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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -44.568734 0.0000000) to (15.757427 44.568734 5.1123844) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8053678 4.6914457 5.1123844 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -44.568734 0.0000000) to (15.757427 44.568734 5.1123844) create_atoms CPU = 0.002 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8053678 4.6914457 5.1123844 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -44.568734 0.0000000) to (15.757427 44.568734 5.1123844) create_atoms CPU = 0.002 seconds 306 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 22 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 608 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 4.949 | 4.949 | 4.949 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2013.1973 0 -2013.1973 35981.7 106 0 -2145.062 0 -2145.062 6107.6847 Loop time of 3.10372 on 1 procs for 106 steps with 608 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2013.19730546525 -2145.05996328973 -2145.06195661237 Force two-norm initial, final = 198.35773 0.13048927 Force max component initial, final = 56.012855 0.021608448 Final line search alpha, max atom move = 1.0000000 0.021608448 Iterations, force evaluations = 106 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0208 | 3.0208 | 3.0208 | 0.0 | 97.33 Neigh | 0.034834 | 0.034834 | 0.034834 | 0.0 | 1.12 Comm | 0.028341 | 0.028341 | 0.028341 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01975 | | | 0.64 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5697.00 ave 5697 max 5697 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: 126032.0 ave 126032 max 126032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126032 Ave neighs/atom = 207.28947 Neighbor list builds = 2 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.946 | 4.946 | 4.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -2145.062 0 -2145.062 6107.6847 7180.7383 113 0 -2145.1805 0 -2145.1805 -232.02437 7213.4135 Loop time of 0.137634 on 1 procs for 7 steps with 608 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 = -2145.06195661237 -2145.18017405351 -2145.18049421443 Force two-norm initial, final = 51.246026 2.0116402 Force max component initial, final = 42.675201 1.3915725 Final line search alpha, max atom move = 0.00053041880 0.00073811623 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13315 | 0.13315 | 0.13315 | 0.0 | 96.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010412 | 0.0010412 | 0.0010412 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00344 | | | 2.50 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5713.00 ave 5713 max 5713 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: 125908.0 ave 125908 max 125908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125908 Ave neighs/atom = 207.08553 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.085 | 5.085 | 5.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2145.1805 0 -2145.1805 -232.02437 Loop time of 6.224e-06 on 1 procs for 0 steps with 608 atoms 176.7% 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 | | 6.224e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5731.00 ave 5731 max 5731 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: 124268.0 ave 124268 max 124268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124268 Ave neighs/atom = 204.38816 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.085 | 5.085 | 5.085 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 -2145.1805 -2145.1805 15.735627 89.701378 5.1104325 -232.02437 -232.02437 -308.63397 -78.473979 -308.96517 2.386243 556.71964 Loop time of 6.655e-06 on 1 procs for 0 steps with 608 atoms 285.5% 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 | | 6.655e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5731.00 ave 5731 max 5731 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62134.0 ave 62134 max 62134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 124268.0 ave 124268 max 124268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124268 Ave neighs/atom = 204.38816 Neighbor list builds = 0 Dangerous builds = 0 608 -2145.18049421443 eV 2.38624300045429 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03