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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -51.608251 0.0000000) to (36.490517 51.608251 4.0545019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9555023 4.7782763 4.0545019 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.608251 0.0000000) to (36.490517 51.608251 4.0545019) create_atoms CPU = 0.006 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9555023 4.7782763 4.0545019 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.608251 0.0000000) to (36.490517 51.608251 4.0545019) create_atoms CPU = 0.005 seconds 650 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1298 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.464 | 5.464 | 5.464 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4913.1898 0 -4913.1898 96144.995 405 0 -5243.6009 0 -5243.6009 -61162.651 Loop time of 18.1669 on 1 procs for 405 steps with 1298 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 = -4913.18981999334 -5243.59673380883 -5243.60085485489 Force two-norm initial, final = 529.66165 0.31743876 Force max component initial, final = 115.61035 0.12734096 Final line search alpha, max atom move = 0.67500953 0.085956364 Iterations, force evaluations = 405 797 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.789 | 17.789 | 17.789 | 0.0 | 97.92 Neigh | 0.088912 | 0.088912 | 0.088912 | 0.0 | 0.49 Comm | 0.16526 | 0.16526 | 0.16526 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1233 | | | 0.68 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9267.00 ave 9267 max 9267 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: 200174.0 ave 200174 max 200174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200174 Ave neighs/atom = 154.21726 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 405 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.464 | 5.464 | 5.464 Mbytes Step Temp E_pair E_mol TotEng Press Volume 405 0 -5243.6009 0 -5243.6009 -61162.651 15270.971 428 0 -5254.0924 0 -5254.0924 -20467.446 14678.655 Loop time of 0.595113 on 1 procs for 23 steps with 1298 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 = -5243.60085485489 -5254.09057807838 -5254.09237553439 Force two-norm initial, final = 739.58864 7.3804146 Force max component initial, final = 576.75994 5.5490574 Final line search alpha, max atom move = 0.00022404040 0.0012432131 Iterations, force evaluations = 23 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57265 | 0.57265 | 0.57265 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049168 | 0.0049168 | 0.0049168 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01755 | | | 2.95 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9262.00 ave 9262 max 9262 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: 200046.0 ave 200046 max 200046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200046 Ave neighs/atom = 154.11864 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.603 | 5.603 | 5.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5254.0924 0 -5254.0924 -20467.446 Loop time of 6.645e-06 on 1 procs for 0 steps with 1298 atoms 180.6% 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 | | 6.645e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9302.00 ave 9302 max 9302 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: 205980.0 ave 205980 max 205980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205980 Ave neighs/atom = 158.69029 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.603 | 5.603 | 5.603 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 -5254.0924 -5254.0924 35.807092 103.2165 3.9716236 -20467.446 -20467.446 -594.33641 -60757.123 -50.877554 2.2347392 5868.8705 Loop time of 6.545e-06 on 1 procs for 0 steps with 1298 atoms 320.9% 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 | | 6.545e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9302.00 ave 9302 max 9302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102990.0 ave 102990 max 102990 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205980.0 ave 205980 max 205980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205980 Ave neighs/atom = 158.69029 Neighbor list builds = 0 Dangerous builds = 0 1298 -5254.09237553439 eV 2.23473919528504 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19