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 = 2.8659524 2.8659524 2.8659524 Created orthogonal box = (0.0000000 -53.155499 0.0000000) to (18.793307 53.155499 4.0530688) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8075901 4.9446976 4.0530688 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -53.155499 0.0000000) to (18.793307 53.155499 4.0530688) create_atoms CPU = 0.002 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8075901 4.9446976 4.0530688 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.155499 0.0000000) to (18.793307 53.155499 4.0530688) create_atoms CPU = 0.001 seconds 346 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 29 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 688 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1584.4044 0 -1584.4044 308492.43 91 0 -2938.772 0 -2938.772 5861.3314 Loop time of 0.983983 on 1 procs for 91 steps with 688 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1584.40443905294 -2938.76919354536 -2938.7720124195 Force two-norm initial, final = 3559.0287 0.20820340 Force max component initial, final = 989.62133 0.049534019 Final line search alpha, max atom move = 1.0000000 0.049534019 Iterations, force evaluations = 91 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95089 | 0.95089 | 0.95089 | 0.0 | 96.64 Neigh | 0.014652 | 0.014652 | 0.014652 | 0.0 | 1.49 Comm | 0.010644 | 0.010644 | 0.010644 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007792 | | | 0.79 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6392.00 ave 6392 max 6392 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: 114112.0 ave 114112 max 114112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114112 Ave neighs/atom = 165.86047 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.946 | 4.946 | 4.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -2938.772 0 -2938.772 5861.3314 8097.7687 95 0 -2938.8674 0 -2938.8674 268.98964 8125.1424 Loop time of 0.0359192 on 1 procs for 4 steps with 688 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 = -2938.77201241949 -2938.86559081892 -2938.86743632953 Force two-norm initial, final = 60.565092 2.6186408 Force max component initial, final = 55.808917 2.1182783 Final line search alpha, max atom move = 0.00019115955 0.00040492912 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034199 | 0.034199 | 0.034199 | 0.0 | 95.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030386 | 0.00030386 | 0.00030386 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001416 | | | 3.94 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6397.00 ave 6397 max 6397 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: 114168.0 ave 114168 max 114168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114168 Ave neighs/atom = 165.94186 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2938.8674 0 -2938.8674 268.98964 Loop time of 2.105e-06 on 1 procs for 0 steps with 688 atoms 142.5% 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 | | 2.105e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6397.00 ave 6397 max 6397 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: 114092.0 ave 114092 max 114092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114092 Ave neighs/atom = 165.83140 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.084 | 5.084 | 5.084 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 -2938.8674 -2938.8674 18.798797 106.65736 4.0523793 268.98964 268.98964 278.05959 419.05887 109.85047 2.2964783 316.82953 Loop time of 2.299e-06 on 1 procs for 0 steps with 688 atoms 261.0% 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 | | 2.299e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6397.00 ave 6397 max 6397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57046.0 ave 57046 max 57046 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114092.0 ave 114092 max 114092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114092 Ave neighs/atom = 165.83140 Neighbor list builds = 0 Dangerous builds = 0 688 -2938.86743632953 eV 2.29647829213817 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01