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 -31.9175 0) to (22.5668 31.9175 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.98238 5.00617 4.4689 Created 206 atoms create_atoms CPU = 0.0001719 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.98238 5.00617 4.4689 Created 206 atoms create_atoms CPU = 6.07967e-05 secs 206 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXwjXXB7/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-XXXXXXwjXXB7/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 = 7 20 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 8 atoms, new total = 404 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 = 7 20 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) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8988.4946 0 -8988.4946 18669.749 29 0 -9028.6068 0 -9028.6068 7470.3024 Loop time of 2.9098 on 1 procs for 29 steps with 404 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8988.4946222 -9028.60268679 -9028.60681724 Force two-norm initial, final = 60.5323 0.202565 Force max component initial, final = 18.7935 0.0278753 Final line search alpha, max atom move = 1 0.0278753 Iterations, force evaluations = 29 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9072 | 2.9072 | 2.9072 | 0.0 | 99.91 Neigh | 0.0010729 | 0.0010729 | 0.0010729 | 0.0 | 0.04 Comm | 0.0009253 | 0.0009253 | 0.0009253 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006306 | | | 0.02 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2700 ave 2700 max 2700 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: 25968 ave 25968 max 25968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25968 Ave neighs/atom = 64.2772 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -9028.6068 0 -9028.6068 7470.3024 6437.6825 31 0 -9028.6262 0 -9028.6262 2921.8785 6449.0478 Loop time of 0.299267 on 1 procs for 2 steps with 404 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9028.60681724 -9028.62527369 -9028.62616177 Force two-norm initial, final = 29.207 2.00967 Force max component initial, final = 25.808 1.89755 Final line search alpha, max atom move = 0.000212294 0.000402839 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29899 | 0.29899 | 0.29899 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.9857e-05 | 6.9857e-05 | 6.9857e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002069 | | | 0.07 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2712 ave 2712 max 2712 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: 25936 ave 25936 max 25936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25936 Ave neighs/atom = 64.198 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 = 7 20 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) = 4.349 | 4.349 | 4.349 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9028.6262 0 -9028.6262 2921.8785 Loop time of 9.53674e-07 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2712 ave 2712 max 2712 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: 25928 ave 25928 max 25928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25928 Ave neighs/atom = 64.1782 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) = 4.349 | 4.349 | 4.349 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 -9028.6262 -9028.6262 22.597154 63.834953 4.47078 2921.8785 2921.8785 -156.43336 9393.688 -471.61908 2.533713 500.29223 Loop time of 1.90735e-06 on 1 procs for 0 steps with 404 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 | | 1.907e-06 | | |100.00 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2712 ave 2712 max 2712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12964 ave 12964 max 12964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25928 ave 25928 max 25928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25928 Ave neighs/atom = 64.1782 Neighbor list builds = 0 Dangerous builds = 0 404 -2049.20464224883 eV 2.53371296466784 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03