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[lectures/latex.git] / posic / thesis / vasp_patch.tex

diff --git a/posic/thesis/vasp_patch.tex b/posic/thesis/vasp_patch.tex
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--- a/posic/thesis/vasp_patch.tex
+++ b/posic/thesis/vasp_patch.tex
@@ -2,33 +2,48 @@
 \label{app:patch_vasp}
 
 \section{Description}
-The modifications to the VASP code allow to rotate all atom coordinates individually in the particle position evaluation routine of VASP.
-In that way constraints for every atom can be applied independently of the chosen basis.
-A patch against version 4.6 of the VASP code containing these modifications is available for download\footnote{http://www.physik.uni-augsburg.de/\~{}zirkelfr/download/posic/sd\_rot\_all-atoms.patch}.
+In the {\textsc vasp} code, the {\em selective dynamics} mode provides a feature to allow or constrain the change of each of the three coordinates for every single atom.
+By this, however, applied constraints are restricted to the chosen basis.
+For the investigation of migration pathways utilizing the constrained relaxation technique as detailed in section~\ref{section:basics:migration}, the required constraint not necessarily corresponds to one of the coordinate axes as defined by the basis, which, in turn, is determined to enable a construction within the supercell approach.
 
-\section{Usage}
+Thus, the functionality of the {\em selective dynamics} mode had to be extended by modifications in the particle position evaluation routine of {\textsc vasp}.
+These modifications allow for a rotation of all atom coordinates individually before respective constraints are applied and a following, final inverse transformation.
+In that way, constraints for every single atom can be applied independently of the chosen basis.
+A patch against version 4.6 of the {\textsc vasp} code containing these modifications is available for download\footnote{http://www.physik.uni-augsburg.de/\~{}zirkelfr/download/posic/sd\_rot\_all-atoms.patch}.
 
-Since this feature only makes sense in selective dynamics mode, it can be switched on by adding the word {\em Transformed} in front of the {\em selective dynamics} switch.
-This feature only works in direct mode.
+\section{Mode of operation}
+
+The extended capabilities can only be used within the {\em selective dynamics} mode.
+It is enabled by adding the word {\em transformed} in front of the {\em selective dynamics} switch.
+This feature only works in {\em direct} mode.
 Two values of angles need to be added after the extra flags of each atom.
 The first angle corresponds to the rotation of the basis about the $z$-axis.
 The second angle determines the rotation about the transformed $x$-axis, $x'$.
 All values have to be supplied in degrees.
-All these information is given in the POSCAR file as can be seen in the follwing example:
-\begin{verbatim}
-cubic diamond                           
-   5.48000000000000     
-     2.9909698580839312    0.0039546630279804   -0.0039658085666586
-     0.0039548953566878    2.9909698596656376   -0.0039660323646892
-    -0.0039680658132861   -0.0039674231313905    2.9909994291263242
- 216   1
-Transformed selective dynamics
-Direct
- 0.994174 0.994174 -0.000408732 T F T 45 36.5145
- 0.182792 0.182792 0.981597 T F T -135 -5.95043
- ...
- 0.119896 0.119896 0.0385525 T F T -135 21.8036
-\end{verbatim}
-In case of the first atom the basis is transformed by a rotation of $45^{\circ}$ and $36.5145^{\circ}$ about the $z$ and $x'$ axis.
-Relaxation of this atom is constrained to the $y''$-axis.
+The entire information is given in the POSCAR file as can be seen in the example displayed in Fig.~\ref{fig:vasp_input}.
+\begin{figure}[t]
+\begin{Verbatim}[frame=single]
+cubic diamond
+ 5.429
+ 1.00000 0.00000 0.00000
+ 0.00000 1.00000 0.00000
+ 0.00000 0.00000 1.00000
+ 8
+transformed selective dynamics
+direct
+ 0.00000 0.00000 0.00000 T F T 45.0 30.0
+ 0.50000 0.50000 0.00000 T T T 0.0 0.0
+ 0.50000 0.00000 0.50000 T T T 0.0 0.0
+ 0.00000 0.50000 0.50000 T T T 0.0 0.0
+ 0.25000 0.25000 0.25000 T F T 135.0 -10.0
+ 0.75000 0.75000 0.25000 T T T 0.0 0.0
+ 0.75000 0.25000 0.75000 T T T 0.0 0.0
+ 0.25000 0.75000 0.75000 T T T 0.0 0.0
+\end{Verbatim}
+\caption{Example {\textsc vasp} input file utilizing the {\em transformed selective dynamics} mode of operation.}
+\label{fig:vasp_input}
+\end{figure}
+In case of the first atom, the basis is transformed by a rotation of $45^{\circ}$ and $30^{\circ}$ about the $z$ and $x'$ axis.
+The basis of the fifth atom is likewise rotated by $135^{\circ}$ and $-10^{\circ}$ respectively.
+Relaxation of both atoms is only allowed within the plane perpendicular to the $y''$-axis.