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 -41.9251 0) to (25.6719 41.9251 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.66761 4.76386 5.16024 Created 533 atoms create_atoms CPU = 0.000326872 secs 533 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.66761 4.76386 5.16024 Created 533 atoms create_atoms CPU = 0.000200033 secs 533 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXIcPJq3/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-XXXXXXIcPJq3/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 = 8 26 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 22 atoms, new total = 1044 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 = 8 26 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) = 5.168 | 5.168 | 5.168 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23290.748 0 -23290.748 1294.4589 34 0 -23341.768 0 -23341.768 -7984.6067 Loop time of 10.8141 on 1 procs for 34 steps with 1044 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 = -23290.7481335 -23341.7453098 -23341.7676319 Force two-norm initial, final = 63.9649 0.555428 Force max component initial, final = 12.9444 0.0775046 Final line search alpha, max atom move = 1 0.0775046 Iterations, force evaluations = 34 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.811 | 10.811 | 10.811 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017571 | 0.0017571 | 0.0017571 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001667 | | | 0.02 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4101 ave 4101 max 4101 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: 66888 ave 66888 max 66888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66888 Ave neighs/atom = 64.069 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.175 | 5.175 | 5.175 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -23341.768 0 -23341.768 -7984.6067 16661.843 36 0 -23341.916 0 -23341.916 -74.631845 16610.503 Loop time of 0.762961 on 1 procs for 2 steps with 1044 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -23341.7676319 -23341.8966715 -23341.916308 Force two-norm initial, final = 135.65 2.47108 Force max component initial, final = 97.4189 1.71296 Final line search alpha, max atom move = 2.70644e-05 4.63604e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76249 | 0.76249 | 0.76249 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010204 | 0.00010204 | 0.00010204 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003657 | | | 0.05 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3794 ave 3794 max 3794 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: 66888 ave 66888 max 66888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66888 Ave neighs/atom = 64.069 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 = 8 26 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) = 4.804 | 4.804 | 4.804 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23341.916 0 -23341.916 -74.631845 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1044 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: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3794 ave 3794 max 3794 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: 66888 ave 66888 max 66888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66888 Ave neighs/atom = 64.069 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) = 4.804 | 4.804 | 4.804 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 -23341.916 -23341.916 25.633503 83.850282 7.7280567 -74.631845 -74.631845 163.01112 -221.94429 -164.96237 2.4404225 924.32503 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1044 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: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3794 ave 3794 max 3794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33444 ave 33444 max 33444 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66888 ave 66888 max 66888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66888 Ave neighs/atom = 64.069 Neighbor list builds = 0 Dangerous builds = 0 1044 -5305.9854505828 eV 2.44042252172183 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12