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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -58.612544 0.0000000) to (20.722664 58.612544 5.1015671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6516355 4.4403442 5.1015671 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.612544 0.0000000) to (20.722664 58.612544 5.1015671) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6516355 4.4403442 5.1015671 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.612544 0.0000000) to (20.722664 58.612544 5.1015671) create_atoms CPU = 0.001 seconds 530 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.149 | 7.149 | 7.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3411.8558 0 -3411.8558 46649.36 77 0 -3719.0693 0 -3719.0693 3274.5966 Loop time of 4.36488 on 1 procs for 77 steps with 1056 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 = -3411.85577925311 -3719.06620073607 -3719.06930662932 Force two-norm initial, final = 420.71460 0.21486941 Force max component initial, final = 120.22401 0.025139569 Final line search alpha, max atom move = 1.0000000 0.025139569 Iterations, force evaluations = 77 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2622 | 4.2622 | 4.2622 | 0.0 | 97.65 Neigh | 0.064879 | 0.064879 | 0.064879 | 0.0 | 1.49 Comm | 0.025773 | 0.025773 | 0.025773 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01199 | | | 0.27 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14931.0 ave 14931 max 14931 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: 664744.0 ave 664744 max 664744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664744 Ave neighs/atom = 629.49242 Neighbor list builds = 2 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.149 | 7.149 | 7.149 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -3719.0693 0 -3719.0693 3274.5966 12392.809 82 0 -3719.1478 0 -3719.1478 2.753301 12421.861 Loop time of 0.249272 on 1 procs for 5 steps with 1056 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 = -3719.06930662933 -3719.14776460256 -3719.1478279035 Force two-norm initial, final = 52.289870 0.30503758 Force max component initial, final = 42.185476 0.061691779 Final line search alpha, max atom move = 0.00072157976 4.4515539e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2443 | 0.2443 | 0.2443 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095288 | 0.00095288 | 0.00095288 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004017 | | | 1.61 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14892.0 ave 14892 max 14892 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: 666424.0 ave 666424 max 666424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 666424 Ave neighs/atom = 631.08333 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.287 | 7.287 | 7.287 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3719.1478 0 -3719.1478 2.753301 Loop time of 1.857e-06 on 1 procs for 0 steps with 1056 atoms 161.6% 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 | | 1.857e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14892.0 ave 14892 max 14892 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: 665360.0 ave 665360 max 665360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665360 Ave neighs/atom = 630.07576 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.287 | 7.287 | 7.287 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 -3719.1478 -3719.1478 20.691771 117.67226 5.1016998 2.753301 2.753301 0.59933745 -0.29667159 7.957237 2.3863472 630.31254 Loop time of 2.318e-06 on 1 procs for 0 steps with 1056 atoms 215.7% 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 | | 2.318e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14892.0 ave 14892 max 14892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 332680.0 ave 332680 max 332680 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 665360.0 ave 665360 max 665360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 665360 Ave neighs/atom = 630.07576 Neighbor list builds = 0 Dangerous builds = 0 1056 -3719.1478279035 eV 2.38634719913714 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05