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 -56.8829 0) to (40.2201 56.8829 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.46199 5.26665 4.4689 Created 650 atoms create_atoms CPU = 0.000613928 secs 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.46199 5.26665 4.4689 Created 650 atoms create_atoms CPU = 0.00048089 secs 650 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX66QFN2/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-XXXXXX66QFN2/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 = 13 35 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 4 atoms, new total = 1296 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 = 13 35 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) = 5.351 | 5.351 | 5.351 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -28882.901 0 -28882.901 27819.062 24 0 -29003.709 0 -29003.709 12718.71 Loop time of 7.30186 on 1 procs for 24 steps with 1296 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -28882.9013198 -29003.6874043 -29003.7094436 Force two-norm initial, final = 117.992 0.516204 Force max component initial, final = 29.1011 0.117994 Final line search alpha, max atom move = 0.922879 0.108894 Iterations, force evaluations = 24 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2958 | 7.2958 | 7.2958 | 0.0 | 99.92 Neigh | 0.003449 | 0.003449 | 0.003449 | 0.0 | 0.05 Comm | 0.0014634 | 0.0014634 | 0.0014634 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00116 | | | 0.02 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368 ave 6368 max 6368 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: 83288 ave 83288 max 83288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83288 Ave neighs/atom = 64.2654 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.351 | 5.351 | 5.351 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -29003.709 0 -29003.709 12718.71 20448.22 27 0 -29003.908 0 -29003.908 4458.0297 20513.329 Loop time of 1.35489 on 1 procs for 3 steps with 1296 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -29003.7094436 -29003.9051463 -29003.9079286 Force two-norm initial, final = 170.762 0.509812 Force max component initial, final = 134.673 0.102708 Final line search alpha, max atom move = 0.000102293 1.05064e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3538 | 1.3538 | 1.3538 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023079 | 0.00023079 | 0.00023079 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008352 | | | 0.06 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368 ave 6368 max 6368 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: 83200 ave 83200 max 83200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83200 Ave neighs/atom = 64.1975 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 = 13 35 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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -29003.908 0 -29003.908 4458.0297 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1296 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: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368 ave 6368 max 6368 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: 83192 ave 83192 max 83192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83192 Ave neighs/atom = 64.1914 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) = 4.982 | 4.982 | 4.982 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 -29003.908 -29003.908 40.308221 113.7659 4.4733246 4458.0297 4458.0297 -1.2390659 13374.157 1.1708878 2.5007458 644.26328 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1296 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: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368 ave 6368 max 6368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41596 ave 41596 max 41596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83192 ave 83192 max 83192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83192 Ave neighs/atom = 64.1914 Neighbor list builds = 0 Dangerous builds = 0 1296 -6614.4765194534 eV 2.5007457543128 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09