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 = 2.85531 2.85531 2.85531 Created orthogonal box = (0 -46.7463 0) to (33.0526 46.7463 4.03802) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.93323 4.53482 4.03802 Created 538 atoms create_atoms CPU = 0.000487089 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.93323 4.53482 4.03802 Created 538 atoms create_atoms CPU = 0.000339985 secs 538 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 22 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1068 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.439 | 5.439 | 5.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4202.8761 0 -4202.8761 22481.255 26 0 -4271.3606 0 -4271.3606 -2714.0598 Loop time of 0.294326 on 1 procs for 26 steps with 1068 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4202.87607898 -4271.3570725 -4271.36064952 Force two-norm initial, final = 143.365 0.163741 Force max component initial, final = 34.6803 0.0219947 Final line search alpha, max atom move = 0.966112 0.0212494 Iterations, force evaluations = 26 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28401 | 0.28401 | 0.28401 | 0.0 | 96.50 Neigh | 0.006588 | 0.006588 | 0.006588 | 0.0 | 2.24 Comm | 0.0024118 | 0.0024118 | 0.0024118 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001312 | | | 0.45 Nlocal: 1068 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8477 ave 8477 max 8477 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: 239684 ave 239684 max 239684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239684 Ave neighs/atom = 224.423 Neighbor list builds = 1 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.439 | 5.439 | 5.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -4271.3606 0 -4271.3606 -2714.0598 12478.21 28 0 -4271.3762 0 -4271.3762 -281.93345 12460.823 Loop time of 0.036886 on 1 procs for 2 steps with 1068 atoms 81.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4271.36064952 -4271.37617131 -4271.37619221 Force two-norm initial, final = 31.4962 0.173634 Force max component initial, final = 22.3 0.0392673 Final line search alpha, max atom move = 0.00169443 6.65357e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035929 | 0.035929 | 0.035929 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007119 | | | 1.93 Nlocal: 1068 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8477 ave 8477 max 8477 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: 239748 ave 239748 max 239748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239748 Ave neighs/atom = 224.483 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 8 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.577 | 5.577 | 5.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4271.3762 0 -4271.3762 -281.93345 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1068 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 | | 1.192e-06 | | |100.00 Nlocal: 1068 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8477 ave 8477 max 8477 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: 240112 ave 240112 max 240112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240112 Ave neighs/atom = 224.824 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) = 5.577 | 5.577 | 5.577 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 -4271.3762 -4271.3762 33.03078 93.492674 4.0350629 -281.93345 -281.93345 -5.0455342 -842.32839 1.5735577 2.2224543 469.51124 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1068 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 | | 1.192e-06 | | |100.00 Nlocal: 1068 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8477 ave 8477 max 8477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120056 ave 120056 max 120056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240112 ave 240112 max 240112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240112 Ave neighs/atom = 224.824 Neighbor list builds = 0 Dangerous builds = 0 1068 -4271.37619221112 eV 2.2224543414324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00