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 -34.0373 0) to (17.0171 34.0373 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.10757 4.10757 3.15999 Created 117 atoms create_atoms CPU = 0.000181913 secs 117 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.10757 4.10757 3.15999 Created 117 atoms create_atoms CPU = 4.50611e-05 secs 117 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXXw4yDe/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-XXXXXXXw4yDe/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 = 6 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 = 230 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 = 6 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5128.343 0 -5128.343 15379.178 12 0 -5139.0647 0 -5139.0647 9275.6112 Loop time of 0.859711 on 1 procs for 12 steps with 230 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 = -5128.34303579 -5139.0609965 -5139.06469112 Force two-norm initial, final = 25.986 0.182507 Force max component initial, final = 10.0923 0.0353076 Final line search alpha, max atom move = 0.762282 0.0269143 Iterations, force evaluations = 12 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85921 | 0.85921 | 0.85921 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002036 | | | 0.02 Nlocal: 230 ave 230 max 230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2220 ave 2220 max 2220 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: 14824 ave 14824 max 14824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14824 Ave neighs/atom = 64.4522 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -5139.0647 0 -5139.0647 9275.6112 3660.6204 14 0 -5139.0823 0 -5139.0823 4269.0482 3667.6572 Loop time of 0.182738 on 1 procs for 2 steps with 230 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5139.06469112 -5139.07808221 -5139.08229816 Force two-norm initial, final = 18.9436 3.08636 Force max component initial, final = 18.5756 2.97161 Final line search alpha, max atom move = 0.00012633 0.000375404 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18251 | 0.18251 | 0.18251 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.0081e-05 | 6.0081e-05 | 6.0081e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001707 | | | 0.09 Nlocal: 230 ave 230 max 230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2220 ave 2220 max 2220 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: 14764 ave 14764 max 14764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14764 Ave neighs/atom = 64.1913 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 = 6 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) = 4.237 | 4.237 | 4.237 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5139.0823 0 -5139.0823 4269.0482 Loop time of 2.14577e-06 on 1 procs for 0 steps with 230 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 | | 2.146e-06 | | |100.00 Nlocal: 230 ave 230 max 230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2210 ave 2210 max 2210 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: 14764 ave 14764 max 14764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14764 Ave neighs/atom = 64.1913 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) = 4.237 | 4.237 | 4.237 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 -5139.0823 -5139.0823 17.050971 68.074549 3.1597655 4269.0482 4269.0482 -355.98466 14461.152 -1298.0225 2.5336022 264.53443 Loop time of 9.53674e-07 on 1 procs for 0 steps with 230 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: 230 ave 230 max 230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2210 ave 2210 max 2210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7382 ave 7382 max 7382 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 14764 ave 14764 max 14764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14764 Ave neighs/atom = 64.1913 Neighbor list builds = 0 Dangerous builds = 0 230 -1165.64925486403 eV 2.53360218033503 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01