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 = 3.52152 3.52152 3.52152 Created orthogonal box = (0 -46.7218 0) to (28.609 46.7218 8.62593) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.20163 5.30889 5.75062 Created 1077 atoms create_atoms CPU = 0.00052309 secs 1077 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.20163 5.30889 5.75062 Created 1077 atoms create_atoms CPU = 0.000378132 secs 1077 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 31 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 2112 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.11 | 5.11 | 5.11 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12179.48 0 -12179.48 5177.4038 33 0 -12196.719 0 -12196.719 2335.0323 Loop time of 100.483 on 1 procs for 33 steps with 2112 atoms 58.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12179.4796552 -12196.7117652 -12196.7192445 Force two-norm initial, final = 22.8932 0.211265 Force max component initial, final = 4.65281 0.0177026 Final line search alpha, max atom move = 1 0.0177026 Iterations, force evaluations = 33 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 100.48 | 100.48 | 100.48 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025194 | 0.0025194 | 0.0025194 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002764 | | | 0.00 Nlocal: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6114 ave 6114 max 6114 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: 181680 ave 181680 max 181680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181680 Ave neighs/atom = 86.0227 Neighbor list builds = 0 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 : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.11 | 5.11 | 5.11 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -12196.719 0 -12196.719 2335.0323 23059.919 34 0 -12196.721 0 -12196.721 2997.6255 23052.529 Loop time of 4.94175 on 1 procs for 1 steps with 2112 atoms 53.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12196.7192445 -12196.7192445 -12196.7210132 Force two-norm initial, final = 15.5127 0.406131 Force max component initial, final = 11.7548 0.258703 Final line search alpha, max atom move = 8.5072e-05 2.20084e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9212 | 4.9212 | 4.9212 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001092 | 0.0001092 | 0.0001092 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02043 | | | 0.41 Nlocal: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6114 ave 6114 max 6114 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: 179634 ave 179634 max 179634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179634 Ave neighs/atom = 85.054 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.248 | 5.248 | 5.248 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12196.721 0 -12196.721 2997.6255 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2112 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: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6114 ave 6114 max 6114 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: 179664 ave 179664 max 179664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179664 Ave neighs/atom = 85.0682 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) = 5.248 | 5.248 | 5.248 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 -12196.721 -12196.721 28.604736 93.443574 8.6244459 2997.6255 2997.6255 16.031551 8994.8221 -17.977038 2.3316628 634.72742 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2112 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: 2112 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6114 ave 6114 max 6114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89832 ave 89832 max 89832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179664 ave 179664 max 179664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179664 Ave neighs/atom = 85.0682 Neighbor list builds = 0 Dangerous builds = 0 2112 -6085.51619541032 eV 2.33166281551028 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:51