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 -35.3329 0) to (7.06595 35.3329 3.15999) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.23957 4.23957 3.15999 Created 51 atoms create_atoms CPU = 0.00013113 secs 51 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.23957 4.23957 3.15999 Created 51 atoms create_atoms CPU = 1.90735e-05 secs 51 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXqy18sx/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-XXXXXXqy18sx/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 = 3 22 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 = 98 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 = 3 22 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) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2188.3042 0 -2188.3042 -15358.649 9 0 -2190.2761 0 -2190.2761 -20904.429 Loop time of 0.251341 on 1 procs for 9 steps with 98 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2188.3041775 -2190.27448753 -2190.27610004 Force two-norm initial, final = 4.5338 0.120696 Force max component initial, final = 1.93535 0.0216517 Final line search alpha, max atom move = 1 0.0216517 Iterations, force evaluations = 9 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25105 | 0.25105 | 0.25105 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018215 | 0.00018215 | 0.00018215 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001068 | | | 0.04 Nlocal: 98 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1753 ave 1753 max 1753 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: 6228 ave 6228 max 6228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6228 Ave neighs/atom = 63.551 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 : 9 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 9 0 -2190.2761 0 -2190.2761 -20904.429 1577.8483 13 0 -2190.3248 0 -2190.3248 -6312.3307 1568.8272 Loop time of 0.093138 on 1 procs for 4 steps with 98 atoms 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2190.27610004 -2190.3247672 -2190.32478496 Force two-norm initial, final = 23.8727 0.21104 Force max component initial, final = 17.506 0.101831 Final line search alpha, max atom move = 0.00784517 0.000798879 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092857 | 0.092857 | 0.092857 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.534e-05 | 7.534e-05 | 7.534e-05 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002053 | | | 0.22 Nlocal: 98 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1753 ave 1753 max 1753 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: 6268 ave 6268 max 6268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6268 Ave neighs/atom = 63.9592 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 = 3 22 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) = 4.145 | 4.145 | 4.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2190.3248 0 -2190.3248 -6312.3307 Loop time of 1.19209e-06 on 1 procs for 0 steps with 98 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: 98 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1753 ave 1753 max 1753 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: 6268 ave 6268 max 6268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6268 Ave neighs/atom = 63.9592 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) = 4.145 | 4.145 | 4.145 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 -2190.3248 -2190.3248 7.0457449 70.665804 3.150931 -6312.3307 -6312.3307 103.69806 -18939.716 -100.97359 2.6472406 117.05452 Loop time of 9.53674e-07 on 1 procs for 0 steps with 98 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: 98 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1753 ave 1753 max 1753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3134 ave 3134 max 3134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6268 ave 6268 max 6268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6268 Ave neighs/atom = 63.9592 Neighbor list builds = 0 Dangerous builds = 0 98 -497.29679260019 eV 2.64724059551983 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00