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 -47.346320 0.0000000) to (22.317562 47.346320 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6984342 5.8140157 5.1200000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.346320 0.0000000) to (22.317562 47.346320 5.1200000) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6984342 5.8140157 5.1200000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.346320 0.0000000) to (22.317562 47.346320 5.1200000) create_atoms CPU = 0.001 seconds 458 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 = 8 32 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 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 = 8 32 2 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3169.2668 0 -3169.2668 5384.3723 47 0 -3188.8361 0 -3188.8361 -4357.4702 Loop time of 1.2056 on 1 procs for 47 steps with 904 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 = -3169.26678443296 -3188.83381560173 -3188.83611029537 Force two-norm initial, final = 27.655581 0.12802268 Force max component initial, final = 3.7638697 0.020385955 Final line search alpha, max atom move = 1.0000000 0.020385955 Iterations, force evaluations = 47 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1988 | 1.1988 | 1.1988 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032576 | 0.0032576 | 0.0032576 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00354 | | | 0.29 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 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: 69832.0 ave 69832 max 69832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69832 Ave neighs/atom = 77.247788 Neighbor list builds = 0 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 = 8 32 2 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -3188.8361 0 -3188.8361 -4357.4702 10820.141 49 0 -3188.8603 0 -3188.8603 -1446.6052 10797.873 Loop time of 0.0541468 on 1 procs for 2 steps with 904 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 = -3188.83611029537 -3188.8598759458 -3188.86034513688 Force two-norm initial, final = 32.948745 0.55445463 Force max component initial, final = 25.998141 0.45864234 Final line search alpha, max atom move = 0.00025427686 0.00011662213 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053465 | 0.053465 | 0.053465 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012813 | 0.00012813 | 0.00012813 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005532 | | | 1.02 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 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: 69800.0 ave 69800 max 69800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69800 Ave neighs/atom = 77.212389 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 = 8 32 2 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) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3188.8603 0 -3188.8603 -1446.6052 Loop time of 1.652e-06 on 1 procs for 0 steps with 904 atoms 181.6% 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 | | 1.652e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 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: 69808.0 ave 69808 max 69808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69808 Ave neighs/atom = 77.221239 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 = 8 32 2 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) = 4.718 | 4.718 | 4.718 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 -3188.8603 -3188.8603 22.297879 94.692639 5.1139729 -1446.6052 -1446.6052 67.992826 -4366.0099 -41.79868 2.415881 568.04401 Loop time of 1.595e-06 on 1 procs for 0 steps with 904 atoms 125.4% 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 | | 1.595e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34904.0 ave 34904 max 34904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69808.0 ave 69808 max 69808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69808 Ave neighs/atom = 77.221239 Neighbor list builds = 0 Dangerous builds = 0 904 -3188.86034513688 eV 2.41588097442732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01