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 = 3.52 3.52 3.52 Created orthogonal box = (0 -44.8058 0) to (31.68 44.8058 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.86667 6.08426 4.97803 Created 650 atoms create_atoms CPU = 0.000524998 secs 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.86667 6.08426 4.97803 Created 650 atoms create_atoms CPU = 0.000439882 secs 650 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 21 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1288 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 5.899 | 5.899 | 5.899 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5688.0011 0 -5688.0011 3861.8192 67 0 -5718.3428 0 -5718.3428 -6568.8365 Loop time of 1.09605 on 1 procs for 67 steps with 1288 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5688.00107268 -5718.33786073 -5718.34283988 Force two-norm initial, final = 23.9486 0.245663 Force max component initial, final = 5.44649 0.0410642 Final line search alpha, max atom move = 1 0.0410642 Iterations, force evaluations = 67 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0745 | 1.0745 | 1.0745 | 0.0 | 98.04 Neigh | 0.0088921 | 0.0088921 | 0.0088921 | 0.0 | 0.81 Comm | 0.0082588 | 0.0082588 | 0.0082588 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004379 | | | 0.40 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10085 ave 10085 max 10085 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: 318128 ave 318128 max 318128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318128 Ave neighs/atom = 246.994 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.903 | 5.903 | 5.903 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -5718.3428 0 -5718.3428 -6568.8365 14132.114 69 0 -5718.3831 0 -5718.3831 -2975.3697 14103.599 Loop time of 0.0259781 on 1 procs for 2 steps with 1288 atoms 115.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5718.34283988 -5718.3811332 -5718.38308983 Force two-norm initial, final = 54.8513 3.60852 Force max component initial, final = 46.3662 3.58125 Final line search alpha, max atom move = 9.12642e-05 0.00032684 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025255 | 0.025255 | 0.025255 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019407 | 0.00019407 | 0.00019407 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005291 | | | 2.04 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10078 ave 10078 max 10078 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: 318116 ave 318116 max 318116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318116 Ave neighs/atom = 246.984 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 6.041 | 6.041 | 6.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5718.3831 0 -5718.3831 -2975.3697 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1288 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: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10087 ave 10087 max 10087 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: 318212 ave 318212 max 318212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318212 Ave neighs/atom = 247.059 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) = 6.041 | 6.041 | 6.041 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 -5718.3831 -5718.3831 31.637147 89.611612 4.9747165 -2975.3697 -2975.3697 -41.447689 -9291.2223 406.5608 2.2752875 457.7315 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1288 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: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10087 ave 10087 max 10087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159106 ave 159106 max 159106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 318212 ave 318212 max 318212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318212 Ave neighs/atom = 247.059 Neighbor list builds = 0 Dangerous builds = 0 1288 -5689.33914043289 eV 2.27528752386611 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01