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 -38.705 0) to (4.4689 38.705 5.47326) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4689 5.16024 5.47326 Created 62 atoms create_atoms CPU = 0.000148058 secs 62 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4689 5.16024 5.47326 Created 62 atoms create_atoms CPU = 4.29153e-05 secs 62 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXC7Afjh/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-XXXXXXC7Afjh/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 = 2 24 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 4 atoms, new total = 120 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 = 2 24 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) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2688.7165 0 -2688.7165 -209.46295 1 0 -2688.7168 0 -2688.7168 -210.54473 Loop time of 0.0585451 on 1 procs for 1 steps with 120 atoms 102.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2688.716512 -2688.716512 -2688.71684409 Force two-norm initial, final = 0.107521 0.0345497 Force max component initial, final = 0.0461278 0.0156821 Final line search alpha, max atom move = 1 0.0156821 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.058469 | 0.058469 | 0.058469 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 3.4809e-05 | 3.4809e-05 | 3.4809e-05 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.148e-05 | | | 0.07 Nlocal: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1616 ave 1616 max 1616 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: 7680 ave 7680 max 7680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7680 Ave neighs/atom = 64 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 : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.534 | 4.534 | 4.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -2688.7168 0 -2688.7168 -210.54473 1893.4032 2 0 -2688.7168 0 -2688.7168 -82.733585 1893.3097 Loop time of 0.0417981 on 1 procs for 1 steps with 120 atoms 95.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2688.71684409 -2688.71684409 -2688.71684847 Force two-norm initial, final = 0.2459 0.0364483 Force max component initial, final = 0.180541 0.0156555 Final line search alpha, max atom move = 0.0055389 8.67145e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041681 | 0.041681 | 0.041681 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.917e-05 | | | 0.21 Nlocal: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1616 ave 1616 max 1616 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: 7680 ave 7680 max 7680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7680 Ave neighs/atom = 64 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 = 2 24 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) = 4.165 | 4.165 | 4.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2688.7168 0 -2688.7168 -82.733585 Loop time of 9.53674e-07 on 1 procs for 0 steps with 120 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: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1616 ave 1616 max 1616 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: 7680 ave 7680 max 7680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7680 Ave neighs/atom = 64 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) = 4.165 | 4.165 | 4.165 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 -2688.7168 -2688.7168 4.4687934 77.409907 5.4731182 -82.733585 -82.733585 8.7330323 -252.1744 -4.7593864 2.7365591 5.4605023e-05 Loop time of 1.90735e-06 on 1 procs for 0 steps with 120 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: 120 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1616 ave 1616 max 1616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3840 ave 3840 max 3840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7680 ave 7680 max 7680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7680 Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0 120 -615.62134761948 eV 2.73655911261521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00