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 -33.0555 0) to (23.3717 33.0555 4.03802) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.53482 4.93323 4.03802 Created 269 atoms create_atoms CPU = 0.000283957 secs 269 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.53482 4.93323 4.03802 Created 269 atoms create_atoms CPU = 0.000170946 secs 269 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 16 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 532 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.91 | 4.91 | 4.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2095.2527 0 -2095.2527 15771.112 28 0 -2119.7405 0 -2119.7405 684.09547 Loop time of 0.18491 on 1 procs for 28 steps with 532 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2095.25265321 -2119.73882028 -2119.74052064 Force two-norm initial, final = 61.4571 0.137053 Force max component initial, final = 16.4575 0.0269272 Final line search alpha, max atom move = 1 0.0269272 Iterations, force evaluations = 28 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18226 | 0.18226 | 0.18226 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017562 | 0.0017562 | 0.0017562 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008924 | | | 0.48 Nlocal: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5258 ave 5258 max 5258 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: 119772 ave 119772 max 119772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119772 Ave neighs/atom = 225.135 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.91 | 4.91 | 4.91 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -2119.7405 0 -2119.7405 684.09547 6239.2629 29 0 -2119.7424 0 -2119.7424 1850.0434 6235.0203 Loop time of 0.0103981 on 1 procs for 1 steps with 532 atoms 96.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2119.74052064 -2119.74052064 -2119.74240742 Force two-norm initial, final = 7.80808 0.439293 Force max component initial, final = 5.90549 0.308323 Final line search alpha, max atom move = 0.000169334 5.22096e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010061 | 0.010061 | 0.010061 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.0361e-05 | 9.0361e-05 | 9.0361e-05 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002468 | | | 2.37 Nlocal: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5243 ave 5243 max 5243 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: 119308 ave 119308 max 119308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119308 Ave neighs/atom = 224.263 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2119.7424 0 -2119.7424 1850.0434 Loop time of 2.14577e-06 on 1 procs for 0 steps with 532 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: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5243 ave 5243 max 5243 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: 119384 ave 119384 max 119384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119384 Ave neighs/atom = 224.406 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) = 5.048 | 5.048 | 5.048 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 -2119.7424 -2119.7424 23.363216 66.110976 4.0367483 1850.0434 1850.0434 -72.438422 5543.3654 79.203064 2.2563123 408.15999 Loop time of 1.90735e-06 on 1 procs for 0 steps with 532 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 | | 1.907e-06 | | |100.00 Nlocal: 532 ave 532 max 532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5243 ave 5243 max 5243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59692 ave 59692 max 59692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119384 ave 119384 max 119384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119384 Ave neighs/atom = 224.406 Neighbor list builds = 0 Dangerous builds = 0 532 -2119.74240742475 eV 2.25631234082171 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00