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 -33.7426 0) to (23.8574 33.7426 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.44116 5.32728 4.4689 Created 229 atoms create_atoms CPU = 0.000196934 secs 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.44116 5.32728 4.4689 Created 229 atoms create_atoms CPU = 9.91821e-05 secs 229 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXB03Q68/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-XXXXXXB03Q68/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 21 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 6 atoms, new total = 452 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 21 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) = 4.75 | 4.75 | 4.75 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10070.435 0 -10070.435 16473.386 22 0 -10104.656 0 -10104.656 1983.1637 Loop time of 2.48376 on 1 procs for 22 steps with 452 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 = -10070.4347667 -10104.6493298 -10104.6561644 Force two-norm initial, final = 54.0323 0.262211 Force max component initial, final = 16.4064 0.051007 Final line search alpha, max atom move = 1 0.051007 Iterations, force evaluations = 22 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4819 | 2.4819 | 2.4819 | 0.0 | 99.92 Neigh | 0.00076604 | 0.00076604 | 0.00076604 | 0.0 | 0.03 Comm | 0.00061941 | 0.00061941 | 0.00061941 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004823 | | | 0.02 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2491 ave 2491 max 2491 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: 29030 ave 29030 max 29030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29030 Ave neighs/atom = 64.2257 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.75 | 4.75 | 4.75 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -10104.656 0 -10104.656 1983.1637 7195.0184 23 0 -10104.663 0 -10104.663 -287.59344 7201.4398 Loop time of 0.273068 on 1 procs for 1 steps with 452 atoms 102.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10104.6561644 -10104.6561644 -10104.6625064 Force two-norm initial, final = 15.6712 6.7191 Force max component initial, final = 15.583 6.67984 Final line search alpha, max atom move = 6.41725e-05 0.000428662 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27283 | 0.27283 | 0.27283 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.5327e-05 | 6.5327e-05 | 6.5327e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000175 | | | 0.06 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2490 ave 2490 max 2490 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: 29042 ave 29042 max 29042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29042 Ave neighs/atom = 64.2522 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 21 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) = 4.382 | 4.382 | 4.382 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10104.663 0 -10104.663 -287.59344 Loop time of 9.53674e-07 on 1 procs for 0 steps with 452 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: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2490 ave 2490 max 2490 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: 29042 ave 29042 max 29042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29042 Ave neighs/atom = 64.2522 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) = 4.382 | 4.382 | 4.382 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 -10104.663 -10104.663 23.876652 67.485203 4.4692778 -287.59344 -287.59344 150.75447 472.72335 -1486.2581 2.5000116 369.32115 Loop time of 9.53674e-07 on 1 procs for 0 steps with 452 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: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2490 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14521 ave 14521 max 14521 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29042 ave 29042 max 29042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29042 Ave neighs/atom = 64.2522 Neighbor list builds = 0 Dangerous builds = 0 452 -2296.0027865782 eV 2.50001158309095 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03