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 = 3.4921275 3.4921275 3.4921275 Created orthogonal box = (0.0000000 -56.308865 0.0000000) to (28.154432 56.308865 3.4921275) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8983060 3.8983060 3.4921275 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -56.308865 0.0000000) to (28.154432 56.308865 3.4921275) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8983060 3.8983060 3.4921275 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -56.308865 0.0000000) to (28.154432 56.308865 3.4921275) create_atoms CPU = 0.000 seconds 522 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 29 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_270337113239_005#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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 5.439 | 5.439 | 5.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3076.219 0 -3076.219 77081.472 61 0 -3433.8829 0 -3433.8829 -1094.1912 Loop time of 1.15674 on 1 procs for 61 steps with 1036 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3076.21899543456 -3433.87989891676 -3433.88294250037 Force two-norm initial, final = 1070.8200 0.13388619 Force max component initial, final = 364.34958 0.015398985 Final line search alpha, max atom move = 1.0000000 0.015398985 Iterations, force evaluations = 61 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1308 | 1.1308 | 1.1308 | 0.0 | 97.76 Neigh | 0.011631 | 0.011631 | 0.011631 | 0.0 | 1.01 Comm | 0.0083772 | 0.0083772 | 0.0083772 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00592 | | | 0.51 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9154.00 ave 9154 max 9154 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: 206376.0 ave 206376 max 206376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206376 Ave neighs/atom = 199.20463 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.439 | 5.439 | 5.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -3433.8829 0 -3433.8829 -1094.1912 11072.448 64 0 -3433.8954 0 -3433.8954 -286.30274 11063.471 Loop time of 0.0617461 on 1 procs for 3 steps with 1036 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3433.88294250036 -3433.8946407294 -3433.89540733759 Force two-norm initial, final = 14.534204 3.7814309 Force max component initial, final = 11.946787 3.0046949 Final line search alpha, max atom move = 0.00038205906 0.0011479709 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059742 | 0.059742 | 0.059742 | 0.0 | 96.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004091 | 0.0004091 | 0.0004091 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001595 | | | 2.58 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9149.00 ave 9149 max 9149 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: 206332.0 ave 206332 max 206332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206332 Ave neighs/atom = 199.16216 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 5.577 | 5.577 | 5.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3433.8954 0 -3433.8954 -286.30274 Loop time of 1.551e-06 on 1 procs for 0 steps with 1036 atoms 193.4% 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 | | 1.551e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9165.00 ave 9165 max 9165 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: 206408.0 ave 206408 max 206408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206408 Ave neighs/atom = 199.23552 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 5.577 | 5.577 | 5.577 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 -3433.8954 -3433.8954 28.144611 112.41806 3.4967135 -286.30274 -286.30274 -312.19644 -434.35885 -112.35292 2.2572181 196.83569 Loop time of 2.906e-06 on 1 procs for 0 steps with 1036 atoms 206.5% 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 | | 2.906e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9165.00 ave 9165 max 9165 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103204.0 ave 103204 max 103204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206408.0 ave 206408 max 206408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206408 Ave neighs/atom = 199.23552 Neighbor list builds = 0 Dangerous builds = 0 1036 -3390.15172447163 eV 2.25721813682614 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01