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 = 3.1472 3.1472 3.1472 Created orthogonal box = (0 -33.606 0) to (19.4006 33.606 5.45111) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.10543 4.7162 5.45111 Created 229 atoms create_atoms CPU = 0.000233889 secs 229 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.10543 4.7162 5.45111 Created 230 atoms create_atoms CPU = 0.000118017 secs 230 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 22 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 456 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2990.718 0 -2990.718 77123.632 58 0 -3086.7785 0 -3086.7785 12051.862 Loop time of 0.089921 on 1 procs for 58 steps with 456 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 = -2990.71799368 -3086.77579983 -3086.77851997 Force two-norm initial, final = 190.828 0.164076 Force max component initial, final = 53.8522 0.0500116 Final line search alpha, max atom move = 0.808352 0.040427 Iterations, force evaluations = 58 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087005 | 0.087005 | 0.087005 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016518 | 0.0016518 | 0.0016518 | 0.0 | 1.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001264 | | | 1.41 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2337 ave 2337 max 2337 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: 26736 ave 26736 max 26736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26736 Ave neighs/atom = 58.6316 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 : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3086.7785 0 -3086.7785 12051.862 7108.0183 63 0 -3086.8979 0 -3086.8979 2919.3912 7130.7177 Loop time of 0.00694704 on 1 procs for 5 steps with 456 atoms 143.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3086.77851997 -3086.89765726 -3086.89794598 Force two-norm initial, final = 70.9621 0.263088 Force max component initial, final = 66.8524 0.0373405 Final line search alpha, max atom move = 0.000246979 9.22232e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0063887 | 0.0063887 | 0.0063887 | 0.0 | 91.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 1.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000428 | | | 6.16 Nlocal: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2369 ave 2369 max 2369 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: 26928 ave 26928 max 26928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26928 Ave neighs/atom = 59.0526 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 7 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.589 | 4.589 | 4.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3086.8979 0 -3086.8979 2919.3912 Loop time of 9.53674e-07 on 1 procs for 0 steps with 456 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: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 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: 26880 ave 26880 max 26880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26880 Ave neighs/atom = 58.9474 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) = 4.589 | 4.589 | 4.589 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 -3086.8979 -3086.8979 19.390889 67.212095 5.4712692 2919.3912 2919.3912 4.1627236 8753.9836 0.02735905 2.4986549 390.64904 Loop time of 1.19209e-06 on 1 procs for 0 steps with 456 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: 456 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13440 ave 13440 max 13440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26880 ave 26880 max 26880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26880 Ave neighs/atom = 58.9474 Neighbor list builds = 0 Dangerous builds = 0 456 -3086.89794597682 eV 2.49865489910011 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42