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 -38.1854 0) to (46.7636 38.1854 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.48418 4.7074 5.16024 Created 881 atoms create_atoms CPU = 0.000289202 secs 881 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.48418 4.7074 5.16024 Created 881 atoms create_atoms CPU = 0.000211 secs 881 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXLTgVgi/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-XXXXXXLTgVgi/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 = 15 24 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 23 atoms, new total = 1739 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 = 15 24 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) = 5.951 | 5.951 | 5.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -38712.765 0 -38712.765 23719.214 34 0 -38869.996 0 -38869.996 5384.4436 Loop time of 17.0563 on 1 procs for 34 steps with 1739 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 = -38712.7648317 -38869.9634131 -38869.9960195 Force two-norm initial, final = 112.39 0.635893 Force max component initial, final = 13.0353 0.120411 Final line search alpha, max atom move = 0.818396 0.0985436 Iterations, force evaluations = 34 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.048 | 17.048 | 17.048 | 0.0 | 99.95 Neigh | 0.0034039 | 0.0034039 | 0.0034039 | 0.0 | 0.02 Comm | 0.0021014 | 0.0021014 | 0.0021014 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002363 | | | 0.01 Nlocal: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5242 ave 5242 max 5242 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: 111874 ave 111874 max 111874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111874 Ave neighs/atom = 64.3324 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.953 | 5.953 | 5.953 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -38869.996 0 -38869.996 5384.4436 27643.717 35 0 -38870.003 0 -38870.003 4016.1375 27658.256 Loop time of 1.02359 on 1 procs for 1 steps with 1739 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 = -38869.9960195 -38869.9960195 -38870.0033937 Force two-norm initial, final = 38.4929 5.6906 Force max component initial, final = 33.3491 4.9874 Final line search alpha, max atom move = 2.99858e-05 0.000149551 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0231 | 1.0231 | 1.0231 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.203e-05 | 9.203e-05 | 9.203e-05 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003569 | | | 0.03 Nlocal: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223 ave 5223 max 5223 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: 111782 ave 111782 max 111782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111782 Ave neighs/atom = 64.2795 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 = 15 24 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) = 5.584 | 5.584 | 5.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -38870.003 0 -38870.003 4016.1375 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1739 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: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223 ave 5223 max 5223 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: 111778 ave 111778 max 111778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111778 Ave neighs/atom = 64.2772 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) = 5.584 | 5.584 | 5.584 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 -38870.003 -38870.003 46.779158 76.370886 7.7418466 4016.1375 4016.1375 154.46832 12182.908 -288.96342 2.4075845 1766.4046 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1739 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: 1739 ave 1739 max 1739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223 ave 5223 max 5223 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55889 ave 55889 max 55889 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111778 ave 111778 max 111778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111778 Ave neighs/atom = 64.2772 Neighbor list builds = 0 Dangerous builds = 0 1739 -8827.3944272614 eV 2.40758453643702 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19