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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -38.590065 0.0000000) to (12.862166 38.590065 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9469869 4.9469869 3.5673230 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.590065 0.0000000) to (12.862166 38.590065 3.5673230) create_atoms CPU = 0.002 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9469869 4.9469869 3.5673230 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -38.590065 0.0000000) to (12.862166 38.590065 3.5673230) create_atoms CPU = 0.001 seconds 158 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 306 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.421 | 4.421 | 4.421 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1275.1522 0 -1275.1522 -8462.444 53 0 -1288.649 0 -1288.649 7072.2351 Loop time of 2.10055 on 1 procs for 53 steps with 306 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 = -1275.15220711936 -1288.64852534193 -1288.64898043583 Force two-norm initial, final = 22.835786 0.55363179 Force max component initial, final = 7.1226670 0.13620595 Final line search alpha, max atom move = 0.35945777 0.048960289 Iterations, force evaluations = 53 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0896 | 2.0896 | 2.0896 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058543 | 0.0058543 | 0.0058543 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00512 | | | 0.24 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2334.00 ave 2334 max 2334 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: 16408.0 ave 16408 max 16408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16408 Ave neighs/atom = 53.620915 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.421 | 4.421 | 4.421 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1288.649 0 -1288.649 7072.2351 3541.2945 68 0 -1289.2973 0 -1289.2973 3099.1326 3564.8061 Loop time of 0.353496 on 1 procs for 15 steps with 306 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 = -1288.64898043583 -1289.29683025677 -1289.29729001567 Force two-norm initial, final = 89.675330 1.0428491 Force max component initial, final = 66.108466 0.32069757 Final line search alpha, max atom move = 0.00024920214 7.9918522e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34928 | 0.34928 | 0.34928 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090505 | 0.00090505 | 0.00090505 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003309 | | | 0.94 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2326.00 ave 2326 max 2326 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: 17460.0 ave 17460 max 17460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17460 Ave neighs/atom = 57.058824 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1289.2973 0 -1289.2973 3099.1326 Loop time of 6.505e-06 on 1 procs for 0 steps with 306 atoms 169.1% 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 | | 6.505e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2298.00 ave 2298 max 2298 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: 17412.0 ave 17412 max 17412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17412 Ave neighs/atom = 56.901961 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.559 | 4.559 | 4.559 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 -1289.2973 -1289.2973 13.029979 77.18013 3.5447588 3099.1326 3099.1326 -146.01576 9465.1124 -21.698726 2.2928428 166.0514 Loop time of 6.415e-06 on 1 procs for 0 steps with 306 atoms 265.0% 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 | | 6.415e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2298.00 ave 2298 max 2298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8706.00 ave 8706 max 8706 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17412.0 ave 17412 max 17412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17412 Ave neighs/atom = 56.901961 Neighbor list builds = 0 Dangerous builds = 0 306 -1289.29729001567 eV 2.29284283947944 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02