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 = 4.0737181 4.0737181 4.0737181 Created orthogonal box = (0.0000000 -81.677795 0.0000000) to (47.156697 81.677795 7.0558868) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3344816 6.5017150 7.0558868 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.677795 0.0000000) to (47.156697 81.677795 7.0558868) create_atoms CPU = 0.010 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3344816 6.5017150 7.0558868 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.677795 0.0000000) to (47.156697 81.677795 7.0558868) create_atoms CPU = 0.010 seconds 1610 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 = 11 36 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 0 atoms, new total = 3218 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 = 11 36 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) = 11.35 | 11.35 | 11.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9449.668 0 -9449.668 92545.164 118 0 -9851.8976 0 -9851.8976 2140.1813 Loop time of 18.9029 on 1 procs for 118 steps with 3218 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 = -9449.66799379609 -9851.88927761063 -9851.89763418523 Force two-norm initial, final = 892.47471 0.22744675 Force max component initial, final = 203.29590 0.049025806 Final line search alpha, max atom move = 1.0000000 0.049025806 Iterations, force evaluations = 118 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.175 | 18.175 | 18.175 | 0.0 | 96.15 Neigh | 0.57393 | 0.57393 | 0.57393 | 0.0 | 3.04 Comm | 0.082311 | 0.082311 | 0.082311 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07148 | | | 0.38 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14968.0 ave 14968 max 14968 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: 640096.0 ave 640096 max 640096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640096 Ave neighs/atom = 198.91112 Neighbor list builds = 7 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 = 11 36 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 : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.35 | 11.35 | 11.35 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -9851.8976 0 -9851.8976 2140.1813 54353.683 124 0 -9852.3107 0 -9852.3107 29.522707 54586.788 Loop time of 0.729684 on 1 procs for 6 steps with 3218 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 = -9851.89763418524 -9852.30198834989 -9852.31068572212 Force two-norm initial, final = 157.94472 1.9590075 Force max component initial, final = 148.00507 1.5041307 Final line search alpha, max atom move = 7.4732600e-05 0.00011240760 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71727 | 0.71727 | 0.71727 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027329 | 0.0027329 | 0.0027329 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009686 | | | 1.33 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14975.0 ave 14975 max 14975 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: 640104.0 ave 640104 max 640104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 640104 Ave neighs/atom = 198.91361 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 = 11 36 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) = 10.86 | 10.86 | 10.86 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9852.3107 0 -9852.3107 29.522707 Loop time of 8.57e-06 on 1 procs for 0 steps with 3218 atoms 198.4% 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 | | 8.57e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14977.0 ave 14977 max 14977 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: 639676.0 ave 639676 max 639676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 639676 Ave neighs/atom = 198.78061 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 = 11 36 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) = 10.86 | 10.86 | 10.86 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 -9852.3107 -9852.3107 47.161794 164.30263 7.0445409 29.522707 29.522707 10.368038 34.12334 44.076744 2.6163787 1536.9201 Loop time of 9.472e-06 on 1 procs for 0 steps with 3218 atoms 190.0% 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 | | 9.472e-06 | | |100.00 Nlocal: 3218.00 ave 3218 max 3218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14977.0 ave 14977 max 14977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 319838.0 ave 319838 max 319838 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 639676.0 ave 639676 max 639676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 639676 Ave neighs/atom = 198.78061 Neighbor list builds = 0 Dangerous builds = 0 3218 -10312.7917277353 eV 2.61637871320102 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22