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 -63.853661 0.0000000) to (36.865928 63.853661 6.2613666) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6716813 5.7304567 6.2613666 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -63.853661 0.0000000) to (36.865928 63.853661 6.2613666) create_atoms CPU = 0.003 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6716813 5.7304567 6.2613666 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -63.853661 0.0000000) to (36.865928 63.853661 6.2613666) create_atoms CPU = 0.003 seconds 1250 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 = 9 31 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 0 atoms, new total = 2496 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 = 9 31 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) = 6.934 | 6.934 | 6.934 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8481.4201 0 -8481.4201 26745.892 91 0 -8809.4603 0 -8809.4603 5287.2154 Loop time of 4.02263 on 1 procs for 91 steps with 2496 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 = -8481.42010372031 -8809.45192181639 -8809.46027169519 Force two-norm initial, final = 296.78657 0.31223369 Force max component initial, final = 66.985060 0.053704837 Final line search alpha, max atom move = 1.0000000 0.053704837 Iterations, force evaluations = 91 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8448 | 3.8448 | 3.8448 | 0.0 | 95.58 Neigh | 0.12838 | 0.12838 | 0.12838 | 0.0 | 3.19 Comm | 0.026781 | 0.026781 | 0.026781 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02268 | | | 0.56 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12556.0 ave 12556 max 12556 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: 514374.0 ave 514374 max 514374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514374 Ave neighs/atom = 206.07933 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 31 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.934 | 6.934 | 6.934 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -8809.4603 0 -8809.4603 5287.2154 29478.82 98 0 -8810.016 0 -8810.016 12.132632 29589.927 Loop time of 0.264845 on 1 procs for 7 steps with 2496 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 = -8809.46027169516 -8810.01600159102 -8810.01604354205 Force two-norm initial, final = 214.08914 0.84115514 Force max component initial, final = 204.56167 0.67672647 Final line search alpha, max atom move = 0.00052568177 0.00035574277 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25847 | 0.25847 | 0.25847 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010468 | 0.0010468 | 0.0010468 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005333 | | | 2.01 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12591.0 ave 12591 max 12591 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: 514370.0 ave 514370 max 514370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514370 Ave neighs/atom = 206.07772 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 = 9 31 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) = 7.072 | 7.072 | 7.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8810.016 0 -8810.016 12.132632 Loop time of 2.286e-06 on 1 procs for 0 steps with 2496 atoms 218.7% 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 | | 2.286e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12595.0 ave 12595 max 12595 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: 503668.0 ave 503668 max 503668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503668 Ave neighs/atom = 201.79006 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 = 9 31 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) = 7.072 | 7.072 | 7.072 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 -8810.016 -8810.016 36.802004 128.45797 6.2590927 12.132632 12.132632 -4.9685618 4.7377256 36.628732 2.3067767 1025.9116 Loop time of 2.93e-06 on 1 procs for 0 steps with 2496 atoms 273.0% 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 | | 2.93e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12595.0 ave 12595 max 12595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251834.0 ave 251834 max 251834 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 503668.0 ave 503668 max 503668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503668 Ave neighs/atom = 201.79006 Neighbor list builds = 0 Dangerous builds = 0 2496 -8810.01604354205 eV 2.30677671918592 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04