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 -55.8197 0) to (32.2257 55.8197 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9578 5.00917 5.47326 Created 627 atoms create_atoms CPU = 0.000525951 secs 627 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9578 5.00917 5.47326 Created 628 atoms create_atoms CPU = 0.0003829 secs 628 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXHIS0l7/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-XXXXXXHIS0l7/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 = 10 34 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 = 1248 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 = 10 34 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) = 5.319 | 5.319 | 5.319 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27810.423 0 -27810.423 30577.501 18 0 -27916.156 0 -27916.156 15731.671 Loop time of 5.87627 on 1 procs for 18 steps with 1248 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -27810.423123 -27916.1282186 -27916.1559001 Force two-norm initial, final = 112.1 0.557754 Force max component initial, final = 22.3468 0.0551417 Final line search alpha, max atom move = 1 0.0551417 Iterations, force evaluations = 18 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8743 | 5.8743 | 5.8743 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011282 | 0.0011282 | 0.0011282 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008848 | | | 0.02 Nlocal: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5612 ave 5612 max 5612 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: 80736 ave 80736 max 80736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80736 Ave neighs/atom = 64.6923 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.319 | 5.319 | 5.319 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -27916.156 0 -27916.156 15731.671 19690.9 21 0 -27916.484 0 -27916.484 4617.346 19774.674 Loop time of 1.08295 on 1 procs for 3 steps with 1248 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 = -27916.1559001 -27916.482066 -27916.4844045 Force two-norm initial, final = 220.086 0.640952 Force max component initial, final = 160.18 0.265094 Final line search alpha, max atom move = 7.60542e-05 2.01615e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0823 | 1.0823 | 1.0823 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015926 | 0.00015926 | 0.00015926 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005205 | | | 0.05 Nlocal: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5573 ave 5573 max 5573 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: 80344 ave 80344 max 80344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80344 Ave neighs/atom = 64.3782 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 = 10 34 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) = 4.95 | 4.95 | 4.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -27916.484 0 -27916.484 4617.346 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1248 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: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5573 ave 5573 max 5573 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: 80328 ave 80328 max 80328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80328 Ave neighs/atom = 64.3654 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) = 4.95 | 4.95 | 4.95 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 -27916.484 -27916.484 32.296071 111.63936 5.4845663 4617.346 4617.346 -21.525292 13869.188 4.3750693 2.5123782 629.85394 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1248 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: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5573 ave 5573 max 5573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40164 ave 40164 max 40164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80328 ave 80328 max 80328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80328 Ave neighs/atom = 64.3654 Neighbor list builds = 0 Dangerous builds = 0 1248 -6356.2911956398 eV 2.51237815160789 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07