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 Lattice spacing in x,y,z = 2.86 2.86 2.86 Created orthogonal box = (0 -53.048 0) to (18.7543 53.048 4.04465) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7976 4.93443 4.04465 Created 346 atoms create_atoms CPU = 0.000309944 secs 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7976 4.93443 4.04465 Created 346 atoms create_atoms CPU = 0.000180006 secs 346 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 7 40 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 5.44 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 684 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 7 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.44 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1023.1529 0 -1023.1529 6407.7977 18 0 -1040.6731 0 -1040.6731 1030.7531 Loop time of 0.011812 on 1 procs for 18 steps with 684 atoms 84.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1023.15293497 -1040.67244747 -1040.67311521 Force two-norm initial, final = 33.8237 0.116663 Force max component initial, final = 8.77136 0.0384216 Final line search alpha, max atom move = 1 0.0384216 Iterations, force evaluations = 18 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010855 | 0.010855 | 0.010855 | 0.0 | 91.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055909 | 0.00055909 | 0.00055909 | 0.0 | 4.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003977 | | | 3.37 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 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: 39432 ave 39432 max 39432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39432 Ave neighs/atom = 57.6491 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -1040.6731 0 -1040.6731 1030.7531 8047.85 21 0 -1040.6841 0 -1040.6841 446.07128 8051.638 Loop time of 0.00242305 on 1 procs for 3 steps with 684 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1040.67311521 -1040.68406114 -1040.6840984 Force two-norm initial, final = 14.0558 0.124588 Force max component initial, final = 13.032 0.0404993 Final line search alpha, max atom move = 0.000982818 3.98034e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.002032 | 0.002032 | 0.002032 | 0.0 | 83.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.4652e-05 | 9.4652e-05 | 9.4652e-05 | 0.0 | 3.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002964 | | | 12.23 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 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: 39480 ave 39480 max 39480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39480 Ave neighs/atom = 57.7193 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 7 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.44 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.652 | 4.652 | 4.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1040.6841 0 -1040.6841 446.07128 Loop time of 9.53674e-07 on 1 procs for 0 steps with 684 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: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 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: 39480 ave 39480 max 39480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39480 Ave neighs/atom = 57.7193 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) = 4.652 | 4.652 | 4.652 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 -1040.6841 -1040.6841 18.779365 106.09591 4.0411474 446.07128 446.07128 -3.1465837 1342.3415 -0.98111696 2.3263535 303.26231 Loop time of 9.53674e-07 on 1 procs for 0 steps with 684 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: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19740 ave 19740 max 19740 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39480 ave 39480 max 39480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39480 Ave neighs/atom = 57.7193 Neighbor list builds = 0 Dangerous builds = 0 684 -1040.68409839744 eV 2.32635349671039 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00