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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -43.451852 0.0000000) to (25.086938 43.451852 4.2608046) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8595290 3.8995252 4.2608046 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -43.451852 0.0000000) to (25.086938 43.451852 4.2608046) create_atoms CPU = 0.002 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8595290 3.8995252 4.2608046 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -43.451852 0.0000000) to (25.086938 43.451852 4.2608046) create_atoms CPU = 0.001 seconds 626 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 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, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1247 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_677328661525_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.888 | 5.888 | 5.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13090.528 0 -13090.528 816605.99 316 0 -15793.477 0 -15793.477 229428.89 Loop time of 51.6584 on 1 procs for 316 steps with 1247 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 = -13090.5277081143 -15793.4617837147 -15793.4772249468 Force two-norm initial, final = 6834.5827 1.1374959 Force max component initial, final = 1597.3980 0.39682619 Final line search alpha, max atom move = 0.22348035 0.088682857 Iterations, force evaluations = 316 619 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 51.376 | 51.376 | 51.376 | 0.0 | 99.45 Neigh | 0.16488 | 0.16488 | 0.16488 | 0.0 | 0.32 Comm | 0.0702 | 0.0702 | 0.0702 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04722 | | | 0.09 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9529.00 ave 9529 max 9529 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: 304392.0 ave 304392 max 304392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304392 Ave neighs/atom = 244.09944 Neighbor list builds = 9 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 316 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.889 | 5.889 | 5.889 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -15793.477 0 -15793.477 229428.89 9289.184 356 0 -15854.793 0 -15854.793 -1877.3012 9577.7167 Loop time of 3.19722 on 1 procs for 40 steps with 1247 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15793.4772249468 -15854.7854025194 -15854.7929400949 Force two-norm initial, final = 3211.0352 24.429688 Force max component initial, final = 2896.1397 11.865802 Final line search alpha, max atom move = 6.1315017e-05 0.00072755184 Iterations, force evaluations = 40 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1606 | 3.1606 | 3.1606 | 0.0 | 98.86 Neigh | 0.016749 | 0.016749 | 0.016749 | 0.0 | 0.52 Comm | 0.0033876 | 0.0033876 | 0.0033876 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01646 | | | 0.51 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9014.00 ave 9014 max 9014 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: 293796.0 ave 293796 max 293796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293796 Ave neighs/atom = 235.60225 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.641 | 5.641 | 5.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15854.793 0 -15854.793 -1877.3012 Loop time of 1.767e-06 on 1 procs for 0 steps with 1247 atoms 169.8% 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 | | 1.767e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8971.00 ave 8971 max 8971 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: 294148.0 ave 294148 max 294148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294148 Ave neighs/atom = 235.88452 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.641 | 5.641 | 5.641 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 -15854.793 -15854.793 25.461441 85.230952 4.4134852 -1877.3012 -1877.3012 -1914.679 -1946.7246 -1770.5 1.9206832 4888.1639 Loop time of 1.784e-06 on 1 procs for 0 steps with 1247 atoms 224.2% 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 | | 1.784e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8971.00 ave 8971 max 8971 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147074.0 ave 147074 max 147074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 294148.0 ave 294148 max 294148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294148 Ave neighs/atom = 235.88452 Neighbor list builds = 0 Dangerous builds = 0 1247 -15854.7929400948 eV 1.92068317952505 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:55