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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -38.526752 0.0000000) to (38.523129 38.526752 3.6239511) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1136896 5.1136896 3.6239511 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.526752 0.0000000) to (38.523129 38.526752 3.6239511) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1136896 5.1136896 3.6239511 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.526752 0.0000000) to (38.523129 38.526752 3.6239511) create_atoms CPU = 0.001 seconds 454 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 23 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 903 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_427873955970_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3710.4878 0 -3710.4878 23695.594 57 0 -3777.0534 0 -3777.0534 -800.10838 Loop time of 5.57649 on 1 procs for 57 steps with 903 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 = -3710.48783730694 -3777.04976027183 -3777.05337521029 Force two-norm initial, final = 46.101842 0.20491464 Force max component initial, final = 11.947003 0.069922404 Final line search alpha, max atom move = 1.0000000 0.069922404 Iterations, force evaluations = 57 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5568 | 5.5568 | 5.5568 | 0.0 | 99.65 Neigh | 0.0069814 | 0.0069814 | 0.0069814 | 0.0 | 0.13 Comm | 0.0067167 | 0.0067167 | 0.0067167 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005947 | | | 0.11 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6377.00 ave 6377 max 6377 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: 119458.0 ave 119458 max 119458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119458 Ave neighs/atom = 132.29014 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -3777.0534 0 -3777.0534 -800.10838 10757.127 97 0 -3783.7867 0 -3783.7867 -16230.243 10854.973 Loop time of 2.44541 on 1 procs for 40 steps with 903 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3777.0533752103 -3783.78321989172 -3783.78665854429 Force two-norm initial, final = 232.58008 6.8524105 Force max component initial, final = 198.74759 5.1139833 Final line search alpha, max atom move = 0.00017062824 0.00087258996 Iterations, force evaluations = 40 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4242 | 2.4242 | 2.4242 | 0.0 | 99.13 Neigh | 0.0072552 | 0.0072552 | 0.0072552 | 0.0 | 0.30 Comm | 0.0022589 | 0.0022589 | 0.0022589 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01173 | | | 0.48 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6472.00 ave 6472 max 6472 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: 118474.0 ave 118474 max 118474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118474 Ave neighs/atom = 131.20044 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3783.7867 0 -3783.7867 -16230.243 Loop time of 2.079e-06 on 1 procs for 0 steps with 903 atoms 144.3% 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 | | 2.079e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6482.00 ave 6482 max 6482 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: 117302.0 ave 117302 max 117302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117302 Ave neighs/atom = 129.90255 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.096 | 5.096 | 5.096 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 -3783.7867 -3783.7867 37.408853 77.053505 3.7658409 -16230.243 -16230.243 -732.98274 -47348.054 -609.69295 2.3352083 226.55873 Loop time of 2.345e-06 on 1 procs for 0 steps with 903 atoms 170.6% 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 | | 2.345e-06 | | |100.00 Nlocal: 903.000 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6482.00 ave 6482 max 6482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58651.0 ave 58651 max 58651 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117302.0 ave 117302 max 117302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117302 Ave neighs/atom = 129.90255 Neighbor list builds = 0 Dangerous builds = 0 903 -3783.78665854429 eV 2.33520830717576 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08