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 = 3.51812 3.51812 3.51812 Created orthogonal box = (0 -36.9019 0) to (45.1911 36.9019 8.6176) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.75159 5.36704 5.74507 Created 1324 atoms create_atoms CPU = 0.00069809 secs 1324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.75159 5.36704 5.74507 Created 1324 atoms create_atoms CPU = 0.000524044 secs 1324 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 = 10 16 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 50 atoms, new total = 2598 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 = 10 16 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) = 8.16 | 8.16 | 8.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11211.716 0 -11211.716 16548.832 67 0 -11333.775 0 -11333.775 -15441.867 Loop time of 2.40895 on 1 procs for 67 steps with 2598 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 = -11211.7163941 -11333.7649963 -11333.7752935 Force two-norm initial, final = 171.016 0.333206 Force max component initial, final = 24.0912 0.05217 Final line search alpha, max atom move = 1 0.05217 Iterations, force evaluations = 67 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3471 | 2.3471 | 2.3471 | 0.0 | 97.43 Neigh | 0.043082 | 0.043082 | 0.043082 | 0.0 | 1.79 Comm | 0.011185 | 0.011185 | 0.011185 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007553 | | | 0.31 Nlocal: 2598 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12502 ave 12502 max 12502 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: 841004 ave 841004 max 841004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 841004 Ave neighs/atom = 323.712 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.16 | 8.16 | 8.16 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -11333.775 0 -11333.775 -15441.867 28742.048 71 0 -11334.44 0 -11334.44 -5383.7141 28568.19 Loop time of 0.13725 on 1 procs for 4 steps with 2598 atoms 102.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11333.7752935 -11334.435018 -11334.439575 Force two-norm initial, final = 306.965 1.74598 Force max component initial, final = 231.454 1.35312 Final line search alpha, max atom move = 4.74254e-05 6.41721e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1352 | 0.1352 | 0.1352 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001589 | | | 1.16 Nlocal: 2598 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12460 ave 12460 max 12460 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: 841350 ave 841350 max 841350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 841350 Ave neighs/atom = 323.845 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 = 10 16 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) = 8.297 | 8.297 | 8.297 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11334.44 0 -11334.44 -5383.7141 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2598 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: 2598 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12486 ave 12486 max 12486 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: 858828 ave 858828 max 858828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 858828 Ave neighs/atom = 330.573 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) = 8.297 | 8.297 | 8.297 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 -11334.44 -11334.44 45.042329 73.803768 8.5937627 -5383.7141 -5383.7141 -57.221891 -16169.597 75.676314 2.2207927 1347.6934 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2598 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: 2598 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12486 ave 12486 max 12486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 429414 ave 429414 max 429414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 858828 ave 858828 max 858828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 858828 Ave neighs/atom = 330.573 Neighbor list builds = 0 Dangerous builds = 0 2598 -11334.4395750309 eV 2.22079268389334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02