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— exercises:2016_ethz_mmm:wannier [2016/02/03 09:54] (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.
 +
 +<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
 +    &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
 +</​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>​
  
exercises/2016_ethz_mmm/wannier.txt · Last modified: 2016/02/03 09:54 (external edit)

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