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 = 3.65837 3.65837 3.65837 Created orthogonal box = (0 -42.0351 0) to (29.7207 42.0351 5.17371) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.50314 5.73156 5.17371 Created 532 atoms create_atoms CPU = 0.000242949 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.50314 5.73156 5.17371 Created 532 atoms create_atoms CPU = 0.000153065 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 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, cut 7.3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4142.6907 0 -4142.6907 6174.8121 812 0 -4250.5197 0 -4250.5197 -74796.426 Loop time of 5.3924 on 1 procs for 812 steps with 1048 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4142.69069709 -4250.51562463 -4250.51966576 Force two-norm initial, final = 38.9659 0.252889 Force max component initial, final = 8.60679 0.0612943 Final line search alpha, max atom move = 1 0.0612943 Iterations, force evaluations = 812 1566 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2432 | 5.2432 | 5.2432 | 0.0 | 97.23 Neigh | 0.044833 | 0.044833 | 0.044833 | 0.0 | 0.83 Comm | 0.062498 | 0.062498 | 0.062498 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04187 | | | 0.78 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5942 ave 5942 max 5942 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: 140892 ave 140892 max 140892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140892 Ave neighs/atom = 134.439 Neighbor list builds = 12 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 : 812 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.009 | 5.009 | 5.009 Mbytes Step Temp E_pair E_mol TotEng Press Volume 812 0 -4250.5197 0 -4250.5197 -74796.426 12927.166 855 0 -4276.2956 0 -4276.2956 4131.6372 12231.368 Loop time of 0.159297 on 1 procs for 43 steps with 1048 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4250.51966576 -4276.29524128 -4276.29557122 Force two-norm initial, final = 1081.22 3.26888 Force max component initial, final = 909.457 1.76671 Final line search alpha, max atom move = 0.000570435 0.00100779 Iterations, force evaluations = 43 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15161 | 0.15161 | 0.15161 | 0.0 | 95.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015807 | 0.0015807 | 0.0015807 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006104 | | | 3.83 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5990 ave 5990 max 5990 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: 140824 ave 140824 max 140824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140824 Ave neighs/atom = 134.374 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.148 | 5.148 | 5.148 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4276.2956 0 -4276.2956 4131.6372 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: 6199 ave 6199 max 6199 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: 146128 ave 146128 max 146128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146128 Ave neighs/atom = 139.435 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) = 5.148 | 5.148 | 5.148 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 -4276.2956 -4276.2956 29.346748 84.070176 4.9576184 4131.6372 4131.6372 -228.5079 12814.742 -191.3222 2.2417417 3359.4265 Loop time of 1.19209e-06 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 | | 1.192e-06 | | |100.00 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6199 ave 6199 max 6199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73064 ave 73064 max 73064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146128 ave 146128 max 146128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146128 Ave neighs/atom = 139.435 Neighbor list builds = 0 Dangerous builds = 0 1048 -4276.29557122339 eV 2.24174171285786 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05