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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -47.465813 0.0000000) to (33.563399 47.465813 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2994840 5.4127682 4.4455807 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.465813 0.0000000) to (33.563399 47.465813 4.4455807) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2994840 5.4127682 4.4455807 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.465813 0.0000000) to (33.563399 47.465813 4.4455807) create_atoms CPU = 0.001 seconds 458 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 19 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4467.6305 0 -4467.6305 222781.55 81 0 -6066.0339 0 -6066.0339 12450.63 Loop time of 1.51945 on 1 procs for 81 steps with 912 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 = -4467.63047961262 -6066.0278287248 -6066.03387723725 Force two-norm initial, final = 2678.8203 0.44290017 Force max component initial, final = 752.45483 0.044613357 Final line search alpha, max atom move = 1.0000000 0.044613357 Iterations, force evaluations = 81 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4584 | 1.4584 | 1.4584 | 0.0 | 95.98 Neigh | 0.042404 | 0.042404 | 0.042404 | 0.0 | 2.79 Comm | 0.010909 | 0.010909 | 0.010909 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007716 | | | 0.51 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8785.00 ave 8785 max 8785 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: 253936.0 ave 253936 max 253936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253936 Ave neighs/atom = 278.43860 Neighbor list builds = 3 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -6066.0339 0 -6066.0339 12450.63 14164.634 84 0 -6066.3113 0 -6066.3113 -236.88213 14227.05 Loop time of 0.054552 on 1 procs for 3 steps with 912 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 = -6066.03387723721 -6066.30610249288 -6066.31130404674 Force two-norm initial, final = 199.40981 4.5101766 Force max component initial, final = 149.13914 3.2408829 Final line search alpha, max atom move = 7.3402811e-05 0.00023788991 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052802 | 0.052802 | 0.052802 | 0.0 | 96.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034216 | 0.00034216 | 0.00034216 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001408 | | | 2.58 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8785.00 ave 8785 max 8785 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: 253940.0 ave 253940 max 253940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253940 Ave neighs/atom = 278.44298 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.555 | 5.555 | 5.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6066.3113 0 -6066.3113 -236.88213 Loop time of 2.186e-06 on 1 procs for 0 steps with 912 atoms 137.2% 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 | | 2.186e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8785.00 ave 8785 max 8785 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: 253176.0 ave 253176 max 253176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253176 Ave neighs/atom = 277.60526 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.555 | 5.555 | 5.555 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 -6066.3113 -6066.3113 33.619896 95.152913 4.4472997 -236.88213 -236.88213 4.4377321 -365.82216 -349.26198 2.5716403 970.74489 Loop time of 2.204e-06 on 1 procs for 0 steps with 912 atoms 181.5% 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 | | 2.204e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8785.00 ave 8785 max 8785 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126588.0 ave 126588 max 126588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 253176.0 ave 253176 max 253176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253176 Ave neighs/atom = 277.60526 Neighbor list builds = 0 Dangerous builds = 0 912 -6066.31130404674 eV 2.5716402743715 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01