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 -54.0011 0) to (26.999 54.0011 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.06834 4.06834 3.15999 Created 293 atoms create_atoms CPU = 0.000174046 secs 293 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.06834 4.06834 3.15999 Created 293 atoms create_atoms CPU = 5.79357e-05 secs 293 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXbOZtwS/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-XXXXXXbOZtwS/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 = 9 33 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 6 atoms, new total = 580 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 = 9 33 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) = 4.861 | 4.861 | 4.861 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12925.877 0 -12925.877 12857.868 23 0 -12973.437 0 -12973.437 114.14579 Loop time of 2.89169 on 1 procs for 23 steps with 580 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12925.8768804 -12973.4257503 -12973.4372501 Force two-norm initial, final = 83.1545 0.323001 Force max component initial, final = 23.1124 0.0450832 Final line search alpha, max atom move = 1 0.0450832 Iterations, force evaluations = 23 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8892 | 2.8892 | 2.8892 | 0.0 | 99.91 Neigh | 0.00099301 | 0.00099301 | 0.00099301 | 0.0 | 0.03 Comm | 0.00093412 | 0.00093412 | 0.00093412 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006089 | | | 0.02 Nlocal: 580 ave 580 max 580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4274 ave 4274 max 4274 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: 37250 ave 37250 max 37250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37250 Ave neighs/atom = 64.2241 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.861 | 4.861 | 4.861 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -12973.437 0 -12973.437 114.14579 9214.3489 24 0 -12973.446 0 -12973.446 2418.4271 9206.1723 Loop time of 0.276236 on 1 procs for 1 steps with 580 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12973.4372501 -12973.4372501 -12973.4464023 Force two-norm initial, final = 23.0518 6.63801 Force max component initial, final = 22.8559 6.57096 Final line search alpha, max atom move = 4.37523e-05 0.000287494 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27593 | 0.27593 | 0.27593 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.9182e-05 | 9.9182e-05 | 9.9182e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002053 | | | 0.07 Nlocal: 580 ave 580 max 580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4253 ave 4253 max 4253 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: 37198 ave 37198 max 37198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37198 Ave neighs/atom = 64.1345 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 = 9 33 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) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12973.446 0 -12973.446 2418.4271 Loop time of 2.14577e-06 on 1 procs for 0 steps with 580 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 | | 2.146e-06 | | |100.00 Nlocal: 580 ave 580 max 580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4255 ave 4255 max 4255 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: 37200 ave 37200 max 37200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37200 Ave neighs/atom = 64.1379 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) = 4.492 | 4.492 | 4.492 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 -12973.446 -12973.446 26.996186 108.00212 3.1575075 2418.4271 2418.4271 1143.4452 6265.3215 -153.48538 2.4836233 333.12157 Loop time of 9.53674e-07 on 1 procs for 0 steps with 580 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: 580 ave 580 max 580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4255 ave 4255 max 4255 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18600 ave 18600 max 18600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37200 ave 37200 max 37200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37200 Ave neighs/atom = 64.1379 Neighbor list builds = 0 Dangerous builds = 0 580 -2953.4848148309 eV 2.48362328678004 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03