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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -51.545625 0.0000000) to (36.448261 51.545625 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9497638 4.7727430 4.0498067 Created 647 atoms using lattice units in orthogonal box = (0.0000000 -51.545625 0.0000000) to (36.448261 51.545625 4.0498067) create_atoms CPU = 0.002 seconds 647 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9497638 4.7727430 4.0498067 Created 649 atoms using lattice units in orthogonal box = (0.0000000 -51.545625 0.0000000) to (36.448261 51.545625 4.0498067) create_atoms CPU = 0.001 seconds 649 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1296 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_179420363944_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5413.9231 0 -5413.9231 30678.377 65 0 -5545.0839 0 -5545.0839 3948.857 Loop time of 11.6387 on 1 procs for 65 steps with 1296 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 = -5413.9230855943 -5545.07854280455 -5545.08393800674 Force two-norm initial, final = 188.39307 0.24703788 Force max component initial, final = 75.758953 0.050639381 Final line search alpha, max atom move = 1.0000000 0.050639381 Iterations, force evaluations = 65 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.603 | 11.603 | 11.603 | 0.0 | 99.69 Neigh | 0.017109 | 0.017109 | 0.017109 | 0.0 | 0.15 Comm | 0.0097509 | 0.0097509 | 0.0097509 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008705 | | | 0.07 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7588.00 ave 7588 max 7588 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: 142526.0 ave 142526 max 142526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142526 Ave neighs/atom = 109.97377 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -5545.0839 0 -5545.0839 3948.857 15217.136 68 0 -5545.1731 0 -5545.1731 337.9751 15248.835 Loop time of 0.513819 on 1 procs for 3 steps with 1296 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 = -5545.08393800674 -5545.16886149931 -5545.17308492133 Force two-norm initial, final = 77.816401 6.7317667 Force max component initial, final = 68.603959 5.7044294 Final line search alpha, max atom move = 6.8445918e-05 0.00039044491 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51231 | 0.51231 | 0.51231 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027716 | 0.00027716 | 0.00027716 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001235 | | | 0.24 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7611.00 ave 7611 max 7611 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: 142432.0 ave 142432 max 142432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142432 Ave neighs/atom = 109.90123 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5545.1731 0 -5545.1731 337.9751 Loop time of 2.133e-06 on 1 procs for 0 steps with 1296 atoms 187.5% 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 | | 2.133e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7602.00 ave 7602 max 7602 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: 142274.0 ave 142274 max 142274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142274 Ave neighs/atom = 109.77932 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.187 | 5.187 | 5.187 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 -5545.1731 -5545.1731 36.472286 103.31164 4.0469184 337.9751 337.9751 372.66599 600.63874 40.620574 2.2938439 499.0442 Loop time of 2.038e-06 on 1 procs for 0 steps with 1296 atoms 245.3% 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 | | 2.038e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7602.00 ave 7602 max 7602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71137.0 ave 71137 max 71137 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142274.0 ave 142274 max 142274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142274 Ave neighs/atom = 109.77932 Neighbor list builds = 0 Dangerous builds = 0 1296 -5545.17308492133 eV 2.29384393632153 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12