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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -59.429793 0.0000000) to (29.714896 59.429793 4.0816549) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0459258 5.0459258 4.0816549 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -59.429793 0.0000000) to (29.714896 59.429793 4.0816549) create_atoms CPU = 0.002 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0459258 5.0459258 4.0816549 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -59.429793 0.0000000) to (29.714896 59.429793 4.0816549) create_atoms CPU = 0.001 seconds 426 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_049243498555_000#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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.831 | 5.831 | 5.831 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2951.9218 0 -2951.9218 13217.754 41 0 -3029.7876 0 -3029.7876 4595.8689 Loop time of 3.33745 on 1 procs for 41 steps with 848 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2951.92180481604 -3029.78486320163 -3029.78764576803 Force two-norm initial, final = 107.48746 0.10211830 Force max component initial, final = 30.803027 0.016650029 Final line search alpha, max atom move = 1.0000000 0.016650029 Iterations, force evaluations = 41 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2708 | 3.2708 | 3.2708 | 0.0 | 98.00 Neigh | 0.042319 | 0.042319 | 0.042319 | 0.0 | 1.27 Comm | 0.015719 | 0.015719 | 0.015719 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008628 | | | 0.26 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11177.0 ave 11177 max 11177 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: 362392.0 ave 362392 max 362392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 362392 Ave neighs/atom = 427.34906 Neighbor list builds = 1 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.833 | 5.833 | 5.833 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3029.7876 0 -3029.7876 4595.8689 14415.998 48 0 -3029.9648 0 -3029.9648 140.96731 14484.443 Loop time of 0.495727 on 1 procs for 7 steps with 848 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3029.78764576805 -3029.96407134824 -3029.96483947454 Force two-norm initial, final = 76.190041 3.0700164 Force max component initial, final = 62.550580 2.9465235 Final line search alpha, max atom move = 0.00024963506 0.00073555557 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48781 | 0.48781 | 0.48781 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021859 | 0.0021859 | 0.0021859 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005728 | | | 1.16 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11179.0 ave 11179 max 11179 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: 361796.0 ave 361796 max 361796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361796 Ave neighs/atom = 426.64623 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.971 | 5.971 | 5.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3029.9648 0 -3029.9648 140.96731 Loop time of 6.444e-06 on 1 procs for 0 steps with 848 atoms 170.7% 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 | | 6.444e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11179.0 ave 11179 max 11179 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: 361432.0 ave 361432 max 361432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361432 Ave neighs/atom = 426.21698 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.971 | 5.971 | 5.971 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 -3029.9648 -3029.9648 29.705641 119.57926 4.0776222 140.96731 140.96731 93.537293 327.89904 1.465601 2.5497619 467.71217 Loop time of 6.856e-06 on 1 procs for 0 steps with 848 atoms 248.0% 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 | | 6.856e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11179.0 ave 11179 max 11179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 180716.0 ave 180716 max 180716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 361432.0 ave 361432 max 361432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361432 Ave neighs/atom = 426.21698 Neighbor list builds = 0 Dangerous builds = 0 848 -3029.96483947454 eV 2.54976190619052 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04