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 -35.7543 0) to (5.47326 35.7543 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.47326 4.4689 5.16024 Created 102 atoms create_atoms CPU = 0.000169039 secs 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.47326 4.4689 5.16024 Created 102 atoms create_atoms CPU = 4.60148e-05 secs 102 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX915mWu/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-XXXXXX915mWu/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 22 3 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 12 atoms, new total = 192 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 22 3 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4301.9464 0 -4301.9464 -226.70781 1 0 -4301.9469 0 -4301.9469 -227.90341 Loop time of 0.0984821 on 1 procs for 1 steps with 192 atoms 101.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4301.94639134 -4301.94639134 -4301.9469268 Force two-norm initial, final = 0.135877 0.0451983 Force max component initial, final = 0.0391059 0.0129164 Final line search alpha, max atom move = 1 0.0129164 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.098401 | 0.098401 | 0.098401 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.8147e-05 | 3.8147e-05 | 3.8147e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.315e-05 | | | 0.04 Nlocal: 192 ave 192 max 192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2006 ave 2006 max 2006 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: 12288 ave 12288 max 12288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12288 Ave neighs/atom = 64 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -4301.9469 0 -4301.9469 -227.90341 3029.4655 2 0 -4301.9469 0 -4301.9469 -90.833269 3029.305 Loop time of 0.0973799 on 1 procs for 1 steps with 192 atoms 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4301.9469268 -4301.9469268 -4301.94693486 Force two-norm initial, final = 0.423824 0.0493261 Force max component initial, final = 0.31268 0.0154188 Final line search alpha, max atom move = 0.00319816 4.93118e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.097263 | 0.097263 | 0.097263 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.059e-05 | | | 0.08 Nlocal: 192 ave 192 max 192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2006 ave 2006 max 2006 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: 12288 ave 12288 max 12288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12288 Ave neighs/atom = 64 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 22 3 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) = 4.234 | 4.234 | 4.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4301.9469 0 -4301.9469 -90.833269 Loop time of 1.19209e-06 on 1 procs for 0 steps with 192 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: 192 ave 192 max 192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2006 ave 2006 max 2006 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: 12288 ave 12288 max 12288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12288 Ave neighs/atom = 64 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) = 4.234 | 4.234 | 4.234 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 -4301.9469 -4301.9469 5.4731078 71.508691 7.7401641 -90.833269 -90.833269 -6.5919308 -274.06257 8.1546964 2.7365539 8.6644325e-05 Loop time of 9.53674e-07 on 1 procs for 0 steps with 192 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: 192 ave 192 max 192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2006 ave 2006 max 2006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6144 ave 6144 max 6144 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12288 ave 12288 max 12288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12288 Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0 192 -984.99413350812 eV 2.73655392420173 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00