LAMMPS (24 Jan 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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -44.2578 0) to (9.03326 44.2578 9.89544) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.41996 5.9005 6.59696 Created 242 atoms create_atoms CPU = 0.000575066 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.41996 5.9005 6.59696 Created 242 atoms create_atoms CPU = 0.000391006 secs 242 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 2 16 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 476 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.452 | 5.452 | 5.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1351.4582 0 -1351.4582 3497.9359 21 0 -1364.5007 0 -1364.5007 -2615.8447 Loop time of 0.207509 on 1 procs for 21 steps with 476 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 = -1351.45816737 -1364.49978679 -1364.50072689 Force two-norm initial, final = 19.7922 0.0842737 Force max component initial, final = 5.60035 0.0105726 Final line search alpha, max atom move = 1 0.0105726 Iterations, force evaluations = 21 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20493 | 0.20493 | 0.20493 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001893 | 0.001893 | 0.001893 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006866 | | | 0.33 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7124 ave 7124 max 7124 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: 201264 ave 201264 max 201264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201264 Ave neighs/atom = 422.824 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.452 | 5.452 | 5.452 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -1364.5007 0 -1364.5007 -2615.8447 7912.2497 23 0 -1364.511 0 -1364.511 -1007.0185 7895.2686 Loop time of 0.021373 on 1 procs for 2 steps with 476 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 = -1364.50072689 -1364.51064957 -1364.51101223 Force two-norm initial, final = 13.3531 0.145534 Force max component initial, final = 10.6865 0.0983066 Final line search alpha, max atom move = 0.000473958 4.65931e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02081 | 0.02081 | 0.02081 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003843 | | | 1.80 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7068 ave 7068 max 7068 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: 188056 ave 188056 max 188056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188056 Ave neighs/atom = 395.076 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.208 | 5.208 | 5.208 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1364.511 0 -1364.511 -1007.0185 Loop time of 9.53674e-07 on 1 procs for 0 steps with 476 atoms 209.7% 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: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7068 ave 7068 max 7068 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: 192852 ave 192852 max 192852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192852 Ave neighs/atom = 405.151 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) = 5.208 | 5.208 | 5.208 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 -1364.511 -1364.511 9.0250881 88.515629 9.8831526 -1007.0185 -1007.0185 19.931167 -3027.5897 -13.397051 2.5887489 327.70576 Loop time of 1.19209e-06 on 1 procs for 0 steps with 476 atoms 167.8% 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: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7068 ave 7068 max 7068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96426 ave 96426 max 96426 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192852 ave 192852 max 192852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192852 Ave neighs/atom = 405.151 Neighbor list builds = 0 Dangerous builds = 0 476 -1364.51101222693 eV 2.58874887886618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00