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 -47.7179 0) to (33.7394 47.7179 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.32728 4.60406 4.4689 Created 458 atoms create_atoms CPU = 0.000383139 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.32728 4.60406 4.4689 Created 458 atoms create_atoms CPU = 0.000226021 secs 458 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXqrS8LL/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-XXXXXXqrS8LL/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 = 11 29 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 12 atoms, new total = 904 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 = 11 29 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) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20147.598 0 -20147.598 5369.1655 38 0 -20214.29 0 -20214.29 -1946.0675 Loop time of 11.0184 on 1 procs for 38 steps with 904 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20147.5979365 -20214.2716642 -20214.289883 Force two-norm initial, final = 104.576 0.496361 Force max component initial, final = 32.6338 0.0737554 Final line search alpha, max atom move = 1 0.0737554 Iterations, force evaluations = 38 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.012 | 11.012 | 11.012 | 0.0 | 99.94 Neigh | 0.0023091 | 0.0023091 | 0.0023091 | 0.0 | 0.02 Comm | 0.0026503 | 0.0026503 | 0.0026503 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001652 | | | 0.01 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4812 ave 4812 max 4812 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: 57996 ave 57996 max 57996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57996 Ave neighs/atom = 64.1549 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -20214.29 0 -20214.29 -1946.0675 14389.642 40 0 -20214.315 0 -20214.315 1124.2482 14372.723 Loop time of 0.781664 on 1 procs for 2 steps with 904 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 = -20214.289883 -20214.3128863 -20214.3151626 Force two-norm initial, final = 48.6251 0.498999 Force max component initial, final = 43.5433 0.0728083 Final line search alpha, max atom move = 0.000129403 9.42161e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78112 | 0.78112 | 0.78112 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013399 | 0.00013399 | 0.00013399 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004139 | | | 0.05 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4808 ave 4808 max 4808 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: 57972 ave 57972 max 57972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57972 Ave neighs/atom = 64.1283 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 = 11 29 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) = 4.704 | 4.704 | 4.704 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20214.315 0 -20214.315 1124.2482 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4808 ave 4808 max 4808 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: 57980 ave 57980 max 57980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57980 Ave neighs/atom = 64.1372 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) = 4.704 | 4.704 | 4.704 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 -20214.315 -20214.315 33.738243 95.435871 4.4638021 1124.2482 1124.2482 -5.9704245 3377.6095 1.1056268 2.4344701 730.95922 Loop time of 1.90735e-06 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4808 ave 4808 max 4808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28990 ave 28990 max 28990 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57980 ave 57980 max 57980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57980 Ave neighs/atom = 64.1372 Neighbor list builds = 0 Dangerous builds = 0 904 -4596.9957228436 eV 2.43447010492673 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12