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 = 3.49213 3.49213 3.49213 Created orthogonal box = (0 -34.9248 0) to (17.4606 34.9248 3.49213) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88898 4.88898 3.49213 Created 202 atoms create_atoms CPU = 0.000201941 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88898 4.88898 3.49213 Created 202 atoms create_atoms CPU = 8.39233e-05 secs 202 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 5 18 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 398 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1300.2183 0 -1300.2183 18977.678 65 0 -1318.1174 0 -1318.1174 -1114.8225 Loop time of 0.203545 on 1 procs for 65 steps with 398 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1300.21831382 -1318.11620025 -1318.11742197 Force two-norm initial, final = 19.8316 0.081031 Force max component initial, final = 6.74496 0.00931101 Final line search alpha, max atom move = 1 0.00931101 Iterations, force evaluations = 65 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19526 | 0.19526 | 0.19526 | 0.0 | 95.93 Neigh | 0.003701 | 0.003701 | 0.003701 | 0.0 | 1.82 Comm | 0.0032556 | 0.0032556 | 0.0032556 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001328 | | | 0.65 Nlocal: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4757 ave 4757 max 4757 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: 78964 ave 78964 max 78964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78964 Ave neighs/atom = 198.402 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.485 | 4.485 | 4.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1318.1174 0 -1318.1174 -1114.8225 4259.0596 68 0 -1318.1251 0 -1318.1251 -427.07404 4256.1805 Loop time of 0.00986385 on 1 procs for 3 steps with 398 atoms 101.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1318.11742197 -1318.12455616 -1318.12507882 Force two-norm initial, final = 6.55064 1.17486 Force max component initial, final = 6.50108 1.08902 Final line search alpha, max atom move = 0.00081716 0.000889902 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0093822 | 0.0093822 | 0.0093822 | 0.0 | 95.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003493 | | | 3.54 Nlocal: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4729 ave 4729 max 4729 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: 79164 ave 79164 max 79164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79164 Ave neighs/atom = 198.905 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 4.623 | 4.623 | 4.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1318.1251 0 -1318.1251 -427.07404 Loop time of 9.53674e-07 on 1 procs for 0 steps with 398 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: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4734 ave 4734 max 4734 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: 79160 ave 79160 max 79160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79160 Ave neighs/atom = 198.894 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) = 4.623 | 4.623 | 4.623 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 -1318.1251 -1318.1251 17.420954 69.849535 3.4977163 -427.07404 -427.07404 -409.01323 -709.37246 -162.83643 2.2210518 144.85833 Loop time of 9.53674e-07 on 1 procs for 0 steps with 398 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: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4734 ave 4734 max 4734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39580 ave 39580 max 39580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79160 ave 79160 max 79160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79160 Ave neighs/atom = 198.894 Neighbor list builds = 0 Dangerous builds = 0 398 -1301.32007324424 eV 2.22105183120835 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00