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 = 6.4001079 6.4001079 6.4001079 Created orthogonal box = (0.0000000 -83.936628 0.0000000) to (59.352159 83.936628 9.0511194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 11.042262 10.736080 9.0511194 Created 685 atoms using lattice units in orthogonal box = (0.0000000 -83.936628 0.0000000) to (59.352159 83.936628 9.0511194) create_atoms CPU = 0.002 seconds 685 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 11.042262 10.736080 9.0511194 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -83.936628 0.0000000) to (59.352159 83.936628 9.0511194) create_atoms CPU = 0.002 seconds 693 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 37 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 1365 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_128037485276_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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5542.2592 0 -5542.2592 323963.8 1 0 -5542.2592 0 -5542.2592 323963.8 Loop time of 0.147221 on 1 procs for 1 steps with 1365 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5542.25916335145 -5542.25916335145 -5542.25916335145 Force two-norm initial, final = 39.246731 39.246731 Force max component initial, final = 4.9615574 4.9615574 Final line search alpha, max atom move = 4.6926927e-12 2.3283064e-11 Iterations, force evaluations = 1 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14469 | 0.14469 | 0.14469 | 0.0 | 98.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001313 | | | 0.89 Nlocal: 1365.00 ave 1365 max 1365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4587.00 ave 4587 max 4587 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: 73122.0 ave 73122 max 73122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73122 Ave neighs/atom = 53.569231 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.650 | 4.650 | 4.650 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -5542.2592 0 -5542.2592 323963.8 90182.097 2 0 -5542.2592 0 -5542.2592 323963.8 90182.097 Loop time of 0.157373 on 1 procs for 1 steps with 1365 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5542.25916335145 -5542.25916335145 -5542.25916335145 Force two-norm initial, final = 31586.638 31586.638 Force max component initial, final = 18422.014 18422.014 Final line search alpha, max atom move = 6.3193591e-18 1.1641532e-13 Iterations, force evaluations = 1 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14888 | 0.14888 | 0.14888 | 0.0 | 94.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012143 | 0.0012143 | 0.0012143 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007279 | | | 4.63 Nlocal: 1365.00 ave 1365 max 1365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4587.00 ave 4587 max 4587 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: 73122.0 ave 73122 max 73122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73122 Ave neighs/atom = 53.569231 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.788 | 4.788 | 4.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5542.2592 0 -5542.2592 323963.8 Loop time of 1.884e-06 on 1 procs for 0 steps with 1365 atoms 159.2% 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 | | 1.884e-06 | | |100.00 Nlocal: 1365.00 ave 1365 max 1365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4587.00 ave 4587 max 4587 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: 73122.0 ave 73122 max 73122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73122 Ave neighs/atom = 53.569231 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.788 | 4.788 | 4.788 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 -5542.2592 -5542.2592 59.352159 167.87326 9.0511194 323963.8 323963.8 326523.81 318081.79 327285.78 3.1149352 2167.2094 Loop time of 1.712e-06 on 1 procs for 0 steps with 1365 atoms 175.2% 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 | | 1.712e-06 | | |100.00 Nlocal: 1365.00 ave 1365 max 1365 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4587.00 ave 4587 max 4587 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36561.0 ave 36561 max 36561 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73122.0 ave 73122 max 73122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73122 Ave neighs/atom = 53.569231 Neighbor list builds = 0 Dangerous builds = 0 1365 -563.162172847632 eV 3.11493524743162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01