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 -44.6921 0) to (22.3445 44.6921 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.57512 3.57512 3.15999 Created 202 atoms create_atoms CPU = 0.000211954 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.57512 3.57512 3.15999 Created 202 atoms create_atoms CPU = 5.29289e-05 secs 202 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXbfSxun/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-XXXXXXbfSxun/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 = 7 28 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 8 atoms, new total = 396 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 = 7 28 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8844.7148 0 -8844.7148 489.59549 11 0 -8857.8267 0 -8857.8267 -7707.2706 Loop time of 1.07381 on 1 procs for 11 steps with 396 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8844.71479472 -8857.82104739 -8857.82674632 Force two-norm initial, final = 18.3776 0.220205 Force max component initial, final = 4.4763 0.0252021 Final line search alpha, max atom move = 0.747592 0.0188409 Iterations, force evaluations = 11 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0732 | 1.0732 | 1.0732 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035739 | 0.00035739 | 0.00035739 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002575 | | | 0.02 Nlocal: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3179 ave 3179 max 3179 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: 25408 ave 25408 max 25408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25408 Ave neighs/atom = 64.1616 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 : 11 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.724 | 4.724 | 4.724 Mbytes Step Temp E_pair E_mol TotEng Press Volume 11 0 -8857.8267 0 -8857.8267 -7707.2706 6311.2748 13 0 -8857.8614 0 -8857.8614 -1582.9959 6296.187 Loop time of 0.262139 on 1 procs for 2 steps with 396 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8857.82674632 -8857.86014165 -8857.86141171 Force two-norm initial, final = 40.798 0.245822 Force max component initial, final = 29.7617 0.0744167 Final line search alpha, max atom move = 0.000172881 1.28653e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26184 | 0.26184 | 0.26184 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002213 | | | 0.08 Nlocal: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3179 ave 3179 max 3179 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: 25352 ave 25352 max 25352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25352 Ave neighs/atom = 64.0202 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 = 7 28 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) = 4.355 | 4.355 | 4.355 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8857.8614 0 -8857.8614 -1582.9959 Loop time of 9.53674e-07 on 1 procs for 0 steps with 396 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: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3179 ave 3179 max 3179 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: 25352 ave 25352 max 25352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25352 Ave neighs/atom = 64.0202 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) = 4.355 | 4.355 | 4.355 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 -8857.8614 -8857.8614 22.318688 89.384284 3.1560785 -1582.9959 -1582.9959 6.5352374 -4736.6097 -18.913223 2.5524951 137.0252 Loop time of 9.53674e-07 on 1 procs for 0 steps with 396 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: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3179 ave 3179 max 3179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12676 ave 12676 max 12676 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25352 ave 25352 max 25352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25352 Ave neighs/atom = 64.0202 Neighbor list builds = 0 Dangerous builds = 0 396 -2016.64625890964 eV 2.55249513379134 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01