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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -45.900738 0.0000000) to (10.818908 45.900738 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0105043 5.1000820 5.1000820 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -45.900738 0.0000000) to (10.818908 45.900738 5.1000820) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0105043 5.1000820 5.1000820 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -45.900738 0.0000000) to (10.818908 45.900738 5.1000820) create_atoms CPU = 0.001 seconds 218 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 432 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1636.9232 0 -1636.9232 64843.365 119 0 -1807.8016 0 -1807.8016 5507.2807 Loop time of 3.08817 on 1 procs for 119 steps with 432 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 = -1636.92323941729 -1807.80013372796 -1807.80164032208 Force two-norm initial, final = 335.28340 0.16738741 Force max component initial, final = 92.699491 0.017734712 Final line search alpha, max atom move = 1.0000000 0.017734712 Iterations, force evaluations = 119 224 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0245 | 3.0245 | 3.0245 | 0.0 | 97.94 Neigh | 0.028511 | 0.028511 | 0.028511 | 0.0 | 0.92 Comm | 0.024794 | 0.024794 | 0.024794 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01035 | | | 0.34 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9126.00 ave 9126 max 9126 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: 267588.0 ave 267588 max 267588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267588 Ave neighs/atom = 619.41667 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.417 | 5.417 | 5.417 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -1807.8016 0 -1807.8016 5507.2807 5065.3592 121 0 -1807.8307 0 -1807.8307 -90.356301 5081.8082 Loop time of 0.0551727 on 1 procs for 2 steps with 432 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 = -1807.8016403221 -1807.82894880928 -1807.83067119431 Force two-norm initial, final = 30.578438 1.2389771 Force max component initial, final = 21.037375 1.1091677 Final line search alpha, max atom move = 0.00017113484 0.00018981724 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05371 | 0.05371 | 0.05371 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033182 | 0.00033182 | 0.00033182 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001131 | | | 2.05 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9498.00 ave 9498 max 9498 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: 267904.0 ave 267904 max 267904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267904 Ave neighs/atom = 620.14815 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.555 | 5.555 | 5.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1807.8307 0 -1807.8307 -90.356301 Loop time of 2.052e-06 on 1 procs for 0 steps with 432 atoms 194.9% 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 | | 2.052e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9498.00 ave 9498 max 9498 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: 267152.0 ave 267152 max 267152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267152 Ave neighs/atom = 618.40741 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.555 | 5.555 | 5.555 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 -1807.8307 -1807.8307 10.833897 91.900254 5.1040725 -90.356301 -90.356301 150.03669 -71.137059 -349.96853 2.4316316 286.05475 Loop time of 2.889e-06 on 1 procs for 0 steps with 432 atoms 207.7% 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 | | 2.889e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9498.00 ave 9498 max 9498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133576.0 ave 133576 max 133576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267152.0 ave 267152 max 267152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267152 Ave neighs/atom = 618.40741 Neighbor list builds = 0 Dangerous builds = 0 432 -1807.83067119431 eV 2.43163159467479 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03