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 -38.4461 0) to (19.2215 38.4461 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.63649 3.63649 3.15999 Created 149 atoms create_atoms CPU = 0.000176907 secs 149 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.63649 3.63649 3.15999 Created 149 atoms create_atoms CPU = 4.91142e-05 secs 149 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXTytgCJ/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-XXXXXXTytgCJ/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 = 6 24 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 = 294 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 = 6 24 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) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6552.1605 0 -6552.1605 19052.621 27 0 -6573.5516 0 -6573.5516 4865.5824 Loop time of 2.2382 on 1 procs for 27 steps with 294 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6552.16053369 -6573.54727247 -6573.5515928 Force two-norm initial, final = 38.8087 0.192474 Force max component initial, final = 16.1951 0.0317411 Final line search alpha, max atom move = 1 0.0317411 Iterations, force evaluations = 27 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2363 | 2.2363 | 2.2363 | 0.0 | 99.91 Neigh | 0.00052595 | 0.00052595 | 0.00052595 | 0.0 | 0.02 Comm | 0.00088573 | 0.00088573 | 0.00088573 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005231 | | | 0.02 Nlocal: 294 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2621 ave 2621 max 2621 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: 18850 ave 18850 max 18850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18850 Ave neighs/atom = 64.1156 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -6573.5516 0 -6573.5516 4865.5824 4670.397 28 0 -6573.5524 0 -6573.5524 4499.4529 4671.0721 Loop time of 0.163601 on 1 procs for 1 steps with 294 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6573.5515928 -6573.5515928 -6573.55243761 Force two-norm initial, final = 3.91167 0.846926 Force max component initial, final = 3.33743 0.695019 Final line search alpha, max atom move = 0.000299632 0.00020825 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16341 | 0.16341 | 0.16341 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.1022e-05 | 5.1022e-05 | 5.1022e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001438 | | | 0.09 Nlocal: 294 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2621 ave 2621 max 2621 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: 18816 ave 18816 max 18816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18816 Ave neighs/atom = 64 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 = 6 24 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) = 4.288 | 4.288 | 4.288 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6573.5524 0 -6573.5524 4499.4529 Loop time of 9.53674e-07 on 1 procs for 0 steps with 294 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: 294 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2621 ave 2621 max 2621 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: 18816 ave 18816 max 18816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18816 Ave neighs/atom = 64 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) = 4.288 | 4.288 | 4.288 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 -6573.5524 -6573.5524 19.22856 76.892151 3.1592776 4499.4529 4499.4529 -152.41076 13889.107 -238.33768 2.5131713 131.88962 Loop time of 1.90735e-06 on 1 procs for 0 steps with 294 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: 294 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2621 ave 2621 max 2621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9408 ave 9408 max 9408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 18816 ave 18816 max 18816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18816 Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0 294 -1494.46846053587 eV 2.51317125332817 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02