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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -57.193626 0.0000000) to (20.221000 57.193626 4.9780662) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5148183 4.3328505 4.9780662 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.193626 0.0000000) to (20.221000 57.193626 4.9780662) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5148183 4.3328505 4.9780662 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.193626 0.0000000) to (20.221000 57.193626 4.9780662) create_atoms CPU = 0.001 seconds 530 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 28 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_532072268679_000#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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.461 | 5.461 | 5.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4100.9466 0 -4100.9466 136360.23 58 0 -4684.6868 0 -4684.6868 6324.6355 Loop time of 1.21638 on 1 procs for 58 steps with 1056 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4100.94657426733 -4684.68228745957 -4684.68676270586 Force two-norm initial, final = 1684.0301 0.22203409 Force max component initial, final = 414.45967 0.029188010 Final line search alpha, max atom move = 1.0000000 0.029188010 Iterations, force evaluations = 58 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1859 | 1.1859 | 1.1859 | 0.0 | 97.50 Neigh | 0.015603 | 0.015603 | 0.015603 | 0.0 | 1.28 Comm | 0.0084719 | 0.0084719 | 0.0084719 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006374 | | | 0.52 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8371.00 ave 8371 max 8371 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: 235368.0 ave 235368 max 235368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235368 Ave neighs/atom = 222.88636 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.461 | 5.461 | 5.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -4684.6868 0 -4684.6868 6324.6355 11514.39 61 0 -4684.7808 0 -4684.7808 37.560877 11554.661 Loop time of 0.073088 on 1 procs for 3 steps with 1056 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4684.68676270586 -4684.77772873636 -4684.78083391652 Force two-norm initial, final = 81.304512 3.9207502 Force max component initial, final = 54.161363 2.8285793 Final line search alpha, max atom move = 0.00011184494 0.00031636229 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.070879 | 0.070879 | 0.070879 | 0.0 | 96.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041433 | 0.00041433 | 0.00041433 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001795 | | | 2.46 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8368.00 ave 8368 max 8368 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: 235852.0 ave 235852 max 235852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235852 Ave neighs/atom = 223.34470 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.599 | 5.599 | 5.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4684.7808 0 -4684.7808 37.560877 Loop time of 1.943e-06 on 1 procs for 0 steps with 1056 atoms 154.4% 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 | | 1.943e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8368.00 ave 8368 max 8368 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: 235772.0 ave 235772 max 235772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235772 Ave neighs/atom = 223.26894 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.599 | 5.599 | 5.599 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 -4684.7808 -4684.7808 20.220367 114.60964 4.9859399 37.560877 37.560877 171.11103 334.40453 -392.83292 2.3219851 383.1535 Loop time of 2.687e-06 on 1 procs for 0 steps with 1056 atoms 223.3% 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 | | 2.687e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8368.00 ave 8368 max 8368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117886.0 ave 117886 max 117886 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235772.0 ave 235772 max 235772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235772 Ave neighs/atom = 223.26894 Neighbor list builds = 0 Dangerous builds = 0 1056 -4655.99279361572 eV 2.32198508861175 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01