LAMMPS (24 Dec 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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -61.711014 0.0000000) to (30.853702 61.711014 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6491879 4.6491879 3.6111526 Created 585 atoms create_atoms CPU = 0.000 seconds 585 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6491879 4.6491879 3.6111526 Created 585 atoms create_atoms CPU = 0.000 seconds 585 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 11 atoms, new total = 1159 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4887.5178 0 -4887.5178 -821.94424 44 0 -4906.1877 0 -4906.1877 -6655.2948 Loop time of 2.56564 on 1 procs for 44 steps with 1159 atoms 88.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4887.51783864508 -4906.18347290296 -4906.18769181477 Force two-norm initial, final = 25.122499 0.24875645 Force max component initial, final = 7.0324825 0.062545697 Final line search alpha, max atom move = 1.0000000 0.062545697 Iterations, force evaluations = 44 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.561 | 2.561 | 2.561 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024737 | 0.0024737 | 0.0024737 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002199 | | | 0.09 Nlocal: 1159.00 ave 1159 max 1159 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62072.0 ave 62072 max 62072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62072 Ave neighs/atom = 53.556514 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -4906.1877 0 -4906.1877 -6655.2948 13751.365 47 0 -4906.2674 0 -4906.2674 -1684.5068 13709.11 Loop time of 0.162884 on 1 procs for 3 steps with 1159 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 = -4906.18769181477 -4906.26598466231 -4906.26735247082 Force two-norm initial, final = 69.130617 0.28004511 Force max component initial, final = 55.223733 0.078601927 Final line search alpha, max atom move = 0.00030284901 2.3804516e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16222 | 0.16222 | 0.16222 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001492 | 0.0001492 | 0.0001492 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005177 | | | 0.32 Nlocal: 1159.00 ave 1159 max 1159 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62212.0 ave 62212 max 62212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62212 Ave neighs/atom = 53.677308 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.514 | 5.514 | 5.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4906.2674 0 -4906.2674 -1684.5068 Loop time of 2e-06 on 1 procs for 0 steps with 1159 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 1159.00 ave 1159 max 1159 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62214.0 ave 62214 max 62214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62214 Ave neighs/atom = 53.679034 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) = 5.514 | 5.514 | 5.514 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 -4906.2674 -4906.2674 30.783488 123.42203 3.6082678 -1684.5068 -1684.5068 0.4641844 -5052.5561 -1.4284518 2.2722625 181.80351 Loop time of 2.70001e-06 on 1 procs for 0 steps with 1159 atoms 111.1% 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 | | 2.7e-06 | | |100.00 Nlocal: 1159.00 ave 1159 max 1159 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31107.0 ave 31107 max 31107 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62214.0 ave 62214 max 62214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62214 Ave neighs/atom = 53.679034 Neighbor list builds = 0 Dangerous builds = 0 1159 -4906.26735247082 eV 2.27226254149383 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02