LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52733 3.52733 3.52733 Created orthogonal box = (0 -41.7395 0) to (51.1159 41.7395 8.64016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.84181 5.36605 5.7601 Created 1687 atoms create_atoms CPU = 0.00146103 secs 1687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.84181 5.36605 5.7601 Created 1687 atoms create_atoms CPU = 0.00138807 secs 1687 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 11 17 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 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 62 atoms, new total = 3312 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 13.77 | 13.77 | 13.77 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13565.092 0 -13565.092 7757.2779 65 0 -13806.295 0 -13806.295 -19009.306 Loop time of 4.43671 on 1 procs for 65 steps with 3312 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13565.0921365 -13806.2859665 -13806.2951535 Force two-norm initial, final = 113.675 0.385627 Force max component initial, final = 10.8247 0.0277552 Final line search alpha, max atom move = 1 0.0277552 Iterations, force evaluations = 65 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.363 | 4.363 | 4.363 | 0.0 | 98.34 Neigh | 0.042494 | 0.042494 | 0.042494 | 0.0 | 0.96 Comm | 0.018536 | 0.018536 | 0.018536 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01265 | | | 0.29 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16295 ave 16295 max 16295 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: 1.25329e+06 ave 1.25329e+06 max 1.25329e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1253294 Ave neighs/atom = 378.41 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.77 | 13.77 | 13.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -13806.295 0 -13806.295 -19009.306 36868.379 71 0 -13807.97 0 -13807.97 -4785.7369 36577.233 Loop time of 0.349249 on 1 procs for 6 steps with 3312 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13806.2951535 -13807.9693271 -13807.9697393 Force two-norm initial, final = 578.038 0.573486 Force max component initial, final = 477.824 0.0710172 Final line search alpha, max atom move = 0.000157737 1.1202e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34395 | 0.34395 | 0.34395 | 0.0 | 98.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012257 | 0.0012257 | 0.0012257 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004076 | | | 1.17 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15971 ave 15971 max 15971 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: 1.25494e+06 ave 1.25494e+06 max 1.25494e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1254944 Ave neighs/atom = 378.908 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 13.28 | 13.28 | 13.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13807.97 0 -13807.97 -4785.7369 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 atoms 157.3% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15999 ave 15999 max 15999 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: 1.25703e+06 ave 1.25703e+06 max 1.25703e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1257034 Ave neighs/atom = 379.539 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) = 13.28 | 13.28 | 13.28 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 -13807.97 -13807.97 50.863232 83.478903 8.6145016 -4785.7369 -4785.7369 -0.21915085 -14353.89 -3.1014972 2.3623487 2126.8324 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 atoms 157.3% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15999 ave 15999 max 15999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 628517 ave 628517 max 628517 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.25703e+06 ave 1.25703e+06 max 1.25703e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1257034 Ave neighs/atom = 379.539 Neighbor list builds = 0 Dangerous builds = 0 3312 -13807.9697393095 eV 2.36234865609512 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05