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 = 3.51962 3.51962 3.51962 Created orthogonal box = (0 -40.4409 0) to (28.5935 40.4409 4.97749) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.06529 5.51418 4.97749 Created 532 atoms create_atoms CPU = 0.000411987 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.06529 5.51418 4.97749 Created 532 atoms create_atoms CPU = 0.000293016 secs 532 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 8 22 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 7.56501 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.56501 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) = 5.028 | 5.028 | 5.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4605.3682 0 -4605.3682 14803.644 31 0 -4649.4535 0 -4649.4535 -5808.4337 Loop time of 0.186955 on 1 procs for 31 steps with 1048 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4605.36816207 -4649.44905247 -4649.45351034 Force two-norm initial, final = 53.4618 0.197956 Force max component initial, final = 13.7327 0.0141438 Final line search alpha, max atom move = 1 0.0141438 Iterations, force evaluations = 31 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17758 | 0.17758 | 0.17758 | 0.0 | 94.99 Neigh | 0.0051949 | 0.0051949 | 0.0051949 | 0.0 | 2.78 Comm | 0.0023675 | 0.0023675 | 0.0023675 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00181 | | | 0.97 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6992 ave 6992 max 6992 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: 180312 ave 180312 max 180312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180312 Ave neighs/atom = 172.053 Neighbor list builds = 1 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 : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.03 | 5.03 | 5.03 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -4649.4535 0 -4649.4535 -5808.4337 11511.408 34 0 -4649.5214 0 -4649.5214 -2867.3555 11491.993 Loop time of 0.0147519 on 1 procs for 3 steps with 1048 atoms 135.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4649.45351034 -4649.51761881 -4649.52136515 Force two-norm initial, final = 51.637 0.225028 Force max component initial, final = 51.5241 0.0304417 Final line search alpha, max atom move = 0.000123093 3.74716e-06 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.01407 | 0.01407 | 0.01407 | 0.0 | 95.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015712 | 0.00015712 | 0.00015712 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000525 | | | 3.56 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7024 ave 7024 max 7024 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: 180008 ave 180008 max 180008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180008 Ave neighs/atom = 171.763 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.56501 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) = 5.168 | 5.168 | 5.168 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4649.5214 0 -4649.5214 -2867.3555 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7024 ave 7024 max 7024 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: 180088 ave 180088 max 180088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180088 Ave neighs/atom = 171.84 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) = 5.168 | 5.168 | 5.168 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 -4649.5214 -4649.5214 28.616036 80.881711 4.9651861 -2867.3555 -2867.3555 -2.662464 -8595.1704 -4.2335861 2.3121912 545.37357 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7024 ave 7024 max 7024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90044 ave 90044 max 90044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180088 ave 180088 max 180088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180088 Ave neighs/atom = 171.84 Neighbor list builds = 0 Dangerous builds = 0 1048 -4649.52136515396 eV 2.31219120431409 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00