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 -58.2705 0) to (29.1337 58.2705 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.45573 4.45573 3.15999 Created 341 atoms create_atoms CPU = 0.000264883 secs 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.45573 4.45573 3.15999 Created 341 atoms create_atoms CPU = 0.000112057 secs 341 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX5DqrNN/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-XXXXXX5DqrNN/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 = 9 36 1 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 = 678 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 = 9 36 1 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) = 4.94 | 4.94 | 4.94 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15115.422 0 -15115.422 17063.054 17 0 -15176.76 0 -15176.76 2321.1423 Loop time of 2.9269 on 1 procs for 17 steps with 678 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 = -15115.4216218 -15176.7487419 -15176.7596551 Force two-norm initial, final = 88.3958 0.347518 Force max component initial, final = 28.6253 0.0593461 Final line search alpha, max atom move = 1 0.0593461 Iterations, force evaluations = 17 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9255 | 2.9255 | 2.9255 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083065 | 0.00083065 | 0.00083065 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000526 | | | 0.02 Nlocal: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4827 ave 4827 max 4827 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: 43730 ave 43730 max 43730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43730 Ave neighs/atom = 64.4985 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 : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.94 | 4.94 | 4.94 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -15176.76 0 -15176.76 2321.1423 10728.99 18 0 -15176.77 0 -15176.77 -107.3606 10739.159 Loop time of 0.33338 on 1 procs for 1 steps with 678 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15176.7596551 -15176.7596551 -15176.7695256 Force two-norm initial, final = 25.4849 7.60557 Force max component initial, final = 24.6643 7.36564 Final line search alpha, max atom move = 4.05444e-05 0.000298636 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33312 | 0.33312 | 0.33312 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.2016e-05 | 8.2016e-05 | 8.2016e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001769 | | | 0.05 Nlocal: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879 ave 4879 max 4879 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: 43542 ave 43542 max 43542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43542 Ave neighs/atom = 64.2212 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 = 9 36 1 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) = 4.572 | 4.572 | 4.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15176.77 0 -15176.77 -107.3606 Loop time of 9.53674e-07 on 1 procs for 0 steps with 678 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: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879 ave 4879 max 4879 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: 43538 ave 43538 max 43538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43538 Ave neighs/atom = 64.2153 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) = 4.572 | 4.572 | 4.572 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 -15176.77 -15176.77 29.155567 116.54093 3.1606056 -107.3606 -107.3606 278.20947 498.80456 -1099.0958 2.4959505 134.43823 Loop time of 9.53674e-07 on 1 procs for 0 steps with 678 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: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879 ave 4879 max 4879 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21769 ave 21769 max 21769 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43538 ave 43538 max 43538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43538 Ave neighs/atom = 64.2153 Neighbor list builds = 0 Dangerous builds = 0 678 -3463.7799457627 eV 2.49595048256914 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03