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 = 3.7004859 3.7004859 3.7004859 Created orthogonal box = (0.0000000 -55.876112 0.0000000) to (39.510378 55.876112 5.2332774) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2384807 6.3718374 5.2332774 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -55.876112 0.0000000) to (39.510378 55.876112 5.2332774) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2384807 6.3718374 5.2332774 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -55.876112 0.0000000) to (39.510378 55.876112 5.2332774) create_atoms CPU = 0.003 seconds 916 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 15 42 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 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_857282754307_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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 15 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 5.133 | 5.133 | 5.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2518.3976 0 -2518.3976 29581.271 107 0 -2738.0432 0 -2738.0432 -1739.0638 Loop time of 0.53878 on 1 procs for 107 steps with 1824 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 = -2518.39758606857 -2738.04052823107 -2738.04322281904 Force two-norm initial, final = 381.72054 0.14320641 Force max component initial, final = 87.816699 0.014432923 Final line search alpha, max atom move = 1.0000000 0.014432923 Iterations, force evaluations = 107 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51247 | 0.51247 | 0.51247 | 0.0 | 95.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010328 | 0.010328 | 0.010328 | 0.0 | 1.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01598 | | | 2.97 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5826.00 ave 5826 max 5826 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: 98520.0 ave 98520 max 98520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98520 Ave neighs/atom = 54.013158 Neighbor list builds = 0 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 15 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.133 | 5.133 | 5.133 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -2738.0432 0 -2738.0432 -1739.0638 23106.87 111 0 -2738.1286 0 -2738.1286 -0.28454081 23070.416 Loop time of 0.0202767 on 1 procs for 4 steps with 1824 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 = -2738.04322281904 -2738.12840812063 -2738.12855264333 Force two-norm initial, final = 70.736472 0.16837960 Force max component initial, final = 69.176806 0.062760211 Final line search alpha, max atom move = 0.00029633465 1.8598025e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.017786 | 0.017786 | 0.017786 | 0.0 | 87.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033235 | 0.00033235 | 0.00033235 | 0.0 | 1.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002158 | | | 10.64 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5890.00 ave 5890 max 5890 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: 98704.0 ave 98704 max 98704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98704 Ave neighs/atom = 54.114035 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 15 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 5.271 | 5.271 | 5.271 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2738.1286 0 -2738.1286 -0.28454081 Loop time of 1.984e-06 on 1 procs for 0 steps with 1824 atoms 151.2% 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 | | 1.984e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5890.00 ave 5890 max 5890 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: 98752.0 ave 98752 max 98752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98752 Ave neighs/atom = 54.140351 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 15 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 5.271 | 5.271 | 5.271 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 -2738.1286 -2738.1286 39.542362 111.48584 5.2332694 -0.28454081 -0.28454081 -4.3620512 -0.39925631 3.9076851 2.3865839 813.33493 Loop time of 2.565e-06 on 1 procs for 0 steps with 1824 atoms 233.9% 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 | | 2.565e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5890.00 ave 5890 max 5890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49376.0 ave 49376 max 49376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98752.0 ave 98752 max 98752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98752 Ave neighs/atom = 54.140351 Neighbor list builds = 0 Dangerous builds = 0 1824 -2738.12855264333 eV 2.38658386736435 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00