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 # Using KIM Simulator Model : Sim_LAMMPS_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 # For Simulator : LAMMPS 12 Dec 2018 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.15999 3.15999 3.15999 Created orthogonal box = (0 -36.8546 0) to (13.029 36.8546 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.36487 5.41934 4.4689 Created 138 atoms create_atoms CPU = 0.000257015 secs 138 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.36487 5.41934 4.4689 Created 138 atoms create_atoms CPU = 0.000108004 secs 138 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX2qVfyv/Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 SNAP Element = Mo, Radius 0.5, Weight 1 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX2qVfyv/Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 SNAP keyword rcutfac 4.615858 SNAP keyword twojmax 6 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 = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 4 23 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 270 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 = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair snap, perpetual attributes: full, newton on 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) = 4.638 | 4.638 | 4.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6001.4895 0 -6001.4895 31196.109 38 0 -6036.2893 0 -6036.2893 5645.5014 Loop time of 3.04242 on 1 procs for 38 steps with 270 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6001.48951581 -6036.28396437 -6036.28933093 Force two-norm initial, final = 58.9302 0.248531 Force max component initial, final = 15.4845 0.0438874 Final line search alpha, max atom move = 1 0.0438874 Iterations, force evaluations = 38 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0406 | 3.0406 | 3.0406 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011075 | 0.0011075 | 0.0011075 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006728 | | | 0.02 Nlocal: 270 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2314 ave 2314 max 2314 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: 17420 ave 17420 max 17420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17420 Ave neighs/atom = 64.5185 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.638 | 4.638 | 4.638 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -6036.2893 0 -6036.2893 5645.5014 4291.7314 40 0 -6036.3048 0 -6036.3048 795.78265 4299.8097 Loop time of 0.219861 on 1 procs for 2 steps with 270 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6036.28933093 -6036.30244867 -6036.30481125 Force two-norm initial, final = 19.849 2.91027 Force max component initial, final = 18.4422 2.73196 Final line search alpha, max atom move = 0.000175635 0.000479827 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21961 | 0.21961 | 0.21961 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.3896e-05 | 6.3896e-05 | 6.3896e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000186 | | | 0.08 Nlocal: 270 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2314 ave 2314 max 2314 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: 17328 ave 17328 max 17328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17328 Ave neighs/atom = 64.1778 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 = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.269 | 4.269 | 4.269 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6036.3048 0 -6036.3048 795.78265 Loop time of 9.53674e-07 on 1 procs for 0 steps with 270 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: 270 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2310 ave 2310 max 2310 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: 17324 ave 17324 max 17324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17324 Ave neighs/atom = 64.163 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) = 4.269 | 4.269 | 4.269 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 -6036.3048 -6036.3048 13.051661 73.709277 4.4695242 795.78265 795.78265 -362.52106 3767.9822 -1018.1132 2.505174 263.61583 Loop time of 1.19209e-06 on 1 procs for 0 steps with 270 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: 270 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2310 ave 2310 max 2310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8662 ave 8662 max 8662 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17324 ave 17324 max 17324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17324 Ave neighs/atom = 64.163 Neighbor list builds = 0 Dangerous builds = 0 270 -1371.83993433855 eV 2.50517399475156 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03