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 = 2.8602 2.8602 2.8602 Created orthogonal box = (0 -30.8081 0) to (15.4026 30.8081 2.8602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.71787 3.71787 2.8602 Created 117 atoms create_atoms CPU = 0.000174999 secs 117 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.71787 3.71787 2.8602 Created 117 atoms create_atoms CPU = 4.91142e-05 secs 117 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 228 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.388 | 4.388 | 4.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -962.11067 0 -962.11067 -6681.9345 27 0 -968.58699 0 -968.58699 -18555.639 Loop time of 0.244824 on 1 procs for 27 steps with 228 atoms 102.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -962.110666077 -968.586052091 -968.586985103 Force two-norm initial, final = 17.7258 0.122248 Force max component initial, final = 8.34696 0.032632 Final line search alpha, max atom move = 1 0.032632 Iterations, force evaluations = 27 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24384 | 0.24384 | 0.24384 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005939 | 0.0005939 | 0.0005939 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003867 | | | 0.16 Nlocal: 228 ave 228 max 228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2037 ave 2037 max 2037 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: 12964 ave 12964 max 12964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12964 Ave neighs/atom = 56.8596 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.77 | 4.77 | 4.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -968.58699 0 -968.58699 -18555.639 2714.4725 36 0 -968.76956 0 -968.76956 -1186.831 2686.0018 Loop time of 0.0875299 on 1 procs for 9 steps with 228 atoms 102.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -968.586985103 -968.768847388 -968.769555569 Force two-norm initial, final = 45.8444 0.601443 Force max component initial, final = 36.0994 0.432836 Final line search alpha, max atom move = 0.000738369 0.000319593 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086849 | 0.086849 | 0.086849 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016737 | 0.00016737 | 0.00016737 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005136 | | | 0.59 Nlocal: 228 ave 228 max 228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2037 ave 2037 max 2037 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: 13044 ave 13044 max 13044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13044 Ave neighs/atom = 57.2105 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -968.76956 0 -968.76956 -1186.831 Loop time of 1.19209e-06 on 1 procs for 0 steps with 228 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: 228 ave 228 max 228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2037 ave 2037 max 2037 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: 13048 ave 13048 max 13048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13048 Ave neighs/atom = 57.2281 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) = 4.908 | 4.908 | 4.908 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 -968.76956 -968.76956 15.375284 61.616216 2.835229 -1186.831 -1186.831 257.72442 -4008.8832 190.66576 2.3062383 174.04414 Loop time of 9.53674e-07 on 1 procs for 0 steps with 228 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: 228 ave 228 max 228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2037 ave 2037 max 2037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6524 ave 6524 max 6524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13048 ave 13048 max 13048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13048 Ave neighs/atom = 57.2281 Neighbor list builds = 0 Dangerous builds = 0 228 -968.769555569045 eV 2.306238285476 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00