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 = 3.51623 3.51623 3.51623 Created orthogonal box = (0 -53.0975 0) to (37.5431 53.0975 4.9727) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.92786 6.05457 4.9727 Created 915 atoms create_atoms CPU = 0.000766039 secs 915 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.92786 6.05457 4.9727 Created 915 atoms create_atoms CPU = 0.000652075 secs 915 atoms in group lower Displacing atoms ... 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 24 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 1815 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 6.413 | 6.413 | 6.413 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8748.0319 0 -8748.0319 24580.546 35 0 -8828.8877 0 -8828.8877 -3744.6765 Loop time of 0.739048 on 1 procs for 35 steps with 1815 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 = -8748.03194561 -8828.87906496 -8828.88768355 Force two-norm initial, final = 150.524 0.372509 Force max component initial, final = 40.9482 0.127273 Final line search alpha, max atom move = 1 0.127273 Iterations, force evaluations = 35 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72281 | 0.72281 | 0.72281 | 0.0 | 97.80 Neigh | 0.0085809 | 0.0085809 | 0.0085809 | 0.0 | 1.16 Comm | 0.0048783 | 0.0048783 | 0.0048783 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002777 | | | 0.38 Nlocal: 1815 ave 1815 max 1815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12238 ave 12238 max 12238 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: 457604 ave 457604 max 457604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457604 Ave neighs/atom = 252.123 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.413 | 6.413 | 6.413 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -8828.8877 0 -8828.8877 -3744.6765 19825.606 37 0 -8828.9059 0 -8828.9059 -1867.8229 19804.856 Loop time of 0.0656869 on 1 procs for 2 steps with 1815 atoms 91.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8828.88768355 -8828.90511798 -8828.90585539 Force two-norm initial, final = 42.6962 0.388012 Force max component initial, final = 37.7798 0.128214 Final line search alpha, max atom move = 0.00019669 2.52185e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06429 | 0.06429 | 0.06429 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034738 | 0.00034738 | 0.00034738 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00105 | | | 1.60 Nlocal: 1815 ave 1815 max 1815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12238 ave 12238 max 12238 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: 456718 ave 456718 max 456718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 456718 Ave neighs/atom = 251.635 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 6.551 | 6.551 | 6.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8828.9059 0 -8828.9059 -1867.8229 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1815 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: 1815 ave 1815 max 1815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12238 ave 12238 max 12238 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: 457030 ave 457030 max 457030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457030 Ave neighs/atom = 251.807 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) = 6.551 | 6.551 | 6.551 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 -8828.9059 -8828.9059 37.510771 106.19493 4.97178 -1867.8229 -1867.8229 -3.170204 -5593.5418 -6.7566973 2.276098 625.58451 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1815 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: 1815 ave 1815 max 1815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12238 ave 12238 max 12238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228515 ave 228515 max 228515 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 457030 ave 457030 max 457030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457030 Ave neighs/atom = 251.807 Neighbor list builds = 0 Dangerous builds = 0 1815 -8828.90585538978 eV 2.27609801281046 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01