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 -31.603 0) to (15.7999 31.603 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.42398 4.42398 3.15999 Created 101 atoms create_atoms CPU = 0.000175953 secs 101 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.42398 4.42398 3.15999 Created 101 atoms create_atoms CPU = 4.50611e-05 secs 101 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXqBynlr/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-XXXXXXqBynlr/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 = 5 20 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 = 198 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 = 5 20 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) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4406.7753 0 -4406.7753 17116.665 24 0 -4425.6687 0 -4425.6687 -1693.1321 Loop time of 1.49922 on 1 procs for 24 steps with 198 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 = -4406.77529725 -4425.66529877 -4425.66867044 Force two-norm initial, final = 37.6655 0.202637 Force max component initial, final = 13.6398 0.0562145 Final line search alpha, max atom move = 1 0.0562145 Iterations, force evaluations = 24 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4978 | 1.4978 | 1.4978 | 0.0 | 99.90 Neigh | 0.00041485 | 0.00041485 | 0.00041485 | 0.0 | 0.03 Comm | 0.00066829 | 0.00066829 | 0.00066829 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003803 | | | 0.03 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2037 ave 2037 max 2037 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: 12782 ave 12782 max 12782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12782 Ave neighs/atom = 64.5556 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -4425.6687 0 -4425.6687 -1693.1321 3155.7298 26 0 -4425.6774 0 -4425.6774 -1442.5243 3155.4877 Loop time of 0.16002 on 1 procs for 2 steps with 198 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 = -4425.66867044 -4425.6762958 -4425.67744879 Force two-norm initial, final = 10.1173 1.08598 Force max component initial, final = 8.70101 0.976896 Final line search alpha, max atom move = 0.000292031 0.000285284 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1598 | 0.1598 | 0.1598 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.6267e-05 | 5.6267e-05 | 5.6267e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001597 | | | 0.10 Nlocal: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2034 ave 2034 max 2034 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: 12776 ave 12776 max 12776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12776 Ave neighs/atom = 64.5253 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 = 5 20 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) = 4.215 | 4.215 | 4.215 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4425.6774 0 -4425.6774 -1442.5243 Loop time of 9.53674e-07 on 1 procs for 0 steps with 198 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: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2043 ave 2043 max 2043 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: 12778 ave 12778 max 12778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12778 Ave neighs/atom = 64.5354 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) = 4.215 | 4.215 | 4.215 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 -4425.6774 -4425.6774 15.818345 63.206084 3.1560695 -1442.5243 -1442.5243 -217.51887 -3614.6571 -495.39694 2.4845909 113.9435 Loop time of 1.19209e-06 on 1 procs for 0 steps with 198 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: 198 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2043 ave 2043 max 2043 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6389 ave 6389 max 6389 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12778 ave 12778 max 12778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12778 Ave neighs/atom = 64.5354 Neighbor list builds = 0 Dangerous builds = 0 198 -1005.06987238779 eV 2.48459087663713 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01