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 -48.1347 0) to (24.0658 48.1347 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.14927 4.14927 3.15999 Created 234 atoms create_atoms CPU = 0.000164032 secs 234 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.14927 4.14927 3.15999 Created 234 atoms create_atoms CPU = 5.00679e-05 secs 234 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXmEAxJp/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-XXXXXXmEAxJp/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 = 8 30 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 8 atoms, new total = 460 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 = 8 30 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) = 4.772 | 4.772 | 4.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10275.915 0 -10275.915 3088.1355 9 0 -10286.366 0 -10286.366 244.43659 Loop time of 1.08385 on 1 procs for 9 steps with 460 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 = -10275.9145897 -10286.3608549 -10286.3660932 Force two-norm initial, final = 23.7187 0.229787 Force max component initial, final = 7.57351 0.0305 Final line search alpha, max atom move = 1 0.0305 Iterations, force evaluations = 9 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0832 | 1.0832 | 1.0832 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038648 | 0.00038648 | 0.00038648 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002282 | | | 0.02 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982 ave 3982 max 3982 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: 29480 ave 29480 max 29480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29480 Ave neighs/atom = 64.087 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 : 9 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.772 | 4.772 | 4.772 Mbytes Step Temp E_pair E_mol TotEng Press Volume 9 0 -10286.366 0 -10286.366 244.43659 7321.0417 10 0 -10286.371 0 -10286.371 2215.4259 7315.5133 Loop time of 0.260624 on 1 procs for 1 steps with 460 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 = -10286.3660932 -10286.3660932 -10286.3706703 Force two-norm initial, final = 15.2492 3.20885 Force max component initial, final = 14.4786 3.02698 Final line search alpha, max atom move = 6.90673e-05 0.000209065 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26038 | 0.26038 | 0.26038 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.0095e-05 | 7.0095e-05 | 7.0095e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001738 | | | 0.07 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982 ave 3982 max 3982 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: 29428 ave 29428 max 29428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29428 Ave neighs/atom = 63.9739 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 = 8 30 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) = 4.404 | 4.404 | 4.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10286.371 0 -10286.371 2215.4259 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982 ave 3982 max 3982 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: 29428 ave 29428 max 29428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29428 Ave neighs/atom = 63.9739 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) = 4.404 | 4.404 | 4.404 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 -10286.371 -10286.371 24.061242 96.269333 3.158194 2215.4259 2215.4259 662.81749 6210.815 -227.35472 2.5097346 311.08586 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982 ave 3982 max 3982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14714 ave 14714 max 14714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29428 ave 29428 max 29428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29428 Ave neighs/atom = 63.9739 Neighbor list builds = 0 Dangerous builds = 0 460 -2339.5045836861 eV 2.50973461829451 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01