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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -78.096856 0.0000000) to (27.611408 78.096856 5.9548295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.0633835 7.2648239 5.9548295 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -78.096856 0.0000000) to (27.611408 78.096856 5.9548295) create_atoms CPU = 0.003 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.0633835 7.2648239 5.9548295 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -78.096856 0.0000000) to (27.611408 78.096856 5.9548295) create_atoms CPU = 0.002 seconds 690 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 35 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_878712978062_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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.523 | 5.523 | 5.523 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5031.7438 0 -5031.7438 18466.962 92 0 -5133.277 0 -5133.277 954.87013 Loop time of 3.19266 on 1 procs for 92 steps with 1378 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 = -5031.74377304194 -5133.27199278088 -5133.27697820274 Force two-norm initial, final = 199.85847 0.12233183 Force max component initial, final = 45.329590 0.026726570 Final line search alpha, max atom move = 1.0000000 0.026726570 Iterations, force evaluations = 92 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.132 | 3.132 | 3.132 | 0.0 | 98.10 Neigh | 0.028311 | 0.028311 | 0.028311 | 0.0 | 0.89 Comm | 0.017636 | 0.017636 | 0.017636 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0147 | | | 0.46 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8762.00 ave 8762 max 8762 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: 236708.0 ave 236708 max 236708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236708 Ave neighs/atom = 171.77649 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.523 | 5.523 | 5.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -5133.277 0 -5133.277 954.87013 25681.562 94 0 -5133.2994 0 -5133.2994 -49.507577 25744.917 Loop time of 0.0579804 on 1 procs for 2 steps with 1378 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 = -5133.27697820274 -5133.29655888736 -5133.29943839551 Force two-norm initial, final = 27.131731 1.3869715 Force max component initial, final = 19.593325 0.88618205 Final line search alpha, max atom move = 0.00028802458 0.00025524221 Iterations, force evaluations = 2 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.056814 | 0.056814 | 0.056814 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022003 | 0.00022003 | 0.00022003 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009459 | | | 1.63 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8778.00 ave 8778 max 8778 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: 236092.0 ave 236092 max 236092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236092 Ave neighs/atom = 171.32946 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.661 | 5.661 | 5.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5133.2994 0 -5133.2994 -49.507577 Loop time of 1.756e-06 on 1 procs for 0 steps with 1378 atoms 170.8% 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 | | 1.756e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8778.00 ave 8778 max 8778 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: 235584.0 ave 235584 max 235584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235584 Ave neighs/atom = 170.96081 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 ghost atom cutoff = 9 binsize = 4.5, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.661 | 5.661 | 5.661 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 -5133.2994 -5133.2994 27.666631 156.30033 5.9535406 -49.507577 -49.507577 -46.92002 -46.465117 -55.137593 2.7912338 1107.6965 Loop time of 2.764e-06 on 1 procs for 0 steps with 1378 atoms 217.1% 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 | | 2.764e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8778.00 ave 8778 max 8778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117792.0 ave 117792 max 117792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235584.0 ave 235584 max 235584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235584 Ave neighs/atom = 170.96081 Neighbor list builds = 0 Dangerous builds = 0 1378 -5133.29943839551 eV 2.79123379444531 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03