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 = 4.1288715 4.1288715 4.1288715 Created orthogonal box = (0.0000000 -42.908491 0.0000000) to (30.340885 42.908491 5.8391060) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7424189 5.5622118 5.8391060 Created 431 atoms using lattice units in orthogonal box = (0.0000000 -42.908491 0.0000000) to (30.340885 42.908491 5.8391060) create_atoms CPU = 0.003 seconds 431 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7424189 5.5622118 5.8391060 Created 439 atoms using lattice units in orthogonal box = (0.0000000 -42.908491 0.0000000) to (30.340885 42.908491 5.8391060) create_atoms CPU = 0.002 seconds 439 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 19 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 864 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_122703700223_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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3073.2989 0 -3073.2989 22979.243 80 0 -3200.9357 0 -3200.9357 2691.7547 Loop time of 4.12456 on 1 procs for 80 steps with 864 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3073.29886057488 -3200.93308230937 -3200.93571599409 Force two-norm initial, final = 173.24293 0.12023175 Force max component initial, final = 29.574179 0.014964197 Final line search alpha, max atom move = 1.0000000 0.014964197 Iterations, force evaluations = 80 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0627 | 4.0627 | 4.0627 | 0.0 | 98.50 Neigh | 0.022971 | 0.022971 | 0.022971 | 0.0 | 0.56 Comm | 0.021257 | 0.021257 | 0.021257 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01766 | | | 0.43 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6268.00 ave 6268 max 6268 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: 157106.0 ave 157106 max 157106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157106 Ave neighs/atom = 181.83565 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -3200.9357 0 -3200.9357 2691.7547 15203.649 88 0 -3201.135 0 -3201.135 191.794 15240.433 Loop time of 0.287164 on 1 procs for 8 steps with 864 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3200.93571599408 -3201.13311087316 -3201.13503751907 Force two-norm initial, final = 58.401142 3.2022544 Force max component initial, final = 54.941507 2.1789579 Final line search alpha, max atom move = 0.00032161213 0.00070077930 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28104 | 0.28104 | 0.28104 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013382 | 0.0013382 | 0.0013382 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004784 | | | 1.67 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6274.00 ave 6274 max 6274 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: 156620.0 ave 156620 max 156620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156620 Ave neighs/atom = 181.27315 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.127 | 5.127 | 5.127 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3201.135 0 -3201.135 191.794 Loop time of 6.875e-06 on 1 procs for 0 steps with 864 atoms 174.5% 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 | | 6.875e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6283.00 ave 6283 max 6283 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: 156140.0 ave 156140 max 156140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156140 Ave neighs/atom = 180.71759 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.127 | 5.127 | 5.127 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 -3201.135 -3201.135 30.214425 86.473326 5.8331187 191.794 191.794 181.95997 230.81861 162.60342 2.7484604 917.98534 Loop time of 6.434e-06 on 1 procs for 0 steps with 864 atoms 248.7% 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 | | 6.434e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6283.00 ave 6283 max 6283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78070.0 ave 78070 max 78070 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156140.0 ave 156140 max 156140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156140 Ave neighs/atom = 180.71759 Neighbor list builds = 0 Dangerous builds = 0 864 -3201.13503751907 eV 2.74846042133095 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05