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 = 2.86385 2.86385 2.86385 Created orthogonal box = (0 -51.5521 0) to (36.4508 51.5521 4.05009) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.95011 4.77308 4.05009 Created 650 atoms create_atoms CPU = 0.000414848 secs 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.95011 4.77308 4.05009 Created 650 atoms create_atoms CPU = 0.000289917 secs 650 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 7 18 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 11.9775 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1284 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 11.4 | 11.4 | 11.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5279.8109 0 -5279.8109 5258.8835 95 0 -5347.598 0 -5347.598 -12126.227 Loop time of 3.11973 on 1 procs for 95 steps with 1284 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 = -5279.8108555 -5347.59310705 -5347.59796434 Force two-norm initial, final = 67.8751 0.297027 Force max component initial, final = 19.9205 0.0484891 Final line search alpha, max atom move = 1 0.0484891 Iterations, force evaluations = 95 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0672 | 3.0672 | 3.0672 | 0.0 | 98.32 Neigh | 0.027699 | 0.027699 | 0.027699 | 0.0 | 0.89 Comm | 0.018178 | 0.018178 | 0.018178 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006644 | | | 0.21 Nlocal: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15734 ave 15734 max 15734 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: 772524 ave 772524 max 772524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 772524 Ave neighs/atom = 601.654 Neighbor list builds = 2 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 : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -5347.598 0 -5347.598 -12126.227 15221.213 104 0 -5348.4707 0 -5348.4707 -2684.1597 15134.896 Loop time of 0.197977 on 1 procs for 9 steps with 1284 atoms 101.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5347.59796434 -5348.47069085 -5348.4707029 Force two-norm initial, final = 223.407 0.661673 Force max component initial, final = 222.629 0.379367 Final line search alpha, max atom move = 0.00204639 0.000776332 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19467 | 0.19467 | 0.19467 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090551 | 0.00090551 | 0.00090551 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002406 | | | 1.22 Nlocal: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15710 ave 15710 max 15710 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: 774004 ave 774004 max 774004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774004 Ave neighs/atom = 602.807 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 10.92 | 10.92 | 10.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5348.4707 0 -5348.4707 -2684.1597 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1284 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: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15703 ave 15703 max 15703 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: 774972 ave 774972 max 774972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774972 Ave neighs/atom = 603.561 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) = 10.92 | 10.92 | 10.92 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 -5348.4707 -5348.4707 36.523046 103.10427 4.0191645 -2684.1597 -2684.1597 -40.239243 -7989.3563 -22.883625 2.3360631 603.602 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1284 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: 1284 ave 1284 max 1284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15703 ave 15703 max 15703 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387486 ave 387486 max 387486 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 774972 ave 774972 max 774972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774972 Ave neighs/atom = 603.561 Neighbor list builds = 0 Dangerous builds = 0 1284 -5348.47070290131 eV 2.33606313728279 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03