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 -33.1454 0) to (40.5908 33.1454 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1661 4.82069 5.16024 Created 664 atoms create_atoms CPU = 0.000411034 secs 664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1661 4.82069 5.16024 Created 664 atoms create_atoms CPU = 0.000277996 secs 664 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXhAAk1s/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-XXXXXXhAAk1s/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 = 13 21 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 20 atoms, new total = 1308 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 = 13 21 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) = 5.296 | 5.296 | 5.296 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -29059.314 0 -29059.314 27509.107 62 0 -29225.625 0 -29225.625 5545.1099 Loop time of 21.4661 on 1 procs for 62 steps with 1308 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 = -29059.313964 -29225.5981087 -29225.6245926 Force two-norm initial, final = 119.174 0.588305 Force max component initial, final = 17.0955 0.0813382 Final line search alpha, max atom move = 0.861987 0.0701124 Iterations, force evaluations = 62 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.453 | 21.453 | 21.453 | 0.0 | 99.94 Neigh | 0.0067322 | 0.0067322 | 0.0067322 | 0.0 | 0.03 Comm | 0.0029252 | 0.0029252 | 0.0029252 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003075 | | | 0.01 Nlocal: 1308 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4206 ave 4206 max 4206 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: 84138 ave 84138 max 84138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84138 Ave neighs/atom = 64.3257 Neighbor list builds = 2 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.296 | 5.296 | 5.296 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -29225.625 0 -29225.625 5545.1099 20827.72 64 0 -29225.674 0 -29225.674 2428.4051 20852.852 Loop time of 0.862702 on 1 procs for 2 steps with 1308 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -29225.6245926 -29225.6676178 -29225.6744022 Force two-norm initial, final = 77.2597 4.04227 Force max component initial, final = 72.4429 3.27604 Final line search alpha, max atom move = 5.98064e-05 0.000195928 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86226 | 0.86226 | 0.86226 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.8228e-05 | 9.8228e-05 | 9.8228e-05 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003395 | | | 0.04 Nlocal: 1308 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4203 ave 4203 max 4203 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: 84188 ave 84188 max 84188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84188 Ave neighs/atom = 64.3639 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 = 13 21 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) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -29225.674 0 -29225.674 2428.4051 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1308 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: 1308 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4203 ave 4203 max 4203 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: 84188 ave 84188 max 84188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84188 Ave neighs/atom = 64.3639 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) = 4.927 | 4.927 | 4.927 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 -29225.674 -29225.674 40.64716 66.290792 7.73895 2428.4051 2428.4051 252.05617 6856.9093 176.24989 2.3975626 1418.9105 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1308 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: 1308 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4203 ave 4203 max 4203 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42094 ave 42094 max 42094 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84188 ave 84188 max 84188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84188 Ave neighs/atom = 64.3639 Neighbor list builds = 0 Dangerous builds = 0 1308 -6628.9334429894 eV 2.39756258687441 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23