Use $ams2026

Compare how fast and accurate mode-tracking is to full normal-modes calculations.

Method: DFT ADF/PBE/DZ, large core, NumericalQuality Normal

1. Construct dydrogesterone: SMILES `CC(=O)[C@H]1CC[C@@H]2[C@@]1(CC[C@@H]3[C@H]2C=CC4=CC(=O)CC[C@@]34C)C`

Identify the O that is double-bonded to a C and which is not in a ring using ChemicalSystem bonds methods. Add the C and O to the "CO" region.

2. Get the DFT-optimized geometry. Use normal convergence for the geometry optimizations.
    - Pre-optimize the geometry with DFTB GFN1-xTB with normal modes. 
    - Continue the optimization with the DFT method and use the initial hessian from the previous job to speed up the optimization. 

From now on, all calculations must be single-points on the DFT-optimized geometry.

3. Get the mode to track with partial hessian calculation.
    - DFT: Use the CO region for the hessian, and EngineRestart from geo opt job. Get the number of the mode that most purely corresponds to a C=O stretch (which has the biggest displacements for those atoms).

4. Run the mode tracking on the mode from the previous step to get the pure correct normal mode.
    - DFTB: single-point on the DFT-optimized geometry with normal modes. 
    - DFT: Run the mode tracking calculation supplying 
        - the correct mode from the partial hessian calculation 
        - DFTB-calculated hessian on the current geometry as the hessian guess 
        - EngineRestart from the DFT geo opt

5. Verification calculation: full normal-modes calculation on the optimized geometry. Use the default analytical Hessian implemented in ADF and use EngineRestart.

Report: 
Introduction: Include a basic recap of the purpose of mode tracking and what the current report will show.
Picture: `plot_image_grid` mode-displaced-negative, optimized geometry, mode-displaced-positive. Show the region as well.
Picture: Spectrum from partial hessian calculation
Picture: Spectrum from mode tracking
Picture: Full spectrum
Table: Frequency and intensity of the selected mode.
Table: Timings of individual jobs. Especially compare the partialhessian+modetracking vs. full normal modes.

References: See $AMSHOME/Doc/text/Tutorials/VibrationalSpectroscopy/ModeTracking.txt

The calculations may take an hour to finish. Run all the calculations and generate the report.