LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -48.029857 0.0000000) to (29.412161 48.029857 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3476656 5.4579383 5.9120667 Created 1042 atoms using lattice units in orthogonal box = (0.0000000 -48.029857 0.0000000) to (29.412161 48.029857 8.8681001) create_atoms CPU = 0.002 seconds 1042 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3476656 5.4579383 5.9120667 Created 1066 atoms using lattice units in orthogonal box = (0.0000000 -48.029857 0.0000000) to (29.412161 48.029857 8.8681001) create_atoms CPU = 0.001 seconds 1066 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2108 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_390178379548_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7225.1981 0 -7225.1981 28258.472 76 0 -7451.8291 0 -7451.8291 1772.1516 Loop time of 3.58653 on 1 procs for 76 steps with 2108 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7225.19812861204 -7451.82203193696 -7451.82906502073 Force two-norm initial, final = 210.51401 0.20489964 Force max component initial, final = 43.935503 0.028678997 Final line search alpha, max atom move = 1.0000000 0.028678997 Iterations, force evaluations = 76 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5128 | 3.5128 | 3.5128 | 0.0 | 97.95 Neigh | 0.050976 | 0.050976 | 0.050976 | 0.0 | 1.42 Comm | 0.0082574 | 0.0082574 | 0.0082574 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01446 | | | 0.40 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5738.00 ave 5738 max 5738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163360.0 ave 163360 max 163360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163360 Ave neighs/atom = 77.495256 Neighbor list builds = 4 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -7451.8291 0 -7451.8291 1772.1516 25055.254 80 0 -7451.9462 0 -7451.9462 -52.551886 25086.842 Loop time of 0.204785 on 1 procs for 4 steps with 2108 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 = -7451.82906502073 -7451.94535323826 -7451.94623050547 Force two-norm initial, final = 75.401489 2.7752473 Force max component initial, final = 75.045369 2.5519084 Final line search alpha, max atom move = 0.00011035941 0.00028162710 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20231 | 0.20231 | 0.20231 | 0.0 | 98.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003288 | 0.0003288 | 0.0003288 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002146 | | | 1.05 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5932.00 ave 5932 max 5932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163400.0 ave 163400 max 163400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163400 Ave neighs/atom = 77.514231 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7451.9462 0 -7451.9462 -52.551886 Loop time of 2.26e-06 on 1 procs for 0 steps with 2108 atoms 177.0% 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 | | 2.26e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5940.00 ave 5940 max 5940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163350.0 ave 163350 max 163350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163350 Ave neighs/atom = 77.490512 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.213 | 5.213 | 5.213 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 -7451.9462 -7451.9462 29.385028 96.363303 8.8594794 -52.551886 -52.551886 -162.82783 50.254885 -45.082716 2.4116952 813.03024 Loop time of 2.252e-06 on 1 procs for 0 steps with 2108 atoms 222.0% 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 | | 2.252e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5940.00 ave 5940 max 5940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81675.0 ave 81675 max 81675 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163350.0 ave 163350 max 163350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163350 Ave neighs/atom = 77.490512 Neighbor list builds = 0 Dangerous builds = 0 2108 -7451.94623050547 eV 2.41169515887531 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04