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 -40.9613 0) to (23.6472 40.9613 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.06725 4.87597 5.47326 Created 340 atoms create_atoms CPU = 0.00022006 secs 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.06725 4.87597 5.47326 Created 339 atoms create_atoms CPU = 0.000123978 secs 339 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXvqSo3H/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-XXXXXXvqSo3H/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 = 8 25 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 7 atoms, new total = 672 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 = 8 25 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) = 4.922 | 4.922 | 4.922 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14947.771 0 -14947.771 42991.566 27 0 -15022.665 0 -15022.665 22216.397 Loop time of 5.18074 on 1 procs for 27 steps with 672 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14947.7712838 -15022.652385 -15022.665421 Force two-norm initial, final = 87.0598 0.347197 Force max component initial, final = 24.257 0.0430205 Final line search alpha, max atom move = 0.532609 0.0229131 Iterations, force evaluations = 27 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1769 | 5.1769 | 5.1769 | 0.0 | 99.93 Neigh | 0.001631 | 0.001631 | 0.001631 | 0.0 | 0.03 Comm | 0.0012712 | 0.0012712 | 0.0012712 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009 | | | 0.02 Nlocal: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3573 ave 3573 max 3573 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: 43340 ave 43340 max 43340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43340 Ave neighs/atom = 64.494 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.922 | 4.922 | 4.922 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -15022.665 0 -15022.665 22216.397 10603.01 31 0 -15023.014 0 -15023.014 6407.4374 10666.825 Loop time of 0.782861 on 1 procs for 4 steps with 672 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15022.665421 -15023.0141709 -15023.014238 Force two-norm initial, final = 166.483 0.991878 Force max component initial, final = 119.262 0.856405 Final line search alpha, max atom move = 0.000656915 0.000562585 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78226 | 0.78226 | 0.78226 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013757 | 0.00013757 | 0.00013757 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004635 | | | 0.06 Nlocal: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471 ave 3471 max 3471 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: 43368 ave 43368 max 43368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43368 Ave neighs/atom = 64.5357 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 = 8 25 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15023.014 0 -15023.014 6407.4374 Loop time of 2.14577e-06 on 1 procs for 0 steps with 672 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: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3382 ave 3382 max 3382 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: 43336 ave 43336 max 43336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43336 Ave neighs/atom = 64.4881 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) = 4.551 | 4.551 | 4.551 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 -15023.014 -15023.014 23.717454 81.922577 5.489888 6407.4374 6407.4374 -129.01579 19395.712 -44.384306 2.545106 525.66627 Loop time of 1.90735e-06 on 1 procs for 0 steps with 672 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: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3382 ave 3382 max 3382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21668 ave 21668 max 21668 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43336 ave 43336 max 43336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43336 Ave neighs/atom = 64.4881 Neighbor list builds = 0 Dangerous builds = 0 672 -3413.6794332061 eV 2.54510597852754 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06