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 = 3.61496 3.61496 3.61496 Created orthogonal box = (0 -63.8565 0) to (36.8655 63.8565 6.26129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.67161 5.73039 6.26129 Created 1250 atoms create_atoms CPU = 0.000545979 secs 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.67161 5.73039 6.26129 Created 1250 atoms create_atoms CPU = 0.000473022 secs 1250 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 = 7.71575 ghost atom cutoff = 7.71575 binsize = 3.85788, bins = 10 34 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 7.71575 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 21 atoms, new total = 2479 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 = 7.71575 ghost atom cutoff = 7.71575 binsize = 3.85788, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.71575 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) = 6.518 | 6.518 | 6.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8715.5842 0 -8715.5842 3270.0601 53 0 -8753.6156 0 -8753.6156 -1215.1048 Loop time of 0.826859 on 1 procs for 53 steps with 2479 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8715.58420675 -8753.60805433 -8753.6155647 Force two-norm initial, final = 45.7821 0.26395 Force max component initial, final = 7.95709 0.0497109 Final line search alpha, max atom move = 0.707613 0.0351761 Iterations, force evaluations = 53 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79222 | 0.79222 | 0.79222 | 0.0 | 95.81 Neigh | 0.022373 | 0.022373 | 0.022373 | 0.0 | 2.71 Comm | 0.0070915 | 0.0070915 | 0.0070915 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005171 | | | 0.63 Nlocal: 2479 ave 2479 max 2479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10575 ave 10575 max 10575 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: 427790 ave 427790 max 427790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 427790 Ave neighs/atom = 172.566 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.518 | 6.518 | 6.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -8753.6156 0 -8753.6156 -1215.1048 29479.444 55 0 -8753.6362 0 -8753.6362 -204.44129 29458.01 Loop time of 0.0454259 on 1 procs for 2 steps with 2479 atoms 88.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8753.6155647 -8753.63496406 -8753.63624037 Force two-norm initial, final = 40.1553 0.276917 Force max component initial, final = 39.8371 0.0646859 Final line search alpha, max atom move = 8.05653e-05 5.21144e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04402 | 0.04402 | 0.04402 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032473 | 0.00032473 | 0.00032473 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001081 | | | 2.38 Nlocal: 2479 ave 2479 max 2479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10575 ave 10575 max 10575 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: 428028 ave 428028 max 428028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428028 Ave neighs/atom = 172.662 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 = 7.71575 ghost atom cutoff = 7.71575 binsize = 3.85788, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.71575 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) = 6.656 | 6.656 | 6.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8753.6362 0 -8753.6362 -204.44129 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2479 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: 2479 ave 2479 max 2479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10575 ave 10575 max 10575 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: 428178 ave 428178 max 428178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428178 Ave neighs/atom = 172.722 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) = 6.656 | 6.656 | 6.656 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 -8753.6362 -8753.6362 36.876239 127.71304 6.2549167 -204.44129 -204.44129 -3.5191953 -610.3505 0.54582742 2.3208564 1015.7931 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2479 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: 2479 ave 2479 max 2479 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10575 ave 10575 max 10575 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 214089 ave 214089 max 214089 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 428178 ave 428178 max 428178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428178 Ave neighs/atom = 172.722 Neighbor list builds = 0 Dangerous builds = 0 2479 -8753.63624037151 eV 2.32085636674952 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01