View source for Resgrp:comp-photo-dyn/mctdh90.56dv/rotation

= Rotation of the Conical Intersection=

Dynamics are performed in internal coordinates, so it is necessary to remove any translations or rotational componentes in the starting and conical intersection reference geometries. To this end it is necessary to perform a rotation/displacement of the conical intersection geometry. Although MCTDH (DD-vMCG) will do this automatically, the program needs to be told (via a question in the generator) by how much to rotate the conical intersection.

There are two ways to proceed: either perform the rotation before hand and providing the {0,0,0} tuple to the program (this is done using the [[#dd_rotation method|dd_rotation method]]); or determine the appropriate rotation angles via the [[#EXCEL spreadsheet method|spreadsheet method]].


==dd_rotation method==

'''Note:'''dd_rotation program only works with the output of gaussian development version gdvh01.

[[Media:Dd_rotation_v2.x]]

The dd_rotation program, written by David, reads a file called ''start.log'' with the gaussian output with the optimized starting geometry and frequencies and a file called ''coin.dat'' with the conical intersection reference geometry in xyz format (but no number of atoms in the file's first line), and will output a file called ''coin.out'' which is a xyz with the rotated conical intersection geometry. The program also outputs to stdout the relevant rotation angles.

The rotated geometry should be visually checked for consistency against the starting geometry.

Taking the rotated geometry it is necessary to perform a new conical intersection optimization to obtain the orbitals and branching space coordinates (see also note in section [[Resgrp:comp-photo-dyn/mctdh90.56dv/input#Note|Optimise the Conical Intersection ]]).


== EXCEL spreadsheet method==

'''Note''': This is the old procedure. The spreadsheet is specific to one molecule making difficult to generalize.

The three angles required can be found using an EXCEL spreadsheet.

[[Media:Cis-butadiene_XQ-transform1.xls]]

The EXCEL spreadsheet contains different coloured  boxes:

1) BLUE: the cartesian coordinates of the ground state minimum (provided by the user)

2) RED: the cartesian coordinates of the conical intersection (provided by the user)

3) YELLOW: Euler angles (calculated by the spreadsheet)

4) GREEN: the frequency-mass-weighted normal coordinates (calculated by the spreadsheet)

5) ORANGE: the geometry of the rotated conical Intersection (calculated by the spreadsheet)

To use the EXCEL spreadsheet, you simply need to:

===1) Input===

Ground state minimum structure

* Paste the cartesian coordinates of the ground state minimum (in start.log) in the BLUE BOX (C2-E2 to C11-E11).


Conical Intersection structure

* Paste the cartesian coordinates of the conical intersection (in coin.log) in the RED BOX (C13-E13 to C22-E22).


Ground state minimum normal modes of vibration

* Paste normal modes of the ground state minimum (in start.log) in the BLUE BOX (Z2-AW2 to Z31-AW31).


Ground state minimum frequencies

* Paste the frequencies of the ground state minimum (in start.log) in the BLUE BOX (L10 to L33).

===2) Run the solver optimization===

* set the three Euler angles in the yellow boxes "Angles deg" (K2, K3 and K4) to zero.
* select: Tools > Solver
* minimise "Mw vib. norm" (M7)

The desired solution is one where "Mw norm" (M6) and "Mw vib. norm" (M7) are equal; "Mw rot. Norm" (M8) is zero; and the three angles (K2-K4) are minimised. If minimising "Mw vib. norm" (M7) does not achieve this, try solving for "Mw rot. Norm" (M8) equal to zero or minimising "Mw norm" (M6) (or combinations of these). 

There is more than one possible solution! The best choice is the one where the three angles are smallest (and all the other criteria are satisfied).

===3) Note the three angles in degrees (K2, K3 and K4)===

These three angles are required as part of the input for MCTDH (DD-vMCG). In this case they are 180.000, 0.000 and 90.000 (in that order).

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