atom move = 1 0.035573 Iterations, force evaluations = 35 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9088 | 5.9088 | 5.9088 | 0.0 | 99.95 Neigh | 0.00078607 | 0.00078607 | 0.00078607 | 0.0 | 0.01 Comm | 0.0013773 | 0.0013773 | 0.0013773 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001007 | | | 0.02 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2483 ave 2483 max 2483 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: 26268 ave 26268 max 26268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26268 Ave neighs/atom = 64.3824 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -4409.6792 0 -4409.6792 10390.6 6494.3884 38 0 -4409.7231 0 -4409.7231 3620.457 6511.093 Loop time of 0.518117 on 1 procs for 3 steps with 408 atoms 70.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4409.67915735 -4409.72222156 -4409.72311248 Force two-norm initial, final = 44.926 0.189472 Force max component initial, final = 37.0468 0.0310609 Final line search alpha, max atom move = 0.000279637 8.68577e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51769 | 0.51769 | 0.51769 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.6308e-05 | 8.6308e-05 | 8.6308e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003452 | | | 0.07 Nlocal: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2483 ave 2483 max 2483 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: 26248 ave 26248 max 26248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26248 Ave neighs/atom = 64.3333 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.58 | 4.58 | 4.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4409.7231 0 -4409.7231 3620.457 Loop time of 9.53674e-07 on 1 procs for 0 steps with 408 atoms 209.7% 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: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2483 ave 2483 max 2483 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: 26248 ave 26248 max 26248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26248 Ave neighs/atom = 64.3333 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) = 4.58 | 4.58 | 4.58 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 -4409.7231 -4409.7231 18.515898 78.409463 4.4847749 3620.457 3620.457 -3.4889824 10862.942 1.918171 2.432882 324.82986 Loop time of 1.90735e-06 on 1 procs for 0 steps with 408 atoms 104.9% 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: 408 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2483 ave 2483 max 2483 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13124 ave 13124 max 13124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26248 ave 26248 max 26248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26248 Ave neighs/atom = 64.3333 Neighbor list builds = 0 Dangerous builds = 0 408 -2225.04398951617 eV 2.43288197629232 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06