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 -33.7426 0) to (19.4795 33.7426 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.12618 4.73536 5.47326 Created 230 atoms create_atoms CPU = 0.000189066 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.12618 4.73536 5.47326 Created 230 atoms create_atoms CPU = 7.48634e-05 secs 230 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXoYP7n4/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-XXXXXXoYP7n4/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 21 2 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 = 452 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 21 2 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) = 4.756 | 4.756 | 4.756 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10062.644 0 -10062.644 17206.449 25 0 -10100.64 0 -10100.64 3248.4964 Loop time of 3.40389 on 1 procs for 25 steps with 452 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 = -10062.6441325 -10100.632765 -10100.6402278 Force two-norm initial, final = 63.9261 0.285714 Force max component initial, final = 20.706 0.0462252 Final line search alpha, max atom move = 1 0.0462252 Iterations, force evaluations = 25 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4023 | 3.4023 | 3.4023 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092959 | 0.00092959 | 0.00092959 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006225 | | | 0.02 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2670 ave 2670 max 2670 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: 29136 ave 29136 max 29136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29136 Ave neighs/atom = 64.4602 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.761 | 4.761 | 4.761 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -10100.64 0 -10100.64 3248.4964 7195.0184 27 0 -10100.659 0 -10100.659 -243.1117 7204.9054 Loop time of 0.319145 on 1 procs for 2 steps with 452 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 = -10100.6402278 -10100.6566681 -10100.6594636 Force two-norm initial, final = 27.9863 1.06954 Force max component initial, final = 25.6696 0.756343 Final line search alpha, max atom move = 0.000190958 0.00014443 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31884 | 0.31884 | 0.31884 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.5565e-05 | 6.5565e-05 | 6.5565e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002372 | | | 0.07 Nlocal: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2707 ave 2707 max 2707 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: 29224 ave 29224 max 29224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29224 Ave neighs/atom = 64.6549 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 21 2 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) = 4.392 | 4.392 | 4.392 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10100.659 0 -10100.659 -243.1117 Loop time of 1.90735e-06 on 1 procs for 0 steps with 452 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: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2707 ave 2707 max 2707 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: 29224 ave 29224 max 29224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29224 Ave neighs/atom = 64.6549 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) = 4.392 | 4.392 | 4.392 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 -10100.659 -10100.659 19.476446 67.485203 5.4816337 -243.1117 -243.1117 154.90472 -1052.6874 168.44761 2.5131564 392.64786 Loop time of 9.53674e-07 on 1 procs for 0 steps with 452 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: 452 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2707 ave 2707 max 2707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14612 ave 14612 max 14612 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29224 ave 29224 max 29224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29224 Ave neighs/atom = 64.6549 Neighbor list builds = 0 Dangerous builds = 0 452 -2291.9997436919 eV 2.51315640875361 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04