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 -44.4681 0) to (10.4805 44.4681 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.76386 5.38969 4.4689 Created 134 atoms create_atoms CPU = 0.000252008 secs 134 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.76386 5.38969 4.4689 Created 134 atoms create_atoms CPU = 0.000128984 secs 134 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX1IAZ1w/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-XXXXXX1IAZ1w/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 27 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 = 264 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 27 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) = 4.644 | 4.644 | 4.644 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5886.8295 0 -5886.8295 30952.418 14 0 -5905.4096 0 -5905.4096 19908.69 Loop time of 1.11773 on 1 procs for 14 steps with 264 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5886.82945428 -5905.40688176 -5905.40960689 Force two-norm initial, final = 37.0801 0.140802 Force max component initial, final = 10.463 0.0270615 Final line search alpha, max atom move = 1 0.0270615 Iterations, force evaluations = 14 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.117 | 1.117 | 1.117 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044799 | 0.00044799 | 0.00044799 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002723 | | | 0.02 Nlocal: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2484 ave 2484 max 2484 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: 17148 ave 17148 max 17148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17148 Ave neighs/atom = 64.9545 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 : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.644 | 4.644 | 4.644 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -5905.4096 0 -5905.4096 19908.69 4165.4429 19 0 -5905.5365 0 -5905.5365 6478.2161 4186.6754 Loop time of 0.287485 on 1 procs for 5 steps with 264 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 = -5905.40960689 -5905.53425652 -5905.53646888 Force two-norm initial, final = 58.9497 0.833358 Force max component initial, final = 52.6244 0.606206 Final line search alpha, max atom move = 0.00023695 0.00014364 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28708 | 0.28708 | 0.28708 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010276 | 0.00010276 | 0.00010276 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003052 | | | 0.11 Nlocal: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2484 ave 2484 max 2484 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: 16944 ave 16944 max 16944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16944 Ave neighs/atom = 64.1818 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 27 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) = 4.275 | 4.275 | 4.275 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5905.5365 0 -5905.5365 6478.2161 Loop time of 9.53674e-07 on 1 procs for 0 steps with 264 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: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2484 ave 2484 max 2484 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: 16944 ave 16944 max 16944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16944 Ave neighs/atom = 64.1818 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) = 4.275 | 4.275 | 4.275 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 -5905.5365 -5905.5365 10.486571 88.936271 4.489075 6478.2161 6478.2161 197.50522 19004.11 233.03295 2.5732167 180.50877 Loop time of 9.53674e-07 on 1 procs for 0 steps with 264 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: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2484 ave 2484 max 2484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8472 ave 8472 max 8472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16944 ave 16944 max 16944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16944 Ave neighs/atom = 64.1818 Neighbor list builds = 0 Dangerous builds = 0 264 -1344.72636701218 eV 2.57321668150959 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01