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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -56.758670 0.0000000) to (34.757445 56.758670 7.0220643) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0195685 4.0541907 4.6813762 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -56.758670 0.0000000) to (34.757445 56.758670 7.0220643) create_atoms CPU = 0.005 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0195685 4.0541907 4.6813762 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.758670 0.0000000) to (34.757445 56.758670 7.0220643) create_atoms CPU = 0.004 seconds 1182 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2352 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_036303866285_000#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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.493 | 6.493 | 6.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7404.8211 0 -7404.8211 155749.86 63 0 -10013.975 0 -10013.975 9399.9163 Loop time of 4.147 on 1 procs for 63 steps with 2352 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 = -7404.82111519372 -10013.9650465823 -10013.9747530085 Force two-norm initial, final = 3057.4783 0.36481486 Force max component initial, final = 449.09432 0.020206391 Final line search alpha, max atom move = 1.0000000 0.020206391 Iterations, force evaluations = 63 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9894 | 3.9894 | 3.9894 | 0.0 | 96.20 Neigh | 0.10059 | 0.10059 | 0.10059 | 0.0 | 2.43 Comm | 0.029011 | 0.029011 | 0.029011 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02797 | | | 0.67 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9984.00 ave 9984 max 9984 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: 392028.0 ave 392028 max 392028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 392028 Ave neighs/atom = 166.67857 Neighbor list builds = 2 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -10013.975 0 -10013.975 9399.9163 27706.065 71 0 -10015.241 0 -10015.241 -90.71171 27833.201 Loop time of 0.365439 on 1 procs for 8 steps with 2352 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 = -10013.9747530085 -10015.2403388746 -10015.2414690129 Force two-norm initial, final = 381.84682 3.1376406 Force max component initial, final = 371.12411 2.3117440 Final line search alpha, max atom move = 0.00015767357 0.00036450093 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35447 | 0.35447 | 0.35447 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022387 | 0.0022387 | 0.0022387 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008734 | | | 2.39 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9995.00 ave 9995 max 9995 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: 391884.0 ave 391884 max 391884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391884 Ave neighs/atom = 166.61735 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.251 | 6.251 | 6.251 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10015.241 0 -10015.241 -90.71171 Loop time of 6.515e-06 on 1 procs for 0 steps with 2352 atoms 230.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9977.00 ave 9977 max 9977 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: 391680.0 ave 391680 max 391680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391680 Ave neighs/atom = 166.53061 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.251 | 6.251 | 6.251 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 -10015.241 -10015.241 34.709166 114.3301 7.0138807 -90.71171 -90.71171 -92.396849 -46.821284 -132.917 2.3033741 1206.8207 Loop time of 7.427e-06 on 1 procs for 0 steps with 2352 atoms 255.8% 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 | | 7.427e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9977.00 ave 9977 max 9977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195840.0 ave 195840 max 195840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391680.0 ave 391680 max 391680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391680 Ave neighs/atom = 166.53061 Neighbor list builds = 0 Dangerous builds = 0 2352 -10015.2414690129 eV 2.30337405425656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05