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 -38.5632 0) to (7.87096 38.5632 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.72258 5.14129 5.74814 Created 242 atoms create_atoms CPU = 0.000254154 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.72258 5.14129 5.74814 Created 242 atoms create_atoms CPU = 0.000135899 secs 242 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 3 23 3 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 3 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2082.8875 0 -2082.8875 -2810.8979 12 0 -2093.0849 0 -2093.0849 9198.5171 Loop time of 0.166156 on 1 procs for 12 steps with 472 atoms 102.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2082.88748817 -2093.08460841 -2093.08490304 Force two-norm initial, final = 12.5891 31.4796 Force max component initial, final = 3.60866 9.56061 Final line search alpha, max atom move = 4.13893e-07 3.95707e-06 Iterations, force evaluations = 12 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16222 | 0.16222 | 0.16222 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002552 | 0.002552 | 0.002552 | 0.0 | 1.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001387 | | | 0.83 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3381 ave 3381 max 3381 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: 61792 ave 61792 max 61792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61792 Ave neighs/atom = 130.915 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -2093.0849 0 -2093.0849 9198.5171 5234.1827 13 0 -2093.0849 0 -2093.0849 49.040076 5234.1837 Loop time of 0.013689 on 1 procs for 1 steps with 472 atoms 73.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2093.08490304 -2093.08490304 -2093.08491351 Force two-norm initial, final = 84.1183 32.7229 Force max component initial, final = 77.0991 24.3069 Final line search alpha, max atom move = 5.06653e-08 1.23152e-06 Iterations, force evaluations = 1 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012838 | 0.012838 | 0.012838 | 0.0 | 93.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 1.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006387 | | | 4.67 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3396 ave 3396 max 3396 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: 61892 ave 61892 max 61892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61892 Ave neighs/atom = 131.127 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 3 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2093.0849 0 -2093.0849 49.040076 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3396 ave 3396 max 3396 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: 61892 ave 61892 max 61892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61892 Ave neighs/atom = 131.127 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) = 4.636 | 4.636 | 4.636 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 -2093.0849 -2093.0849 7.8709595 77.126376 8.6222053 49.040076 49.040076 -557.28981 -6735.9021 7440.3122 2.2097331 318.20673 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3396 ave 3396 max 3396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30946 ave 30946 max 30946 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61892 ave 61892 max 61892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61892 Ave neighs/atom = 131.127 Neighbor list builds = 0 Dangerous builds = 0 472 -2093.08491351364 eV 2.20973308709794 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00