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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -51.2101 0) to (12.0695 51.2101 5.14645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.48613 6.20685 5.14645 Created 266 atoms create_atoms CPU = 0.000350952 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.48613 6.20685 5.14645 Created 266 atoms create_atoms CPU = 0.000252008 secs 266 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 526 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1714.024 0 -1714.024 3333.112 39 0 -1720.5134 0 -1720.5134 447.52529 Loop time of 0.151431 on 1 procs for 39 steps with 526 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1714.02395736 -1720.51188292 -1720.51338337 Force two-norm initial, final = 9.6319 0.101241 Force max component initial, final = 2.57183 0.0133109 Final line search alpha, max atom move = 1 0.0133109 Iterations, force evaluations = 39 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14566 | 0.14566 | 0.14566 | 0.0 | 96.19 Neigh | 0.002435 | 0.002435 | 0.002435 | 0.0 | 1.61 Comm | 0.0021899 | 0.0021899 | 0.0021899 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001145 | | | 0.76 Nlocal: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5218 ave 5218 max 5218 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: 92092 ave 92092 max 92092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92092 Ave neighs/atom = 175.08 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -1720.5134 0 -1720.5134 447.52529 6361.8333 41 0 -1720.5177 0 -1720.5177 1667.6295 6356.4002 Loop time of 0.00883317 on 1 procs for 2 steps with 526 atoms 113.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1720.51338337 -1720.51674927 -1720.51767831 Force two-norm initial, final = 8.65712 0.1047 Force max component initial, final = 8.25287 0.0203483 Final line search alpha, max atom move = 0.000381626 7.76544e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0084009 | 0.0084009 | 0.0084009 | 0.0 | 95.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011849 | 0.00011849 | 0.00011849 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003138 | | | 3.55 Nlocal: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5202 ave 5202 max 5202 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: 92260 ave 92260 max 92260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92260 Ave neighs/atom = 175.399 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1720.5177 0 -1720.5177 1667.6295 Loop time of 9.53674e-07 on 1 procs for 0 steps with 526 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: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5210 ave 5210 max 5210 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: 92268 ave 92268 max 92268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92268 Ave neighs/atom = 175.414 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) = 4.692 | 4.692 | 4.692 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 -1720.5177 -1720.5177 12.055892 102.42028 5.1478508 1667.6295 1667.6295 5.1231586 4996.8161 0.94916839 2.2997646 256.22115 Loop time of 9.53674e-07 on 1 procs for 0 steps with 526 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: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5210 ave 5210 max 5210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46134 ave 46134 max 46134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92268 ave 92268 max 92268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92268 Ave neighs/atom = 175.414 Neighbor list builds = 0 Dangerous builds = 0 526 -1720.51767830937 eV 2.29976464796162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00