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 = 4.0496966 4.0496966 4.0496966 Created orthogonal box = (0.0000000 -42.473576 0.0000000) to (52.019294 42.473576 9.9196902) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6206374 6.1779747 6.6131268 Created 1318 atoms using lattice units in orthogonal box = (0.0000000 -42.473576 0.0000000) to (52.019294 42.473576 9.9196902) create_atoms CPU = 0.008 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6206374 6.1779747 6.6131268 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -42.473576 0.0000000) to (52.019294 42.473576 9.9196902) create_atoms CPU = 0.005 seconds 1324 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 14 23 3 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 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2642 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_284963179498_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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 5.961 | 5.961 | 5.961 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7511.8783 0 -7511.8783 83845.628 98 0 -8876.3273 0 -8876.3273 6631.7566 Loop time of 5.00267 on 1 procs for 98 steps with 2642 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 = -7511.87832152476 -8876.31851107166 -8876.32730230597 Force two-norm initial, final = 880.99321 0.24997411 Force max component initial, final = 151.72248 0.030432547 Final line search alpha, max atom move = 1.0000000 0.030432547 Iterations, force evaluations = 98 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7298 | 4.7298 | 4.7298 | 0.0 | 94.55 Neigh | 0.19588 | 0.19588 | 0.19588 | 0.0 | 3.92 Comm | 0.030318 | 0.030318 | 0.030318 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04666 | | | 0.93 Nlocal: 2642.00 ave 2642 max 2642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7598.00 ave 7598 max 7598 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: 336614.0 ave 336614 max 336614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336614 Ave neighs/atom = 127.40878 Neighbor list builds = 4 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.963 | 5.963 | 5.963 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -8876.3273 0 -8876.3273 6631.7566 43834.029 110 0 -8877.8786 0 -8877.8786 -47.499224 44213.071 Loop time of 0.468238 on 1 procs for 12 steps with 2642 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 = -8876.32730230598 -8877.87841206164 -8877.87864827121 Force two-norm initial, final = 352.38337 2.4289629 Force max component initial, final = 308.58967 1.6755653 Final line search alpha, max atom move = 0.00036640848 0.00061394134 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40387 | 0.40387 | 0.40387 | 0.0 | 86.25 Neigh | 0.049083 | 0.049083 | 0.049083 | 0.0 | 10.48 Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01228 | | | 2.62 Nlocal: 2642.00 ave 2642 max 2642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7720.00 ave 7720 max 7720 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: 328960.0 ave 328960 max 328960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328960 Ave neighs/atom = 124.51173 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.101 | 6.101 | 6.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8877.8786 0 -8877.8786 -47.499224 Loop time of 6.745e-06 on 1 procs for 0 steps with 2642 atoms 192.7% 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 | | 6.745e-06 | | |100.00 Nlocal: 2642.00 ave 2642 max 2642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7719.00 ave 7719 max 7719 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: 330678.0 ave 330678 max 330678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330678 Ave neighs/atom = 125.16200 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 = 7.600044 ghost atom cutoff = 7.600044 binsize = 3.800022, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.600044 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) = 6.101 | 6.101 | 6.101 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 -8877.8786 -8877.8786 52.033948 85.893972 9.8923897 -47.499224 -47.499224 -53.427384 -28.518893 -60.551394 2.627509 1890.3978 Loop time of 7.006e-06 on 1 procs for 0 steps with 2642 atoms 256.9% 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 | | 7.006e-06 | | |100.00 Nlocal: 2642.00 ave 2642 max 2642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7719.00 ave 7719 max 7719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165339.0 ave 165339 max 165339 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 330678.0 ave 330678 max 330678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330678 Ave neighs/atom = 125.16200 Neighbor list builds = 0 Dangerous builds = 0 2642 -8877.87864827121 eV 2.6275090347772 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06