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 = 3.52 3.52 3.52 Created orthogonal box = (0 -40.7505 0) to (28.8124 40.7505 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.59047 6.08163 4.97803 Created 538 atoms create_atoms CPU = 0.000427961 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.59047 6.08163 4.97803 Created 538 atoms create_atoms CPU = 0.000287056 secs 538 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 7 20 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1066 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.43 | 5.43 | 5.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4705.3083 0 -4705.3083 6007.2905 61 0 -4732.0924 0 -4732.0924 -5504.8873 Loop time of 0.542042 on 1 procs for 61 steps with 1066 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4705.30830199 -4732.0878159 -4732.09240457 Force two-norm initial, final = 24.5026 0.222955 Force max component initial, final = 5.90871 0.0229309 Final line search alpha, max atom move = 1 0.0229309 Iterations, force evaluations = 61 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52023 | 0.52023 | 0.52023 | 0.0 | 95.98 Neigh | 0.013106 | 0.013106 | 0.013106 | 0.0 | 2.42 Comm | 0.005481 | 0.005481 | 0.005481 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003228 | | | 0.60 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7979 ave 7979 max 7979 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: 232252 ave 232252 max 232252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232252 Ave neighs/atom = 217.872 Neighbor list builds = 2 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.43 | 5.43 | 5.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -4732.0924 0 -4732.0924 -5504.8873 11689.618 65 0 -4732.2083 0 -4732.2083 -366.41585 11655.721 Loop time of 0.023416 on 1 procs for 4 steps with 1066 atoms 128.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4732.09240457 -4732.20598867 -4732.20827738 Force two-norm initial, final = 75.8925 4.09811 Force max component initial, final = 71.8587 3.9563 Final line search alpha, max atom move = 0.000110894 0.000438728 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022491 | 0.022491 | 0.022491 | 0.0 | 96.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024366 | 0.00024366 | 0.00024366 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006816 | | | 2.91 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7961 ave 7961 max 7961 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: 232080 ave 232080 max 232080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232080 Ave neighs/atom = 217.711 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4732.2083 0 -4732.2083 -366.41585 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1066 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 | | 1.907e-06 | | |100.00 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7970 ave 7970 max 7970 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: 233060 ave 233060 max 233060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233060 Ave neighs/atom = 218.63 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) = 5.568 | 5.568 | 5.568 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 -4732.2083 -4732.2083 28.722484 81.500933 4.9791426 -366.41585 -366.41585 -542.12873 -414.11942 -142.99939 2.301597 511.2213 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1066 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: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7970 ave 7970 max 7970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116530 ave 116530 max 116530 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233060 ave 233060 max 233060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233060 Ave neighs/atom = 218.63 Neighbor list builds = 0 Dangerous builds = 0 1066 -4708.17377589086 eV 2.30159700101613 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00