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 -51.3469 0) to (18.1528 51.3469 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.95075 5.44555 4.4689 Created 266 atoms create_atoms CPU = 0.000370979 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.95075 5.44555 4.4689 Created 266 atoms create_atoms CPU = 0.000243187 secs 266 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXz3ql86/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-XXXXXXz3ql86/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 32 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 8 atoms, new total = 524 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 32 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) = 4.819 | 4.819 | 4.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11675.709 0 -11675.709 14538.655 40 0 -11722.132 0 -11722.132 -1544.4507 Loop time of 5.93507 on 1 procs for 40 steps with 524 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 = -11675.7090011 -11722.1238425 -11722.1315558 Force two-norm initial, final = 79.5864 0.354099 Force max component initial, final = 25.4051 0.0890386 Final line search alpha, max atom move = 0.687858 0.0612459 Iterations, force evaluations = 40 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9312 | 5.9312 | 5.9312 | 0.0 | 99.93 Neigh | 0.00099206 | 0.00099206 | 0.00099206 | 0.0 | 0.02 Comm | 0.001775 | 0.001775 | 0.001775 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001111 | | | 0.02 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3548 ave 3548 max 3548 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: 33608 ave 33608 max 33608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33608 Ave neighs/atom = 64.1374 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.821 | 4.821 | 4.821 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -11722.132 0 -11722.132 -1544.4507 8330.8064 41 0 -11722.142 0 -11722.142 -330.2155 8326.9166 Loop time of 0.197043 on 1 procs for 1 steps with 524 atoms 101.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11722.1315558 -11722.1315558 -11722.1421814 Force two-norm initial, final = 17.6952 5.93069 Force max component initial, final = 15.6085 5.62193 Final line search alpha, max atom move = 6.40678e-05 0.000360184 Iterations, force evaluations = 1 1 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19691 | 0.19691 | 0.19691 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 4.3154e-05 | 4.3154e-05 | 4.3154e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.274e-05 | | | 0.05 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3552 ave 3552 max 3552 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: 33584 ave 33584 max 33584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33584 Ave neighs/atom = 64.0916 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 32 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11722.142 0 -11722.142 -330.2155 Loop time of 9.53674e-07 on 1 procs for 0 steps with 524 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: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 3556 max 3556 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: 33584 ave 33584 max 33584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33584 Ave neighs/atom = 64.0916 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) = 4.452 | 4.452 | 4.452 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 -11722.142 -11722.142 18.134597 102.69378 4.4712829 -330.2155 -330.2155 356.39136 -2429.3267 1082.2888 2.4561964 365.58812 Loop time of 1.19209e-06 on 1 procs for 0 steps with 524 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 | | 1.192e-06 | | |100.00 Nlocal: 524 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3556 ave 3556 max 3556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16792 ave 16792 max 16792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33584 ave 33584 max 33584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33584 Ave neighs/atom = 64.0916 Neighbor list builds = 0 Dangerous builds = 0 524 -2669.6251610426 eV 2.4561963877141 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06