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 = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -38.3503 0) to (38.3467 38.3503 3.60735) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.09027 5.09027 3.60735 Created 454 atoms create_atoms CPU = 0.000279903 secs 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.09027 5.09027 3.60735 Created 454 atoms create_atoms CPU = 0.000140905 secs 454 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 7 13 1 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 904 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 7 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.649 | 6.649 | 6.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3085.8361 0 -3085.8361 31297.601 197 0 -3185.6687 0 -3185.6687 2428.7568 Loop time of 4.99383 on 1 procs for 197 steps with 904 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3085.83611488 -3185.66550946 -3185.66867922 Force two-norm initial, final = 66.2172 0.282512 Force max component initial, final = 15.122 0.0857089 Final line search alpha, max atom move = 1 0.0857089 Iterations, force evaluations = 197 344 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8817 | 4.8817 | 4.8817 | 0.0 | 97.75 Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 1.40 Comm | 0.032324 | 0.032324 | 0.032324 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01002 | | | 0.20 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14656 ave 14656 max 14656 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: 570714 ave 570714 max 570714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 570714 Ave neighs/atom = 631.321 Neighbor list builds = 6 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 : 197 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes Step Temp E_pair E_mol TotEng Press Volume 197 0 -3185.6687 0 -3185.6687 2428.7568 10609.993 204 0 -3185.8277 0 -3185.8277 -527.11267 10632.241 Loop time of 0.14359 on 1 procs for 7 steps with 904 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3185.66867922 -3185.82764628 -3185.82769748 Force two-norm initial, final = 43.6149 0.468674 Force max component initial, final = 38.4046 0.246718 Final line search alpha, max atom move = 0.00234032 0.000577398 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14074 | 0.14074 | 0.14074 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077081 | 0.00077081 | 0.00077081 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002081 | | | 1.45 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14640 ave 14640 max 14640 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: 573438 ave 573438 max 573438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 573438 Ave neighs/atom = 634.334 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 7 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.787 | 6.787 | 6.787 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3185.8277 0 -3185.8277 -527.11267 Loop time of 1.90735e-06 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14664 ave 14664 max 14664 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: 575852 ave 575852 max 575852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575852 Ave neighs/atom = 637.004 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) = 6.787 | 6.787 | 6.787 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 -3185.8277 -3185.8277 38.194033 76.700585 3.6293648 -527.11267 -527.11267 37.029973 -1597.8385 -20.529469 2.154816 108.80692 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14664 ave 14664 max 14664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 287926 ave 287926 max 287926 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575852 ave 575852 max 575852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575852 Ave neighs/atom = 637.004 Neighbor list builds = 0 Dangerous builds = 0 904 -3185.82769748226 eV 2.15481597882635 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05