exercises:2016_ethz_mmm:wannier
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+ | ====== Maximally Localized Wannier Functions ====== | ||
+ | |||
+ | In this exercise we will explore alternative ways to divide the electronic densities into orbitals. By requiring that orbitals should be as localized as possible one obtains a representation, | ||
+ | |||
+ | <note tip> | ||
+ | You should run these calculations on 4 nodes with '' | ||
+ | </ | ||
+ | |||
+ | ===== 1. Task: Caffeine Molecule ===== | ||
+ | Calculate the electronic ground state of the Caffeine molecule by running the provided input file. The simulation will output: | ||
+ | |||
+ | * the molecular orbitals (MOs) as separate cube-files | ||
+ | * the Wannier functions as separate cube-files | ||
+ | * the centers of all Wannier functions combined in a single xyz-file | ||
+ | |||
+ | ===== 2. Task: Water Box ===== | ||
+ | Repeat the previous calculation on a box of 64 water molecules. You can use the following SUBSYS-section. Since the water simulation uses periodic boundary condition, don't forget to turn off the Poisson solver. | ||
+ | |||
+ | < | ||
+ | &SUBSYS | ||
+ | & | ||
+ | ABC 12.4544808085 12.4544808085 12.4544808085 | ||
+ | &END CELL | ||
+ | &COORD | ||
+ | @INCLUDE ' | ||
+ | &END COORD | ||
+ | ... | ||
+ | &END SUBSYS | ||
+ | </ | ||
+ | |||
+ | ===== Questions ===== | ||
+ | - Visualize some of the MO and Wannier functions with vmd. What is the key difference between these two kinds of orbitals? | ||
+ | - Visualize the Wannier centers in vmd. How can you distinguish between lone pairs, single-, and double-bonds? | ||
+ | |||
+ | <note tip> | ||
+ | Howto visualize cube files with VMD was covered in a [[mo_ethene|previous exercise]]. | ||
+ | |||
+ | Initially VMD does not know about the dimensions of the simulations cell. To setup, e.g. a 15Å qubic box, just type the following into vmd's Tk-console: | ||
+ | < | ||
+ | vmd> pbc set {15.0 15.0 15.0} | ||
+ | vmd> pbc wrap | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | |||
+ | ===== Required Files ===== | ||
+ | {{64water.coord.gz|}} | ||
+ | |||
+ | <code - caffeine.inp> | ||
+ | &GLOBAL | ||
+ | PROJECT caffeine | ||
+ | RUN_TYPE ENERGY | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | &DFT | ||
+ | ! Output all occupied molecular orbitals as cube-files | ||
+ | |||
+ | & | ||
+ | NHOMO -1 | ||
+ | &END MO_CUBES | ||
+ | &END PRINT | ||
+ | | ||
+ | ! Calculate the maximally localized Wannier functions | ||
+ | & | ||
+ | METHOD CRAZY | ||
+ | EPS_LOCALIZATION 1.0E-8 | ||
+ | |||
+ | ! Output the Wannier functions as cube-files | ||
+ | & | ||
+ | &END | ||
+ | ! Output the centers of all Wannier functions as xyz-file | ||
+ | & | ||
+ | | ||
+ | &END | ||
+ | &END | ||
+ | & | ||
+ | | ||
+ | ! exchange correlation functional | ||
+ | &XC | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | |||
+ | ! Poisson solver required for non-periodic calculation | ||
+ | & | ||
+ | PERIODIC NONE | ||
+ | PSOLVER | ||
+ | &END POISSON | ||
+ | |||
+ | ! ============ SCF fine tuning ============ | ||
+ | &MGRID | ||
+ | CUTOFF | ||
+ | &END MGRID | ||
+ | &QS | ||
+ | EPS_DEFAULT 1.0E-10 | ||
+ | &END QS | ||
+ | &SCF | ||
+ | SCF_GUESS ATOMIC | ||
+ | EPS_SCF 1.0E-7 | ||
+ | MAX_SCF 30 | ||
+ | &OT | ||
+ | MINIMIZER CG | ||
+ | PRECONDITIONER FULL_SINGLE_INVERSE | ||
+ | &END | ||
+ | & | ||
+ | EPS_SCF | ||
+ | MAX_SCF | ||
+ | &END | ||
+ | &END SCF | ||
+ | ! ============ End of SCF fine tuning ============ | ||
+ | |||
+ | &END DFT | ||
+ | |||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC 15.0 15.0 15.0 | ||
+ | PERIODIC NONE | ||
+ | &END CELL | ||
+ | & | ||
+ | & | ||
+ | &END | ||
+ | &END TOPOLOGY | ||
+ | |||
+ | &COORD | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | &END COORD | ||
+ | |||
+ | &KIND H | ||
+ | BASIS_SET | ||
+ | POTENTIAL | ||
+ | &END KIND | ||
+ | &KIND C | ||
+ | BASIS_SET | ||
+ | POTENTIAL | ||
+ | &END KIND | ||
+ | &KIND N | ||
+ | BASIS_SET | ||
+ | POTENTIAL | ||
+ | &END KIND | ||
+ | &KIND O | ||
+ | BASIS_SET | ||
+ | POTENTIAL | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | <code - BASIS_SET> | ||
+ | H TZV2P-GTH | ||
+ | 2 | ||
+ | 1 0 0 5 3 | ||
+ | | ||
+ | 3.0968750876 | ||
+ | 0.9874518162 | ||
+ | 0.3450687533 | ||
+ | 0.1492693554 | ||
+ | 2 1 1 2 2 | ||
+ | 1.4070000000 | ||
+ | 0.3880000000 | ||
+ | # | ||
+ | C TZV2P-GTH | ||
+ | 2 | ||
+ | 2 0 1 5 3 3 | ||
+ | 5.3685662937 | ||
+ | 1.9830691554 | ||
+ | 0.6978346167 | ||
+ | 0.2430968816 | ||
+ | 0.0812865018 | ||
+ | 3 2 2 2 2 | ||
+ | 1.0970000000 | ||
+ | 0.3180000000 | ||
+ | # | ||
+ | N TZV2P-GTH | ||
+ | 2 | ||
+ | 2 0 1 5 3 3 | ||
+ | 7.6227447102 | ||
+ | 2.7970605447 | ||
+ | 0.9909765447 | ||
+ | 0.3417314862 | ||
+ | 0.1116822743 | ||
+ | 3 2 2 2 2 | ||
+ | 1.6540000000 | ||
+ | 0.4690000000 | ||
+ | # | ||
+ | O TZV2P-GTH | ||
+ | 2 | ||
+ | 2 0 1 5 3 3 | ||
+ | | ||
+ | 3.7480495696 | ||
+ | 1.3308337704 | ||
+ | 0.4556802254 | ||
+ | 0.1462920596 | ||
+ | 3 2 2 2 2 | ||
+ | 2.3140000000 | ||
+ | 0.6450000000 | ||
+ | </ | ||
+ | |||
+ | <code - POTENTIAL> | ||
+ | H GTH-PBE-q1 | ||
+ | 1 | ||
+ | | ||
+ | 0 | ||
+ | # | ||
+ | C GTH-PBE-q4 | ||
+ | 2 2 | ||
+ | | ||
+ | 2 | ||
+ | | ||
+ | | ||
+ | # | ||
+ | N GTH-PBE-q5 | ||
+ | 2 3 | ||
+ | | ||
+ | 2 | ||
+ | | ||
+ | | ||
+ | # | ||
+ | O GTH-PBE-q6 | ||
+ | 2 4 | ||
+ | | ||
+ | 2 | ||
+ | | ||
+ | | ||
+ | </ | ||