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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -31.980817 0.0000000) to (6.3955915 31.980817 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8373549 3.8373549 2.8601955 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -31.980817 0.0000000) to (6.3955915 31.980817 2.8601955) create_atoms CPU = 0.001 seconds 51 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8373549 3.8373549 2.8601955 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -31.980817 0.0000000) to (6.3955915 31.980817 2.8601955) create_atoms CPU = 0.000 seconds 51 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 3 24 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 98 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.360 | 4.360 | 4.360 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -415.19677 0 -415.19677 -11963.182 44 0 -416.6617 0 -416.6617 -25164.139 Loop time of 0.517024 on 1 procs for 44 steps with 98 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 = -415.196768141845 -416.661377984322 -416.661699166017 Force two-norm initial, final = 2.3557549 0.098185605 Force max component initial, final = 0.99496934 0.045051963 Final line search alpha, max atom move = 1.0000000 0.045051963 Iterations, force evaluations = 44 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51558 | 0.51558 | 0.51558 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084693 | 0.00084693 | 0.00084693 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005995 | | | 0.12 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1279.00 ave 1279 max 1279 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: 5558.00 ave 5558 max 5558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5558 Ave neighs/atom = 56.714286 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.360 | 4.360 | 4.360 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -416.6617 0 -416.6617 -25164.139 1170.0273 55 0 -416.78321 0 -416.78321 -3482.7951 1154.6906 Loop time of 0.0759123 on 1 procs for 11 steps with 98 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 = -416.661699166017 -416.783111577427 -416.783210694239 Force two-norm initial, final = 24.874171 0.42300091 Force max component initial, final = 19.140368 0.35116652 Final line search alpha, max atom move = 0.0021620447 0.00075923770 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075284 | 0.075284 | 0.075284 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012163 | 0.00012163 | 0.00012163 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005065 | | | 0.67 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1279.00 ave 1279 max 1279 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: 5604.00 ave 5604 max 5604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5604 Ave neighs/atom = 57.183673 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -416.78321 0 -416.78321 -3482.7951 Loop time of 1.818e-06 on 1 procs for 0 steps with 98 atoms 110.0% 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 | | 1.818e-06 | | |100.00 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1279.00 ave 1279 max 1279 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: 5604.00 ave 5604 max 5604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5604 Ave neighs/atom = 57.183673 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.498 | 4.498 | 4.498 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 -416.78321 -416.78321 6.377795 63.961635 2.8305806 -3482.7951 -3482.7951 485.90085 -11079.88 145.59408 2.3901429 68.492789 Loop time of 1.301e-06 on 1 procs for 0 steps with 98 atoms 230.6% 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 | | 1.301e-06 | | |100.00 Nlocal: 98.0000 ave 98 max 98 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1279.00 ave 1279 max 1279 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2802.00 ave 2802 max 2802 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5604.00 ave 5604 max 5604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5604 Ave neighs/atom = 57.183673 Neighbor list builds = 0 Dangerous builds = 0 98 -416.783210694239 eV 2.39014293467644 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00