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 -60.4573 0) to (34.9032 60.4573 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.14965 4.62491 5.47326 Created 733 atoms create_atoms CPU = 0.000329018 secs 733 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.14965 4.62491 5.47326 Created 734 atoms create_atoms CPU = 0.000251055 secs 734 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXN4aRKI/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-XXXXXXN4aRKI/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 = 11 37 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 3 atoms, new total = 1464 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 = 11 37 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) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -32638.973 0 -32638.973 28258.663 48 0 -32760.118 0 -32760.118 12688.683 Loop time of 20.8479 on 1 procs for 48 steps with 1464 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 = -32638.9729514 -32760.0865888 -32760.1179833 Force two-norm initial, final = 113.042 0.59272 Force max component initial, final = 26.7968 0.0869225 Final line search alpha, max atom move = 0.810771 0.0704743 Iterations, force evaluations = 48 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.841 | 20.841 | 20.841 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0040467 | 0.0040467 | 0.0040467 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002882 | | | 0.01 Nlocal: 1464 ave 1464 max 1464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6425 ave 6425 max 6425 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: 94728 ave 94728 max 94728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94728 Ave neighs/atom = 64.7049 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.471 | 5.471 | 5.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -32760.118 0 -32760.118 12688.683 23098.84 51 0 -32760.385 0 -32760.385 3478.0317 23180.82 Loop time of 1.36288 on 1 procs for 3 steps with 1464 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 = -32760.1179833 -32760.3848924 -32760.3853035 Force two-norm initial, final = 214.146 0.621612 Force max component initial, final = 154.28 0.145898 Final line search alpha, max atom move = 0.000285759 4.16918e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3619 | 1.3619 | 1.3619 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002172 | 0.0002172 | 0.0002172 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007641 | | | 0.06 Nlocal: 1464 ave 1464 max 1464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6361 ave 6361 max 6361 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: 94176 ave 94176 max 94176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94176 Ave neighs/atom = 64.3279 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 = 11 37 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) = 5.102 | 5.102 | 5.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -32760.385 0 -32760.385 3478.0317 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1464 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: 1464 ave 1464 max 1464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6350 ave 6350 max 6350 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: 94152 ave 94152 max 94152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94152 Ave neighs/atom = 64.3115 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) = 5.102 | 5.102 | 5.102 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 -32760.385 -32760.385 34.958849 120.91459 5.4839433 3478.0317 3478.0317 -2.2141073 10446.413 -10.103659 2.5345894 547.51618 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1464 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: 1464 ave 1464 max 1464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6350 ave 6350 max 6350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47076 ave 47076 max 47076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94152 ave 94152 max 94152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94152 Ave neighs/atom = 64.3115 Neighbor list builds = 0 Dangerous builds = 0 1464 -7468.620193172 eV 2.53458941780866 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23