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 = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -58.6162 0) to (20.7227 58.6162 5.10157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.65164 6.21648 5.10157 Created 530 atoms create_atoms CPU = 0.000647068 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.65164 6.21648 5.10157 Created 530 atoms create_atoms CPU = 0.000487804 secs 530 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1044 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 11.03 | 11.03 | 11.03 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3648.8558 0 -3648.8558 156.35143 81 0 -3679.3058 0 -3679.3058 -12876.734 Loop time of 2.4225 on 1 procs for 81 steps with 1044 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3648.85577191 -3679.30234039 -3679.30582486 Force two-norm initial, final = 19.1471 0.22984 Force max component initial, final = 4.75848 0.0219845 Final line search alpha, max atom move = 1 0.0219845 Iterations, force evaluations = 81 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3925 | 2.3925 | 2.3925 | 0.0 | 98.76 Neigh | 0.010319 | 0.010319 | 0.010319 | 0.0 | 0.43 Comm | 0.014873 | 0.014873 | 0.014873 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004757 | | | 0.20 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15348 ave 15348 max 15348 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: 652952 ave 652952 max 652952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 652952 Ave neighs/atom = 625.433 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.03 | 11.03 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -3679.3058 0 -3679.3058 -12876.734 12393.571 90 0 -3679.9314 0 -3679.9314 -1894.4232 12293.035 Loop time of 0.198147 on 1 procs for 9 steps with 1044 atoms 95.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3679.30582486 -3679.93131002 -3679.93140467 Force two-norm initial, final = 164.892 0.656285 Force max component initial, final = 153.824 0.57086 Final line search alpha, max atom move = 0.000493493 0.000281715 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1943 | 0.1943 | 0.1943 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099802 | 0.00099802 | 0.00099802 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002848 | | | 1.44 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15360 ave 15360 max 15360 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: 654328 ave 654328 max 654328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654328 Ave neighs/atom = 626.751 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 10.54 | 10.54 | 10.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3679.9314 0 -3679.9314 -1894.4232 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1044 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 | | 1.907e-06 | | |100.00 Nlocal: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15396 ave 15396 max 15396 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: 658652 ave 658652 max 658652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658652 Ave neighs/atom = 630.893 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) = 10.54 | 10.54 | 10.54 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 -3679.9314 -3679.9314 20.557288 117.2323 5.1008905 -1894.4232 -1894.4232 -73.80761 -5618.6357 9.1738489 2.3768823 633.61301 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1044 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: 1044 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15396 ave 15396 max 15396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 329326 ave 329326 max 329326 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 658652 ave 658652 max 658652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 658652 Ave neighs/atom = 630.893 Neighbor list builds = 0 Dangerous builds = 0 1044 -3679.93140466861 eV 2.37688233185521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02