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 -62.5677 0) to (38.3128 62.5677 7.74036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.43073 4.4689 5.16024 Created 1181 atoms create_atoms CPU = 0.00037694 secs 1181 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.43073 4.4689 5.16024 Created 1181 atoms create_atoms CPU = 0.000262976 secs 1181 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXNPLZNY/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-XXXXXXNPLZNY/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 = 12 38 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 34 atoms, new total = 2328 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 = 12 38 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) = 6.413 | 6.413 | 6.413 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -52017.286 0 -52017.286 -2972.99 62 0 -52081.054 0 -52081.054 -9610.6354 Loop time of 45.5835 on 1 procs for 62 steps with 2328 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 = -52017.2864231 -52081.0041935 -52081.0542633 Force two-norm initial, final = 58.9977 0.789712 Force max component initial, final = 12.0596 0.130891 Final line search alpha, max atom move = 0.695466 0.0910302 Iterations, force evaluations = 62 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 45.565 | 45.565 | 45.565 | 0.0 | 99.96 Neigh | 0.006429 | 0.006429 | 0.006429 | 0.0 | 0.01 Comm | 0.0057731 | 0.0057731 | 0.0057731 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005951 | | | 0.01 Nlocal: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7412 ave 7412 max 7412 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: 149318 ave 149318 max 149318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149318 Ave neighs/atom = 64.14 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.419 | 6.419 | 6.419 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -52081.054 0 -52081.054 -9610.6354 37109.546 64 0 -52081.292 0 -52081.292 -2933.3662 37012.665 Loop time of 1.64896 on 1 procs for 2 steps with 2328 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -52081.0542633 -52081.2755089 -52081.2921443 Force two-norm initial, final = 256.418 7.19218 Force max component initial, final = 187.877 5.55748 Final line search alpha, max atom move = 1.83804e-05 0.000102148 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6482 | 1.6482 | 1.6482 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017476 | 0.00017476 | 0.00017476 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006275 | | | 0.04 Nlocal: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6860 ave 6860 max 6860 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: 149088 ave 149088 max 149088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149088 Ave neighs/atom = 64.0412 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 = 12 38 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) = 6.047 | 6.047 | 6.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -52081.292 0 -52081.292 -2933.3662 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2328 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: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6875 ave 6875 max 6875 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: 149088 ave 149088 max 149088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149088 Ave neighs/atom = 64.0412 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) = 6.047 | 6.047 | 6.047 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 -52081.292 -52081.292 38.266095 125.13547 7.729578 -2933.3662 -2933.3662 240.27462 -8846.3041 -194.06907 2.42855 1352.251 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2328 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: 2328 ave 2328 max 2328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6875 ave 6875 max 6875 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74544 ave 74544 max 74544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149088 ave 149088 max 149088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149088 Ave neighs/atom = 64.0412 Neighbor list builds = 0 Dangerous builds = 0 2328 -11863.2394278533 eV 2.42854996338514 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:48