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 -38.705 0) to (5.47326 38.705 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.47326 5.16024 4.4689 Created 62 atoms create_atoms CPU = 0.000161886 secs 62 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.47326 5.16024 4.4689 Created 62 atoms create_atoms CPU = 5.10216e-05 secs 62 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXZrZPzI/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-XXXXXXZrZPzI/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 = 2 24 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 4 atoms, new total = 120 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 = 2 24 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) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2684.9065 0 -2684.9065 10050.469 9 0 -2686.5908 0 -2686.5908 8121.4599 Loop time of 0.254294 on 1 procs for 9 steps with 120 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2684.90650615 -2686.58940431 -2686.59084978 Force two-norm initial, final = 4.4984 0.106238 Force max component initial, final = 1.65916 0.0218456 Final line search alpha, max atom move = 1 0.0218456 Iterations, force evaluations = 9 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.254 | 0.254 | 0.254 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018048 | 0.00018048 | 0.00018048 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000113 | | | 0.04 Nlocal: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1616 ave 1616 max 1616 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: 7744 ave 7744 max 7744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7744 Ave neighs/atom = 64.5333 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 : 9 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 9 0 -2686.5908 0 -2686.5908 8121.4599 1893.4032 11 0 -2686.5959 0 -2686.5959 3727.1914 1896.6288 Loop time of 0.0734801 on 1 procs for 2 steps with 120 atoms 95.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2686.59084978 -2686.59590199 -2686.59592284 Force two-norm initial, final = 8.42893 0.11182 Force max component initial, final = 6.09887 0.0340611 Final line search alpha, max atom move = 0.00486083 0.000165565 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073305 | 0.073305 | 0.073305 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.0306e-05 | 5.0306e-05 | 5.0306e-05 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001252 | | | 0.17 Nlocal: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1575 ave 1575 max 1575 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: 7704 ave 7704 max 7704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7704 Ave neighs/atom = 64.2 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 = 2 24 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) = 4.176 | 4.176 | 4.176 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2686.5959 0 -2686.5959 3727.1914 Loop time of 9.53674e-07 on 1 procs for 0 steps with 120 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: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1561 ave 1561 max 1561 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: 7704 ave 7704 max 7704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7704 Ave neighs/atom = 64.2 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) = 4.176 | 4.176 | 4.176 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 -2686.5959 -2686.5959 5.4785272 77.409907 4.4722078 3727.1914 3727.1914 -28.800793 11192.86 17.51522 2.7104775 60.67433 Loop time of 9.53674e-07 on 1 procs for 0 steps with 120 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: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1561 ave 1561 max 1561 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3852 ave 3852 max 3852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7704 ave 7704 max 7704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7704 Ave neighs/atom = 64.2 Neighbor list builds = 0 Dangerous builds = 0 120 -613.50042199317 eV 2.71047751572203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00