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 = 3.65837 3.65837 3.65837 Created orthogonal box = (0 -38.8926 0) to (38.889 38.8926 3.65837) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.16225 5.16225 3.65837 Created 454 atoms create_atoms CPU = 0.00018096 secs 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.16225 5.16225 3.65837 Created 454 atoms create_atoms CPU = 8.70228e-05 secs 454 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 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 7.3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.959 | 4.959 | 4.959 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3555.7044 0 -3555.7044 18732.071 224 0 -3620.7455 0 -3620.7455 -8093.6975 Loop time of 1.29257 on 1 procs for 224 steps with 904 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3555.70439244 -3620.74201804 -3620.74548575 Force two-norm initial, final = 42.49 0.179584 Force max component initial, final = 9.69278 0.0280344 Final line search alpha, max atom move = 1 0.0280344 Iterations, force evaluations = 224 432 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2595 | 1.2595 | 1.2595 | 0.0 | 97.44 Neigh | 0.0068362 | 0.0068362 | 0.0068362 | 0.0 | 0.53 Comm | 0.016347 | 0.016347 | 0.016347 | 0.0 | 1.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009849 | | | 0.76 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6526 ave 6526 max 6526 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: 125702 ave 125702 max 125702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125702 Ave neighs/atom = 139.051 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 : 224 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.96 | 4.96 | 4.96 Mbytes Step Temp E_pair E_mol TotEng Press Volume 224 0 -3620.7455 0 -3620.7455 -8093.6975 11066.515 280 0 -3637.4106 0 -3637.4106 -16262.183 11131.531 Loop time of 0.14091 on 1 procs for 56 steps with 904 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3620.74548575 -3637.40910321 -3637.41056832 Force two-norm initial, final = 473.151 4.40974 Force max component initial, final = 383.829 2.28705 Final line search alpha, max atom move = 0.000244702 0.000559647 Iterations, force evaluations = 56 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13067 | 0.13067 | 0.13067 | 0.0 | 92.73 Neigh | 0.0024519 | 0.0024519 | 0.0024519 | 0.0 | 1.74 Comm | 0.0018797 | 0.0018797 | 0.0018797 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005913 | | | 4.20 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6576 ave 6576 max 6576 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: 126712 ave 126712 max 126712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126712 Ave neighs/atom = 140.168 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3637.4106 0 -3637.4106 -16262.183 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: 6611 ave 6611 max 6611 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: 126926 ave 126926 max 126926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126926 Ave neighs/atom = 140.405 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) = 5.098 | 5.098 | 5.098 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 -3637.4106 -3637.4106 37.249098 77.785253 3.8418629 -16262.183 -16262.183 -259.42211 -48181.438 -345.6893 2.302477 344.56497 Loop time of 2.14577e-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 | | 2.146e-06 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6611 ave 6611 max 6611 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63463 ave 63463 max 63463 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126926 ave 126926 max 126926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126926 Ave neighs/atom = 140.405 Neighbor list builds = 0 Dangerous builds = 0 904 -3637.41056831604 eV 2.30247700209356 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01