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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -59.1318 0) to (12.0695 59.1318 8.9139) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.48613 5.37528 5.9426 Created 530 atoms create_atoms CPU = 0.00036788 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.48613 5.37528 5.9426 Created 530 atoms create_atoms CPU = 0.000227928 secs 530 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.971 | 5.971 | 5.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3416.4332 0 -3416.4332 271.89242 50 0 -3428.4118 0 -3428.4118 -5761.8121 Loop time of 0.66281 on 1 procs for 50 steps with 1048 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3416.43324195 -3428.40910009 -3428.41180327 Force two-norm initial, final = 21.4085 0.131581 Force max component initial, final = 6.77706 0.00863497 Final line search alpha, max atom move = 1 0.00863497 Iterations, force evaluations = 50 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6555 | 0.6555 | 0.6555 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002396 | | | 0.36 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8476 ave 8476 max 8476 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: 331940 ave 331940 max 331940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331940 Ave neighs/atom = 316.737 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.974 | 5.974 | 5.974 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -3428.4118 0 -3428.4118 -5761.8121 12723.52 53 0 -3428.4945 0 -3428.4945 -717.8332 12679.348 Loop time of 0.0438311 on 1 procs for 3 steps with 1048 atoms 114.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3428.41180327 -3428.49426889 -3428.494545 Force two-norm initial, final = 65.7332 0.191153 Force max component initial, final = 51.6445 0.0941135 Final line search alpha, max atom move = 0.000561685 5.28622e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042729 | 0.042729 | 0.042729 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027633 | 0.00027633 | 0.00027633 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008261 | | | 1.88 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8867 ave 8867 max 8867 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: 332764 ave 332764 max 332764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332764 Ave neighs/atom = 317.523 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.112 | 6.112 | 6.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3428.4945 0 -3428.4945 -717.8332 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949 ave 8949 max 8949 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: 332800 ave 332800 max 332800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332800 Ave neighs/atom = 317.557 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) = 6.112 | 6.112 | 6.112 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 -3428.4945 -3428.4945 12.053528 118.26355 8.894711 -717.8332 -717.8332 -11.876573 -2131.8554 -9.7676268 2.2210248 432.7697 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949 ave 8949 max 8949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 166400 ave 166400 max 166400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 332800 ave 332800 max 332800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332800 Ave neighs/atom = 317.557 Neighbor list builds = 0 Dangerous builds = 0 1048 -3428.49454499932 eV 2.22102482098981 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00