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 -34.1837 0) to (11.3935 34.1837 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.38212 4.38212 3.15999 Created 79 atoms create_atoms CPU = 0.00019908 secs 79 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.38212 4.38212 3.15999 Created 79 atoms create_atoms CPU = 3.69549e-05 secs 79 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX9lxrHw/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-XXXXXX9lxrHw/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 = 4 21 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 4 atoms, new total = 154 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 = 4 21 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3432.0675 0 -3432.0675 7637.63 28 0 -3441.8093 0 -3441.8093 -7099.9355 Loop time of 1.58063 on 1 procs for 28 steps with 154 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 = -3432.06753528 -3441.80635147 -3441.80930149 Force two-norm initial, final = 25.0148 0.183495 Force max component initial, final = 11.505 0.0498488 Final line search alpha, max atom move = 1 0.0498488 Iterations, force evaluations = 28 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.579 | 1.579 | 1.579 | 0.0 | 99.90 Neigh | 0.00041795 | 0.00041795 | 0.00041795 | 0.0 | 0.03 Comm | 0.0007813 | 0.0007813 | 0.0007813 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004325 | | | 0.03 Nlocal: 154 ave 154 max 154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1841 ave 1841 max 1841 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: 9928 ave 9928 max 9928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9928 Ave neighs/atom = 64.4675 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -3441.8093 0 -3441.8093 -7099.9355 2461.4507 30 0 -3441.8234 0 -3441.8234 -1492.9848 2456.0645 Loop time of 0.0722129 on 1 procs for 2 steps with 154 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3441.80930149 -3441.82024757 -3441.82344938 Force two-norm initial, final = 14.7868 2.32498 Force max component initial, final = 14.2916 2.31543 Final line search alpha, max atom move = 0.000150588 0.000348675 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072065 | 0.072065 | 0.072065 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.966e-05 | | | 0.14 Nlocal: 154 ave 154 max 154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1835 ave 1835 max 1835 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: 9926 ave 9926 max 9926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9926 Ave neighs/atom = 64.4545 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 = 4 21 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) = 4.184 | 4.184 | 4.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3441.8234 0 -3441.8234 -1492.9848 Loop time of 1.19209e-06 on 1 procs for 0 steps with 154 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: 154 ave 154 max 154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1839 ave 1839 max 1839 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: 9926 ave 9926 max 9926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9926 Ave neighs/atom = 64.4545 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) = 4.184 | 4.184 | 4.184 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 -3441.8234 -3441.8234 11.390897 68.367317 3.153794 -1492.9848 -1492.9848 1510.0915 -6049.2081 60.162089 2.4766125 97.024789 Loop time of 9.53674e-07 on 1 procs for 0 steps with 154 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: 154 ave 154 max 154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1839 ave 1839 max 1839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4963 ave 4963 max 4963 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9926 ave 9926 max 9926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9926 Ave neighs/atom = 64.4545 Neighbor list builds = 0 Dangerous builds = 0 154 -781.35088995935 eV 2.47661247575141 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01