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 = 3.7004859 3.7004859 3.7004859 Created orthogonal box = (0.0000000 -68.233589 0.0000000) to (34.116795 68.233589 3.7004859) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2178627 5.2178627 3.7004859 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -68.233589 0.0000000) to (34.116795 68.233589 3.7004859) create_atoms CPU = 0.004 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2178627 5.2178627 3.7004859 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -68.233589 0.0000000) to (34.116795 68.233589 3.7004859) create_atoms CPU = 0.002 seconds 682 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 13 51 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 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_857282754307_003#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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 13 51 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1924.158 0 -1924.158 26294.768 80 0 -2047.3148 0 -2047.3148 1863.1515 Loop time of 0.825662 on 1 procs for 80 steps with 1362 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 = -1924.15795938819 -2047.31280500948 -2047.31480825912 Force two-norm initial, final = 229.33678 0.16609739 Force max component initial, final = 77.294747 0.042085407 Final line search alpha, max atom move = 1.0000000 0.042085407 Iterations, force evaluations = 80 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78055 | 0.78055 | 0.78055 | 0.0 | 94.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021896 | 0.021896 | 0.021896 | 0.0 | 2.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02321 | | | 2.81 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6434.00 ave 6434 max 6434 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: 73608.0 ave 73608 max 73608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73608 Ave neighs/atom = 54.044053 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 13 51 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -2047.3148 0 -2047.3148 1863.1515 17228.807 84 0 -2047.4154 0 -2047.4154 -44.619357 17258.287 Loop time of 0.0412185 on 1 procs for 4 steps with 1362 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 = -2047.31480825912 -2047.41431777188 -2047.41536137026 Force two-norm initial, final = 62.713464 2.3539909 Force max component initial, final = 49.053164 2.2714380 Final line search alpha, max atom move = 0.00013622553 0.00030942785 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036723 | 0.036723 | 0.036723 | 0.0 | 89.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094437 | 0.00094437 | 0.00094437 | 0.0 | 2.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003551 | | | 8.62 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6390.00 ave 6390 max 6390 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: 73512.0 ave 73512 max 73512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73512 Ave neighs/atom = 53.973568 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 13 51 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.800 | 4.800 | 4.800 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2047.4154 0 -2047.4154 -44.619357 Loop time of 6.425e-06 on 1 procs for 0 steps with 1362 atoms 171.2% 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 | | 6.425e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6394.00 ave 6394 max 6394 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: 73492.0 ave 73492 max 73492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73492 Ave neighs/atom = 53.958884 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 13 51 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.800 | 4.800 | 4.800 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 -2047.4154 -2047.4154 34.043199 136.73869 3.707455 -44.619357 -44.619357 33.953078 -211.28895 43.477799 2.3500195 99.411152 Loop time of 6.495e-06 on 1 procs for 0 steps with 1362 atoms 246.3% 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 | | 6.495e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6394.00 ave 6394 max 6394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36746.0 ave 36746 max 36746 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73492.0 ave 73492 max 73492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73492 Ave neighs/atom = 53.958884 Neighbor list builds = 0 Dangerous builds = 0 1362 -2047.41536137026 eV 2.35001945792537 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01