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 = 2.8510000 2.8510000 2.8510000 Created orthogonal box = (0.0000000 -34.686763 0.0000000) to (17.341956 34.686763 2.8510000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2809106 3.2809106 2.8510000 Created 149 atoms using lattice units in orthogonal box = (0.0000000 -34.686763 0.0000000) to (17.341956 34.686763 2.8510000) create_atoms CPU = 0.001 seconds 149 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2809106 3.2809106 2.8510000 Created 149 atoms using lattice units in orthogonal box = (0.0000000 -34.686763 0.0000000) to (17.341956 34.686763 2.8510000) create_atoms CPU = 0.001 seconds 149 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 = 6 24 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 292 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_549900287421_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 = 6 24 1 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) = 4.422 | 4.422 | 4.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1235.2052 0 -1235.2052 -34.033432 52 0 -1246.806 0 -1246.806 -14891.079 Loop time of 1.96709 on 1 procs for 52 steps with 292 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1235.20523663404 -1246.80480277442 -1246.80596497828 Force two-norm initial, final = 18.806054 0.087282167 Force max component initial, final = 6.7975429 0.010409770 Final line search alpha, max atom move = 1.0000000 0.010409770 Iterations, force evaluations = 52 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9519 | 1.9519 | 1.9519 | 0.0 | 99.23 Neigh | 0.0036734 | 0.0036734 | 0.0036734 | 0.0 | 0.19 Comm | 0.0060901 | 0.0060901 | 0.0060901 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005404 | | | 0.27 Nlocal: 292.000 ave 292 max 292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2611.00 ave 2611 max 2611 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: 18824.0 ave 18824 max 18824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18824 Ave neighs/atom = 64.465753 Neighbor list builds = 1 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 = 6 24 1 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.422 | 4.422 | 4.422 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -1246.806 0 -1246.806 -14891.079 3429.9602 62 0 -1247.0182 0 -1247.0182 -142.3583 3400.0579 Loop time of 0.279596 on 1 procs for 10 steps with 292 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 = -1246.80596497828 -1247.01813404419 -1247.01821944854 Force two-norm initial, final = 53.654743 0.20609629 Force max component initial, final = 48.300979 0.035571313 Final line search alpha, max atom move = 0.00086760427 3.0861823e-05 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27631 | 0.27631 | 0.27631 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072 | 0.00072 | 0.00072 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002562 | | | 0.92 Nlocal: 292.000 ave 292 max 292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2598.00 ave 2598 max 2598 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: 18720.0 ave 18720 max 18720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18720 Ave neighs/atom = 64.109589 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 = 6 24 1 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) = 4.560 | 4.560 | 4.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1247.0182 0 -1247.0182 -142.3583 Loop time of 6.185e-06 on 1 procs for 0 steps with 292 atoms 194.0% 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 | | 6.185e-06 | | |100.00 Nlocal: 292.000 ave 292 max 292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2598.00 ave 2598 max 2598 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: 18760.0 ave 18760 max 18760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18760 Ave neighs/atom = 64.246575 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 = 6 24 1 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) = 4.560 | 4.560 | 4.560 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 -1247.0182 -1247.0182 17.341066 69.373527 2.8262901 -142.3583 -142.3583 1.6849121 -445.37647 16.616649 2.3534944 176.73587 Loop time of 6.616e-06 on 1 procs for 0 steps with 292 atoms 211.6% 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 | | 6.616e-06 | | |100.00 Nlocal: 292.000 ave 292 max 292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2598.00 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9380.00 ave 9380 max 9380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 18760.0 ave 18760 max 18760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18760 Ave neighs/atom = 64.246575 Neighbor list builds = 0 Dangerous builds = 0 292 -1247.01821944854 eV 2.35349436147142 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02