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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -37.305438 0.0000000) to (32.307457 37.305438 6.3360136) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7987743 5.7392981 6.3360136 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -37.305438 0.0000000) to (32.307457 37.305438 6.3360136) create_atoms CPU = 0.001 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7987743 5.7392981 6.3360136 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -37.305438 0.0000000) to (32.307457 37.305438 6.3360136) create_atoms CPU = 0.001 seconds 627 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1243 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4598.3739 0 -4598.3739 52851.991 383 0 -4880.3683 0 -4880.3683 -56391.753 Loop time of 6.28392 on 1 procs for 383 steps with 1243 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 = -4598.37393907787 -4880.3637146508 -4880.36832125764 Force two-norm initial, final = 411.90783 0.20736415 Force max component initial, final = 157.30773 0.061448659 Final line search alpha, max atom move = 0.80324497 0.049358327 Iterations, force evaluations = 383 723 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1121 | 6.1121 | 6.1121 | 0.0 | 97.27 Neigh | 0.088581 | 0.088581 | 0.088581 | 0.0 | 1.41 Comm | 0.041678 | 0.041678 | 0.041678 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04155 | | | 0.66 Nlocal: 1243.00 ave 1243 max 1243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5879.00 ave 5879 max 5879 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: 168416.0 ave 168416 max 168416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168416 Ave neighs/atom = 135.49155 Neighbor list builds = 8 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 383 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 383 0 -4880.3683 0 -4880.3683 -56391.753 15272.882 416 0 -4894.5924 0 -4894.5924 7.1634588 14659.89 Loop time of 0.324042 on 1 procs for 33 steps with 1243 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 = -4880.36832125763 -4894.58987892346 -4894.59238942764 Force two-norm initial, final = 967.42356 7.2440912 Force max component initial, final = 705.35928 5.3254402 Final line search alpha, max atom move = 0.00068127387 0.0036280833 Iterations, force evaluations = 33 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30307 | 0.30307 | 0.30307 | 0.0 | 93.53 Neigh | 0.010173 | 0.010173 | 0.010173 | 0.0 | 3.14 Comm | 0.0018007 | 0.0018007 | 0.0018007 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009 | | | 2.78 Nlocal: 1243.00 ave 1243 max 1243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5957.00 ave 5957 max 5957 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: 174508.0 ave 174508 max 174508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174508 Ave neighs/atom = 140.39260 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.189 | 5.189 | 5.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4894.5924 0 -4894.5924 7.1634588 Loop time of 1.965e-06 on 1 procs for 0 steps with 1243 atoms 152.7% 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 | | 1.965e-06 | | |100.00 Nlocal: 1243.00 ave 1243 max 1243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5957.00 ave 5957 max 5957 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: 175750.0 ave 175750 max 175750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175750 Ave neighs/atom = 141.39179 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.189 | 5.189 | 5.189 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 -4894.5924 -4894.5924 31.435474 73.350036 6.3578514 7.1634588 7.1634588 -271.08021 572.18088 -279.6103 2.2106515 3599.5425 Loop time of 2.407e-06 on 1 procs for 0 steps with 1243 atoms 249.3% 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 | | 2.407e-06 | | |100.00 Nlocal: 1243.00 ave 1243 max 1243 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5957.00 ave 5957 max 5957 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87875.0 ave 87875 max 87875 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175750.0 ave 175750 max 175750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175750 Ave neighs/atom = 141.39179 Neighbor list builds = 0 Dangerous builds = 0 1243 -4718.80531090348 eV 2.21065146881721 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07