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 -40.4708 0) to (20.2338 40.4708 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.44157 4.44157 3.15999 Created 165 atoms create_atoms CPU = 0.000185966 secs 165 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.44157 4.44157 3.15999 Created 165 atoms create_atoms CPU = 6.00815e-05 secs 165 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXlow2qE/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-XXXXXXlow2qE/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 = 7 25 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 = 326 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 = 7 25 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) = 4.676 | 4.676 | 4.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7258.8689 0 -7258.8689 19089.932 25 0 -7292.1574 0 -7292.1574 1212.3697 Loop time of 2.61204 on 1 procs for 25 steps with 326 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7258.86888198 -7292.15189246 -7292.15741408 Force two-norm initial, final = 59.4802 0.251344 Force max component initial, final = 22.9529 0.05547 Final line search alpha, max atom move = 0.88765 0.0492379 Iterations, force evaluations = 25 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.61 | 2.61 | 2.61 | 0.0 | 99.92 Neigh | 0.00060797 | 0.00060797 | 0.00060797 | 0.0 | 0.02 Comm | 0.0009191 | 0.0009191 | 0.0009191 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005207 | | | 0.02 Nlocal: 326 ave 326 max 326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2832 ave 2832 max 2832 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: 20996 ave 20996 max 20996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20996 Ave neighs/atom = 64.4049 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.676 | 4.676 | 4.676 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -7292.1574 0 -7292.1574 1212.3697 5175.2835 27 0 -7292.1655 0 -7292.1655 -64.181128 5177.9229 Loop time of 0.224707 on 1 procs for 2 steps with 326 atoms 102.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7292.15741408 -7292.16474025 -7292.16547851 Force two-norm initial, final = 12.96 1.50645 Force max component initial, final = 12.6797 1.47141 Final line search alpha, max atom move = 0.000223614 0.000329028 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22442 | 0.22442 | 0.22442 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.081e-05 | 7.081e-05 | 7.081e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002131 | | | 0.09 Nlocal: 326 ave 326 max 326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2828 ave 2828 max 2828 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: 20992 ave 20992 max 20992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20992 Ave neighs/atom = 64.3926 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 = 7 25 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) = 4.308 | 4.308 | 4.308 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7292.1655 0 -7292.1655 -64.181128 Loop time of 1.19209e-06 on 1 procs for 0 steps with 326 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 | | 1.192e-06 | | |100.00 Nlocal: 326 ave 326 max 326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2830 ave 2830 max 2830 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: 20990 ave 20990 max 20990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20990 Ave neighs/atom = 64.3865 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) = 4.308 | 4.308 | 4.308 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 -7292.1655 -7292.1655 20.254961 80.941508 3.1582963 -64.181128 -64.181128 455.76575 -711.58895 63.27981 2.495993 119.44887 Loop time of 1.19209e-06 on 1 procs for 0 steps with 326 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 | | 1.192e-06 | | |100.00 Nlocal: 326 ave 326 max 326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2830 ave 2830 max 2830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10495 ave 10495 max 10495 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20990 ave 20990 max 20990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20990 Ave neighs/atom = 64.3865 Neighbor list builds = 0 Dangerous builds = 0 326 -1660.25603454212 eV 2.49599295438526 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03