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 -32.2288 0) to (16.1128 32.2288 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.71835 3.71835 3.15999 Created 106 atoms create_atoms CPU = 0.000226021 secs 106 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.71835 3.71835 3.15999 Created 106 atoms create_atoms CPU = 3.8147e-05 secs 106 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXkV4piL/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-XXXXXXkV4piL/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 8 atoms, new total = 204 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) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4548.4713 0 -4548.4713 -1994.9388 31 0 -4559.0727 0 -4559.0727 -20441.959 Loop time of 1.86179 on 1 procs for 31 steps with 204 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 = -4548.47134677 -4559.06987921 -4559.07266931 Force two-norm initial, final = 15.1734 0.128663 Force max component initial, final = 5.70627 0.0178718 Final line search alpha, max atom move = 1 0.0178718 Iterations, force evaluations = 31 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.86 | 1.86 | 1.86 | 0.0 | 99.90 Neigh | 0.00042605 | 0.00042605 | 0.00042605 | 0.0 | 0.02 Comm | 0.00092769 | 0.00092769 | 0.00092769 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004811 | | | 0.03 Nlocal: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2254 ave 2254 max 2254 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: 13088 ave 13088 max 13088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13088 Ave neighs/atom = 64.1569 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 : 31 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 31 0 -4559.0727 0 -4559.0727 -20441.959 3281.9526 35 0 -4559.1873 0 -4559.1873 -5116.7346 3262.1561 Loop time of 0.249292 on 1 procs for 4 steps with 204 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4559.07266931 -4559.18608681 -4559.18730769 Force two-norm initial, final = 52.9943 0.710216 Force max component initial, final = 40.5399 0.590808 Final line search alpha, max atom move = 0.000209905 0.000124013 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24892 | 0.24892 | 0.24892 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.7976e-05 | 8.7976e-05 | 8.7976e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002804 | | | 0.11 Nlocal: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2211 ave 2211 max 2211 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: 13048 ave 13048 max 13048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13048 Ave neighs/atom = 63.9608 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) = 4.214 | 4.214 | 4.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4559.1873 0 -4559.1873 -5116.7346 Loop time of 1.19209e-06 on 1 procs for 0 steps with 204 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: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2223 ave 2223 max 2223 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: 13064 ave 13064 max 13064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13064 Ave neighs/atom = 64.0392 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) = 4.214 | 4.214 | 4.214 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 -4559.1873 -4559.1873 16.070091 64.457686 3.1492831 -5116.7346 -5116.7346 289.39958 -15469.21 -170.39341 2.5594024 142.62521 Loop time of 9.53674e-07 on 1 procs for 0 steps with 204 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: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2223 ave 2223 max 2223 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6532 ave 6532 max 6532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13064 ave 13064 max 13064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13064 Ave neighs/atom = 64.0392 Neighbor list builds = 0 Dangerous builds = 0 204 -1034.92495624982 eV 2.55940235384956 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02