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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -51.796803 0.0000000) to (36.625871 51.796803 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2531975 6.9483517 5.7200000 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.796803 0.0000000) to (36.625871 51.796803 5.7200000) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2531975 6.9483517 5.7200000 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.796803 0.0000000) to (36.625871 51.796803 5.7200000) create_atoms CPU = 0.002 seconds 660 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1316 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_058537087384_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.042 | 5.042 | 5.042 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4225.8892 0 -4225.8892 23977.428 60 0 -4409.7279 0 -4409.7279 5775.0425 Loop time of 7.12801 on 1 procs for 60 steps with 1316 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4225.88918557964 -4409.72359129221 -4409.72793362205 Force two-norm initial, final = 257.76120 0.16689684 Force max component initial, final = 68.921072 0.018144569 Final line search alpha, max atom move = 1.0000000 0.018144569 Iterations, force evaluations = 60 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1106 | 7.1106 | 7.1106 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0091649 | 0.0091649 | 0.0091649 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008192 | | | 0.11 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5894.00 ave 5894 max 5894 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: 103704.0 ave 103704 max 103704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103704 Ave neighs/atom = 78.802432 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -4409.7279 0 -4409.7279 5775.0425 21702.859 69 0 -4410.2158 0 -4410.2158 17.705472 21859.014 Loop time of 0.677138 on 1 procs for 9 steps with 1316 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 = -4409.72793362202 -4410.21572173799 -4410.21579447117 Force two-norm initial, final = 148.20185 0.80905957 Force max component initial, final = 126.58844 0.76368320 Final line search alpha, max atom move = 0.00070197263 0.00053608470 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67383 | 0.67383 | 0.67383 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050032 | 0.00050032 | 0.00050032 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002804 | | | 0.41 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5402.00 ave 5402 max 5402 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: 108408.0 ave 108408 max 108408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108408 Ave neighs/atom = 82.376900 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.177 | 5.177 | 5.177 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4410.2158 0 -4410.2158 17.705472 Loop time of 2.199e-06 on 1 procs for 0 steps with 1316 atoms 181.9% 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 | | 2.199e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5381.00 ave 5381 max 5381 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: 106152.0 ave 106152 max 106152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106152 Ave neighs/atom = 80.662614 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.177 | 5.177 | 5.177 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 -4410.2158 -4410.2158 36.638092 104.42174 5.7135598 17.705472 17.705472 -6.3748301 56.42233 3.0689163 2.616125 756.95458 Loop time of 2.308e-06 on 1 procs for 0 steps with 1316 atoms 173.3% 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 | | 2.308e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5381.00 ave 5381 max 5381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53076.0 ave 53076 max 53076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106152.0 ave 106152 max 106152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106152 Ave neighs/atom = 80.662614 Neighbor list builds = 0 Dangerous builds = 0 1316 -4410.21579447117 eV 2.61612498090829 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08