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 -59.6257 0) to (29.8113 59.6257 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.35446 4.35446 3.15999 Created 357 atoms create_atoms CPU = 0.000249147 secs 357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.35446 4.35446 3.15999 Created 357 atoms create_atoms CPU = 0.000132084 secs 357 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXsSYsF4/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-XXXXXXsSYsF4/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 = 10 37 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 6 atoms, new total = 708 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 = 10 37 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) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15806.371 0 -15806.371 8291.093 15 0 -15839.611 0 -15839.611 925.70866 Loop time of 3.01726 on 1 procs for 15 steps with 708 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 = -15806.3714967 -15839.5997804 -15839.6111811 Force two-norm initial, final = 60.3903 0.367464 Force max component initial, final = 19.6747 0.0921502 Final line search alpha, max atom move = 0.77708 0.0716081 Iterations, force evaluations = 15 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.016 | 3.016 | 3.016 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078678 | 0.00078678 | 0.00078678 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005062 | | | 0.02 Nlocal: 708 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4962 ave 4962 max 4962 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: 45516 ave 45516 max 45516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45516 Ave neighs/atom = 64.2881 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 : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.96 | 4.96 | 4.96 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -15839.611 0 -15839.611 925.70866 11233.87 16 0 -15839.626 0 -15839.626 1485.097 11231.528 Loop time of 0.327865 on 1 procs for 1 steps with 708 atoms 97.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15839.6111811 -15839.6111811 -15839.6257003 Force two-norm initial, final = 24.7612 4.9198 Force max component initial, final = 19.5658 3.87778 Final line search alpha, max atom move = 5.11097e-05 0.000198192 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32755 | 0.32755 | 0.32755 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002198 | | | 0.07 Nlocal: 708 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4986 ave 4986 max 4986 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: 45504 ave 45504 max 45504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45504 Ave neighs/atom = 64.2712 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 = 10 37 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15839.626 0 -15839.626 1485.097 Loop time of 9.53674e-07 on 1 procs for 0 steps with 708 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: 708 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4992 ave 4992 max 4992 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: 45506 ave 45506 max 45506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45506 Ave neighs/atom = 64.274 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) = 4.591 | 4.591 | 4.591 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 -15839.626 -15839.626 29.832657 119.2514 3.1570644 1485.097 1485.097 553.56122 3473.5447 428.18524 2.4539774 314.99507 Loop time of 2.14577e-06 on 1 procs for 0 steps with 708 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 | | 2.146e-06 | | |100.00 Nlocal: 708 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4992 ave 4992 max 4992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22753 ave 22753 max 22753 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45506 ave 45506 max 45506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45506 Ave neighs/atom = 64.274 Neighbor list builds = 0 Dangerous builds = 0 708 -3608.3622452492 eV 2.45397737194593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03