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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -37.477337 0.0000000) to (45.900177 37.477337 7.7585460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2457345 4.8185148 5.1723640 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -37.477337 0.0000000) to (45.900177 37.477337 7.7585460) create_atoms CPU = 0.002 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2457345 4.8185148 5.1723640 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -37.477337 0.0000000) to (45.900177 37.477337 7.7585460) create_atoms CPU = 0.001 seconds 841 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 12 19 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1669 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_269937397263_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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.530 | 5.530 | 5.530 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11048.025 0 -11048.025 3756.5976 107 0 -11281.933 0 -11281.933 -2203.5212 Loop time of 66.6605 on 1 procs for 107 steps with 1669 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 = -11048.0253786276 -11281.9228112884 -11281.9332557522 Force two-norm initial, final = 74.295294 0.38027994 Force max component initial, final = 9.9491148 0.11058906 Final line search alpha, max atom move = 0.48390804 0.053514935 Iterations, force evaluations = 107 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 66.511 | 66.511 | 66.511 | 0.0 | 99.78 Neigh | 0.092088 | 0.092088 | 0.092088 | 0.0 | 0.14 Comm | 0.024217 | 0.024217 | 0.024217 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03327 | | | 0.05 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6461.00 ave 6461 max 6461 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: 224058.0 ave 224058 max 224058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224058 Ave neighs/atom = 134.24685 Neighbor list builds = 3 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.527 | 5.527 | 5.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -11281.933 0 -11281.933 -2203.5212 26692.756 110 0 -11282.034 0 -11282.034 -13.88113 26667.893 Loop time of 1.88289 on 1 procs for 3 steps with 1669 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 = -11281.9332557522 -11282.0316233239 -11282.0342121035 Force two-norm initial, final = 100.46938 0.61047008 Force max component initial, final = 82.388143 0.39796263 Final line search alpha, max atom move = 4.8148053e-05 1.9161126e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8793 | 1.8793 | 1.8793 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049682 | 0.00049682 | 0.00049682 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003054 | | | 0.16 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6455.00 ave 6455 max 6455 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: 224212.0 ave 224212 max 224212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224212 Ave neighs/atom = 134.33913 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.665 | 5.665 | 5.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11282.034 0 -11282.034 -13.88113 Loop time of 3.244e-06 on 1 procs for 0 steps with 1669 atoms 185.0% 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 | | 3.244e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6455.00 ave 6455 max 6455 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: 224156.0 ave 224156 max 224156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224156 Ave neighs/atom = 134.30557 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.665 | 5.665 | 5.665 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 -11282.034 -11282.034 45.866304 75.058322 7.746332 -13.88113 -13.88113 -11.451964 -23.942201 -6.249224 2.3646028 1486.7918 Loop time of 3.604e-06 on 1 procs for 0 steps with 1669 atoms 222.0% 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 | | 3.604e-06 | | |100.00 Nlocal: 1669.00 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6455.00 ave 6455 max 6455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112078.0 ave 112078 max 112078 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224156.0 ave 224156 max 224156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224156 Ave neighs/atom = 134.30557 Neighbor list builds = 0 Dangerous builds = 0 1669 -11282.0342121035 eV 2.3646027771018 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:10