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 -37.3926 0) to (45.7926 37.3926 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.23344 4.80722 5.16024 Created 841 atoms create_atoms CPU = 0.000333071 secs 841 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.23344 4.80722 5.16024 Created 841 atoms create_atoms CPU = 0.000224113 secs 841 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXarHRma/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-XXXXXXarHRma/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 = 14 23 3 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 26 atoms, new total = 1656 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 = 14 23 3 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) = 5.948 | 5.948 | 5.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -36854.476 0 -36854.476 10481.374 69 0 -37010.322 0 -37010.322 -9591.593 Loop time of 31.1701 on 1 procs for 69 steps with 1656 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 = -36854.4759931 -37010.2876541 -37010.322093 Force two-norm initial, final = 127.229 0.649629 Force max component initial, final = 23.6516 0.0997983 Final line search alpha, max atom move = 0.920766 0.0918909 Iterations, force evaluations = 69 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.154 | 31.154 | 31.154 | 0.0 | 99.95 Neigh | 0.0077062 | 0.0077062 | 0.0077062 | 0.0 | 0.02 Comm | 0.0039797 | 0.0039797 | 0.0039797 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004193 | | | 0.01 Nlocal: 1656 ave 1656 max 1656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5407 ave 5407 max 5407 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: 106442 ave 106442 max 106442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106442 Ave neighs/atom = 64.2766 Neighbor list builds = 2 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.959 | 5.959 | 5.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -37010.322 0 -37010.322 -9591.593 26507.72 71 0 -37010.48 0 -37010.48 -3180.3397 26440.996 Loop time of 1.26456 on 1 procs for 2 steps with 1656 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -37010.322093 -37010.4570297 -37010.4795888 Force two-norm initial, final = 170.222 19.3251 Force max component initial, final = 145.008 18.5173 Final line search alpha, max atom move = 1.6895e-05 0.000312849 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.264 | 1.264 | 1.264 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011587 | 0.00011587 | 0.00011587 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000488 | | | 0.04 Nlocal: 1656 ave 1656 max 1656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5021 ave 5021 max 5021 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: 106404 ave 106404 max 106404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106404 Ave neighs/atom = 64.2536 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 = 14 23 3 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) = 5.587 | 5.587 | 5.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -37010.48 0 -37010.48 -3180.3397 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1656 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: 1656 ave 1656 max 1656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5028 ave 5028 max 5028 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: 106422 ave 106422 max 106422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106422 Ave neighs/atom = 64.2645 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) = 5.587 | 5.587 | 5.587 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 -37010.48 -37010.48 45.755124 74.785289 7.7271954 -3180.3397 -3180.3397 1121.1254 -10330.124 -332.0205 2.4631711 1619.0719 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1656 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: 1656 ave 1656 max 1656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5028 ave 5028 max 5028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53211 ave 53211 max 53211 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106422 ave 106422 max 106422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106422 Ave neighs/atom = 64.2645 Neighbor list builds = 0 Dangerous builds = 0 1656 -8401.7616770967 eV 2.46317105962573 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33