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 = 4.0737181 4.0737181 4.0737181 Created orthogonal box = (0.0000000 -52.169047 0.0000000) to (26.084523 52.169047 4.0737181) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7258710 5.7258710 4.0737181 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -52.169047 0.0000000) to (26.084523 52.169047 4.0737181) create_atoms CPU = 0.002 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7258710 5.7258710 4.0737181 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -52.169047 0.0000000) to (26.084523 52.169047 4.0737181) create_atoms CPU = 0.001 seconds 330 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 6 23 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 658 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_128037485276_003#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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1804.5758 0 -1804.5758 267238.09 77 0 -2013.9753 0 -2013.9753 3439.8513 Loop time of 3.06887 on 1 procs for 77 steps with 658 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 = -1804.57576413653 -2013.97360001122 -2013.97530039891 Force two-norm initial, final = 707.82826 0.10391323 Force max component initial, final = 155.23514 0.025056559 Final line search alpha, max atom move = 1.0000000 0.025056559 Iterations, force evaluations = 77 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0137 | 3.0137 | 3.0137 | 0.0 | 98.20 Neigh | 0.016907 | 0.016907 | 0.016907 | 0.0 | 0.55 Comm | 0.023211 | 0.023211 | 0.023211 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01509 | | | 0.49 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6608.00 ave 6608 max 6608 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: 130668.0 ave 130668 max 130668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130668 Ave neighs/atom = 198.58359 Neighbor list builds = 1 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -2013.9753 0 -2013.9753 3439.8513 11087.07 86 0 -2014.1607 0 -2014.1607 -11.074959 11162.332 Loop time of 0.252414 on 1 procs for 9 steps with 658 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2013.97530039892 -2014.16067364587 -2014.16069070504 Force two-norm initial, final = 50.434079 0.26358003 Force max component initial, final = 45.857428 0.16115611 Final line search alpha, max atom move = 0.0027976899 0.00045086483 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24555 | 0.24555 | 0.24555 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016261 | 0.0016261 | 0.0016261 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00524 | | | 2.08 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6635.00 ave 6635 max 6635 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: 130892.0 ave 130892 max 130892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130892 Ave neighs/atom = 198.92401 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2014.1607 0 -2014.1607 -11.074959 Loop time of 6.335e-06 on 1 procs for 0 steps with 658 atoms 189.4% 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 | | 6.335e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6625.00 ave 6625 max 6625 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: 130640.0 ave 130640 max 130640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130640 Ave neighs/atom = 198.54103 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.083 | 5.083 | 5.083 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 -2014.1607 -2014.1607 26.019277 105.16869 4.0791837 -11.074959 -11.074959 -1.9131953 -8.1492314 -23.16245 2.5978604 205.05624 Loop time of 6.906e-06 on 1 procs for 0 steps with 658 atoms 260.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6625.00 ave 6625 max 6625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 65320.0 ave 65320 max 65320 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 130640.0 ave 130640 max 130640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130640 Ave neighs/atom = 198.54103 Neighbor list builds = 0 Dangerous builds = 0 658 -2108.3174730682 eV 2.59786039028393 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04