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 -40.2232 0) to (28.4399 40.2232 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.26665 5.46199 4.4689 Created 326 atoms create_atoms CPU = 0.000359058 secs 326 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.26665 5.46199 4.4689 Created 326 atoms create_atoms CPU = 0.000218868 secs 326 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXpO1On8/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-XXXXXXpO1On8/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 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 8 atoms, new total = 644 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 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) = 4.888 | 4.888 | 4.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14355.957 0 -14355.957 15802.475 12 0 -14400.108 0 -14400.108 7354.2406 Loop time of 2.2875 on 1 procs for 12 steps with 644 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14355.9572039 -14400.0991668 -14400.108173 Force two-norm initial, final = 76.1164 0.326334 Force max component initial, final = 24.2715 0.0587674 Final line search alpha, max atom move = 1 0.0587674 Iterations, force evaluations = 12 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2866 | 2.2866 | 2.2866 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054407 | 0.00054407 | 0.00054407 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003974 | | | 0.02 Nlocal: 644 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3728 ave 3728 max 3728 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: 41444 ave 41444 max 41444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41444 Ave neighs/atom = 64.354 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.888 | 4.888 | 4.888 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -14400.108 0 -14400.108 7354.2406 10224.346 14 0 -14400.149 0 -14400.149 1875.7639 10245.877 Loop time of 0.351034 on 1 procs for 2 steps with 644 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14400.108173 -14400.1466987 -14400.1488889 Force two-norm initial, final = 54.3304 4.47374 Force max component initial, final = 45.0244 4.45214 Final line search alpha, max atom move = 9.08275e-05 0.000404377 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3507 | 0.3507 | 0.3507 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010133 | 0.00010133 | 0.00010133 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002279 | | | 0.06 Nlocal: 644 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3728 ave 3728 max 3728 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: 41348 ave 41348 max 41348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41348 Ave neighs/atom = 64.205 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 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) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14400.149 0 -14400.149 1875.7639 Loop time of 9.53674e-07 on 1 procs for 0 steps with 644 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: 644 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3728 ave 3728 max 3728 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: 41340 ave 41340 max 41340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41340 Ave neighs/atom = 64.1925 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) = 4.519 | 4.519 | 4.519 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 -14400.149 -14400.149 28.479619 80.446487 4.4720627 1875.7639 1875.7639 49.216776 6274.7614 -696.68652 2.4503453 506.34316 Loop time of 1.90735e-06 on 1 procs for 0 steps with 644 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: 644 ave 644 max 644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3728 ave 3728 max 3728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20670 ave 20670 max 20670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41340 ave 41340 max 41340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41340 Ave neighs/atom = 64.1925 Neighbor list builds = 0 Dangerous builds = 0 644 -3274.5363676772 eV 2.45034525415774 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03