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 = 4.05 4.05 4.05 Created orthogonal box = (0 -40.907 0) to (28.9228 40.907 5.72757) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.10402 6.41616 5.72757 Created 410 atoms create_atoms CPU = 0.000231028 secs 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.10402 6.41616 5.72757 Created 410 atoms create_atoms CPU = 0.000132084 secs 410 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 804 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2678.4648 0 -2678.4648 3210.3907 38 0 -2696.9449 0 -2696.9449 -3486.8366 Loop time of 0.140844 on 1 procs for 38 steps with 804 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 = -2678.46478833 -2696.94251628 -2696.94487243 Force two-norm initial, final = 23.8452 0.105022 Force max component initial, final = 8.06879 0.0314269 Final line search alpha, max atom move = 1 0.0314269 Iterations, force evaluations = 38 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13485 | 0.13485 | 0.13485 | 0.0 | 95.75 Neigh | 0.002671 | 0.002671 | 0.002671 | 0.0 | 1.90 Comm | 0.0019319 | 0.0019319 | 0.0019319 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001387 | | | 0.98 Nlocal: 804 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4271 ave 4271 max 4271 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: 103120 ave 103120 max 103120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103120 Ave neighs/atom = 128.259 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -2696.9449 0 -2696.9449 -3486.8366 13553.088 41 0 -2697.018 0 -2697.018 -25.49143 13493.504 Loop time of 0.0112488 on 1 procs for 3 steps with 804 atoms 88.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2696.94487243 -2697.01641153 -2697.01798516 Force two-norm initial, final = 46.724 0.606446 Force max component initial, final = 34.8236 0.468353 Final line search alpha, max atom move = 0.000180458 8.45179e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010673 | 0.010673 | 0.010673 | 0.0 | 94.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013208 | 0.00013208 | 0.00013208 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004437 | | | 3.94 Nlocal: 804 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4271 ave 4271 max 4271 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: 103272 ave 103272 max 103272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103272 Ave neighs/atom = 128.448 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2697.018 0 -2697.018 -25.49143 Loop time of 9.53674e-07 on 1 procs for 0 steps with 804 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: 804 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4271 ave 4271 max 4271 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: 103528 ave 103528 max 103528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103528 Ave neighs/atom = 128.766 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) = 5.074 | 5.074 | 5.074 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 -2697.018 -2697.018 28.864017 81.814091 5.7139948 -25.49143 -25.49143 55.497738 -89.102306 -42.869723 2.5630392 729.60631 Loop time of 1.19209e-06 on 1 procs for 0 steps with 804 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: 804 ave 804 max 804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4271 ave 4271 max 4271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51764 ave 51764 max 51764 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103528 ave 103528 max 103528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103528 Ave neighs/atom = 128.766 Neighbor list builds = 0 Dangerous builds = 0 804 -2697.01798516016 eV 2.56303918073814 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00