# Open SourceMolecular Dynamics

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exercises:2015_ethz_mmm:wannier

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 — exercises:2015_ethz_mmm:wannier [2015/02/06 17:49] (current) Line 1: Line 1: + ====== 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. + + + You should run these calculations on 4 nodes with ''​bsub -n 4''​. ​ + ​ + + ===== 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 + ​ + + ===== 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?​ + + + 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 + ​ + ​ + + + ===== Required Files ===== + {{64water.coord.gz|}} + + ​ + &GLOBAL + PROJECT caffeine + RUN_TYPE ENERGY + &END GLOBAL + + &​FORCE_EVAL + &DFT + ! Output all occupied molecular orbitals as cube-files + &PRINT + &​MO_CUBES + NHOMO -1 + &END MO_CUBES + &END PRINT + ​ + ! Calculate the maximally localized Wannier functions + &​LOCALIZE + METHOD CRAZY + EPS_LOCALIZATION 1.0E-8 + &PRINT + ! 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 + ​ + + ​ + 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 + ​ + + ​ + 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 +