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 -62.1791 0) to (35.8971 62.1791 6.09682) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.52263 5.57986 6.09682 Created 1251 atoms create_atoms CPU = 0.000778913 secs 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.52263 5.57986 6.09682 Created 1251 atoms create_atoms CPU = 0.000674009 secs 1251 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 37 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2480 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.116 | 6.116 | 6.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10947.267 0 -10947.267 7926.324 41 0 -10999.461 0 -10999.461 -3141.8613 Loop time of 0.422418 on 1 procs for 41 steps with 2480 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10947.2668237 -10999.4503783 -10999.4613211 Force two-norm initial, final = 80.0294 0.383464 Force max component initial, final = 13.9847 0.0748567 Final line search alpha, max atom move = 1 0.0748567 Iterations, force evaluations = 41 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41313 | 0.41313 | 0.41313 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0051634 | 0.0051634 | 0.0051634 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00412 | | | 0.98 Nlocal: 2480 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10112 ave 10112 max 10112 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: 328602 ave 328602 max 328602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328602 Ave neighs/atom = 132.501 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.116 | 6.116 | 6.116 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -10999.461 0 -10999.461 -3141.8613 27216.803 43 0 -10999.489 0 -10999.489 -1453.1144 27191.112 Loop time of 0.0219071 on 1 procs for 2 steps with 2480 atoms 91.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10999.4613211 -10999.4876687 -10999.4893271 Force two-norm initial, final = 58.9504 0.394169 Force max component initial, final = 57.2731 0.0732358 Final line search alpha, max atom move = 8.97646e-05 6.57398e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020908 | 0.020908 | 0.020908 | 0.0 | 95.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024319 | 0.00024319 | 0.00024319 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000756 | | | 3.45 Nlocal: 2480 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10107 ave 10107 max 10107 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: 328528 ave 328528 max 328528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328528 Ave neighs/atom = 132.471 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.254 | 6.254 | 6.254 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10999.489 0 -10999.489 -1453.1144 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2480 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: 2480 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10107 ave 10107 max 10107 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: 328556 ave 328556 max 328556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328556 Ave neighs/atom = 132.482 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) = 6.254 | 6.254 | 6.254 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 -10999.489 -10999.489 35.898646 124.35823 6.0908005 -1453.1144 -1453.1144 -4.0740451 -4355.1142 -0.15504349 2.2600496 973.50903 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2480 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 | | 1.192e-06 | | |100.00 Nlocal: 2480 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10107 ave 10107 max 10107 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164278 ave 164278 max 164278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 328556 ave 328556 max 328556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328556 Ave neighs/atom = 132.482 Neighbor list builds = 0 Dangerous builds = 0 2480 -10999.4893271434 eV 2.26004963012049 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00