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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, which closely resembles the typical text-book pictures of molecular orbitals. | ||
+ | |||
+ | <note tip> | ||
+ | You should run these calculations on 4 nodes with ''bsub -n 4''. | ||
+ | </note> | ||
+ | |||
+ | ===== 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. | ||
+ | |||
+ | <code> | ||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC 12.4544808085 12.4544808085 12.4544808085 | ||
+ | &END CELL | ||
+ | &COORD | ||
+ | @INCLUDE '64water.coord' | ||
+ | &END COORD | ||
+ | ... | ||
+ | &END SUBSYS | ||
+ | </code> | ||
+ | |||
+ | ===== 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: | ||
+ | <code> | ||
+ | vmd> pbc set {15.0 15.0 15.0} | ||
+ | vmd> pbc wrap | ||
+ | </code> | ||
+ | </note> | ||
+ | |||
+ | |||
+ | ===== Required Files ===== | ||
+ | {{64water.coord.gz|}} | ||
+ | |||
+ | <code - caffeine.inp> | ||
+ | &GLOBAL | ||
+ | PROJECT caffeine | ||
+ | RUN_TYPE ENERGY | ||
+ | &END GLOBAL | ||
+ | |||
+ | &FORCE_EVAL | ||
+ | &DFT | ||
+ | ! Output all occupied molecular orbitals as cube-files | ||
+ | |||
+ | &MO_CUBES | ||
+ | NHOMO -1 | ||
+ | &END MO_CUBES | ||
+ | &END PRINT | ||
+ | | ||
+ | ! Calculate the maximally localized Wannier functions | ||
+ | &LOCALIZE | ||
+ | METHOD CRAZY | ||
+ | EPS_LOCALIZATION 1.0E-8 | ||
+ | |||
+ | ! Output the Wannier functions as cube-files | ||
+ | &WANNIER_CUBES | ||
+ | &END | ||
+ | ! Output the centers of all Wannier functions as xyz-file | ||
+ | &WANNIER_CENTERS | ||
+ | IONS+CENTERS .TRUE. | ||
+ | &END | ||
+ | &END | ||
+ | &END | ||
+ | | ||
+ | ! exchange correlation functional | ||
+ | &XC | ||
+ | &XC_FUNCTIONAL PBE | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | |||
+ | ! Poisson solver required for non-periodic calculation | ||
+ | &POISSON | ||
+ | PERIODIC NONE | ||
+ | PSOLVER WAVELET | ||
+ | &END POISSON | ||
+ | |||
+ | ! ============ SCF fine tuning ============ | ||
+ | &MGRID | ||
+ | CUTOFF 400 | ||
+ | &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 | ||
+ | &OUTER_SCF | ||
+ | EPS_SCF 1.0E-7 | ||
+ | MAX_SCF 4 | ||
+ | &END | ||
+ | &END SCF | ||
+ | ! ============ End of SCF fine tuning ============ | ||
+ | |||
+ | &END DFT | ||
+ | |||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | ABC 15.0 15.0 15.0 | ||
+ | PERIODIC NONE | ||
+ | &END CELL | ||
+ | &TOPOLOGY | ||
+ | &CENTER_COORDINATES | ||
+ | &END | ||
+ | &END TOPOLOGY | ||
+ | |||
+ | &COORD | ||
+ | H 4.4169009427 5.7654974925 7.9758408247 | ||
+ | N 8.6708423642 5.8343946244 6.6347213084 | ||
+ | C 7.7544572660 7.7275482372 7.8213939469 | ||
+ | N 6.3919654318 5.8642629272 7.3568679126 | ||
+ | C 6.4494839543 7.1525402940 7.9597387862 | ||
+ | C 7.4402138371 5.1755331540 6.7117923744 | ||
+ | C 8.8064058483 7.0850033638 7.1845597858 | ||
+ | N 8.2778986769 8.9446280562 8.2382523594 | ||
+ | O 7.2643506988 4.0529962930 6.2454118622 | ||
+ | C 5.1156137682 5.1424213782 7.4120564649 | ||
+ | O 5.4684099858 7.6593220497 8.5167253955 | ||
+ | H 10.2341485900 9.7932463989 8.0304114260 | ||
+ | C 9.7967248636 5.1907999513 5.9591641231 | ||
+ | H 5.2562171072 4.1726515030 7.9014364748 | ||
+ | H 4.7402775185 4.9652043967 6.3976240445 | ||
+ | H 10.6401430351 5.0886560185 6.6519804958 | ||
+ | H 10.1151718438 5.7973815083 5.1027558576 | ||
+ | H 9.4549428018 4.2086990850 5.6240133244 | ||
+ | C 7.5708564616 9.9966158796 8.9691451507 | ||
+ | C 9.5777006425 8.9511038401 7.8331053451 | ||
+ | N 9.9406928680 7.8388520756 7.1872221397 | ||
+ | H 7.5517578349 10.9193467788 8.3771079019 | ||
+ | H 8.0665429481 10.1847691445 9.9288020634 | ||
+ | H 6.5474923450 9.6514720878 9.1444003294 | ||
+ | &END COORD | ||
+ | |||
+ | &KIND H | ||
+ | BASIS_SET TZV2P-GTH | ||
+ | POTENTIAL GTH-PBE-q1 | ||
+ | &END KIND | ||
+ | &KIND C | ||
+ | BASIS_SET TZV2P-GTH | ||
+ | POTENTIAL GTH-PBE-q4 | ||
+ | &END KIND | ||
+ | &KIND N | ||
+ | BASIS_SET TZV2P-GTH | ||
+ | POTENTIAL GTH-PBE-q5 | ||
+ | &END KIND | ||
+ | &KIND O | ||
+ | BASIS_SET TZV2P-GTH | ||
+ | POTENTIAL GTH-PBE-q6 | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | &END FORCE_EVAL | ||
+ | </code> | ||
+ | |||
+ | <code - BASIS_SET> | ||
+ | H TZV2P-GTH | ||
+ | 2 | ||
+ | 1 0 0 5 3 | ||
+ | 10.8827241585 -0.0167058885 0.0000000000 0.0000000000 | ||
+ | 3.0968750876 -0.0627538300 0.0000000000 0.0000000000 | ||
+ | 0.9874518162 -0.1917521975 0.0000000000 0.0000000000 | ||
+ | 0.3450687533 -0.4173635232 1.0000000000 0.0000000000 | ||
+ | 0.1492693554 -0.4270508887 0.0000000000 1.0000000000 | ||
+ | 2 1 1 2 2 | ||
+ | 1.4070000000 1.0000000000 0.0000000000 | ||
+ | 0.3880000000 0.0000000000 1.0000000000 | ||
+ | # | ||
+ | C TZV2P-GTH | ||
+ | 2 | ||
+ | 2 0 1 5 3 3 | ||
+ | 5.3685662937 0.0974901974 0.0000000000 0.0000000000 -0.0510969367 0.0000000000 0.0000000000 | ||
+ | 1.9830691554 0.1041996677 0.0000000000 0.0000000000 -0.1693035193 0.0000000000 0.0000000000 | ||
+ | 0.6978346167 -0.3645093878 0.0000000000 0.0000000000 -0.3579933930 0.0000000000 0.0000000000 | ||
+ | 0.2430968816 -0.6336931464 1.0000000000 0.0000000000 -0.4327616531 1.0000000000 0.0000000000 | ||
+ | 0.0812865018 -0.1676727564 0.0000000000 1.0000000000 -0.2457672757 0.0000000000 1.0000000000 | ||
+ | 3 2 2 2 2 | ||
+ | 1.0970000000 1.0000000000 0.0000000000 | ||
+ | 0.3180000000 0.0000000000 1.0000000000 | ||
+ | # | ||
+ | N TZV2P-GTH | ||
+ | 2 | ||
+ | 2 0 1 5 3 3 | ||
+ | 7.6227447102 0.0983924689 0.0000000000 0.0000000000 -0.0561654555 0.0000000000 0.0000000000 | ||
+ | 2.7970605447 0.1045217098 0.0000000000 0.0000000000 -0.1798165209 0.0000000000 0.0000000000 | ||
+ | 0.9909765447 -0.3742661352 0.0000000000 0.0000000000 -0.3653986185 0.0000000000 0.0000000000 | ||
+ | 0.3417314862 -0.6278094034 1.0000000000 0.0000000000 -0.4259126207 1.0000000000 0.0000000000 | ||
+ | 0.1116822743 -0.1675236192 0.0000000000 1.0000000000 -0.2366040346 0.0000000000 1.0000000000 | ||
+ | 3 2 2 2 2 | ||
+ | 1.6540000000 1.0000000000 0.0000000000 | ||
+ | 0.4690000000 0.0000000000 1.0000000000 | ||
+ | # | ||
+ | O TZV2P-GTH | ||
+ | 2 | ||
+ | 2 0 1 5 3 3 | ||
+ | 10.2674419938 0.0989598460 0.0000000000 0.0000000000 -0.0595856940 0.0000000000 0.0000000000 | ||
+ | 3.7480495696 0.1041178339 0.0000000000 0.0000000000 -0.1875649045 0.0000000000 0.0000000000 | ||
+ | 1.3308337704 -0.3808255700 0.0000000000 0.0000000000 -0.3700707718 0.0000000000 0.0000000000 | ||
+ | 0.4556802254 -0.6232449802 1.0000000000 0.0000000000 -0.4204922615 1.0000000000 0.0000000000 | ||
+ | 0.1462920596 -0.1677863491 0.0000000000 1.0000000000 -0.2313901687 0.0000000000 1.0000000000 | ||
+ | 3 2 2 2 2 | ||
+ | 2.3140000000 1.0000000000 0.0000000000 | ||
+ | 0.6450000000 0.0000000000 1.0000000000 | ||
+ | </code> | ||
+ | |||
+ | <code - POTENTIAL> | ||
+ | H GTH-PBE-q1 | ||
+ | 1 | ||
+ | 0.20000000 2 -4.17890044 0.72446331 | ||
+ | 0 | ||
+ | # | ||
+ | C GTH-PBE-q4 | ||
+ | 2 2 | ||
+ | 0.33847124 2 -8.80367398 1.33921085 | ||
+ | 2 | ||
+ | 0.30257575 1 9.62248665 | ||
+ | 0.29150694 0 | ||
+ | # | ||
+ | N GTH-PBE-q5 | ||
+ | 2 3 | ||
+ | 0.28379052 2 -12.41522559 1.86809592 | ||
+ | 2 | ||
+ | 0.25540500 1 13.63026257 | ||
+ | 0.24549453 0 | ||
+ | # | ||
+ | O GTH-PBE-q6 | ||
+ | 2 4 | ||
+ | 0.24455430 2 -16.66721480 2.48731132 | ||
+ | 2 | ||
+ | 0.22095592 1 18.33745811 | ||
+ | 0.21133247 0 | ||
+ | </code> | ||