restructured the accelerated md stuff

diff --git a/posic/thesis/md.tex b/posic/thesis/md.tex
index c47633b..3662b69 100644 (file)
--- a/posic/thesis/md.tex
+++ b/posic/thesis/md.tex
@@ -178,7 +178,7 @@ The difference in energy $\Delta$ growing within the carbon insertion process up
 Here is the problem.
 The excess amount of next neighboured strongly bounded C-C bonds in the high concentration simulations make these configurations energetically more favorable compared to the low concentration configuration.
 However, in the same way a lot of energy is needed to break these bonds to get out of the local energy minimum advancing towards the global minimum configuration.
-Thus, this transformation is very unlikely to happen.
+Thus, such conformational chamges are very unlikely to happen.
 This is in accordance with the constant total energy observed in the continuation step of 100 ps inbetween the end of carbon insertion and the cooling process.
 Obviously no energetically favorable relaxation is taking place at a system temperature of $450\,^{\circ}\mathrm{C}$.
 
@@ -217,27 +217,34 @@ Short range order indeed is observed but only hardly visible is the long range o
 This indicates the formation of an amorphous SiC-like phase.
 In fact the resulting Si-C and C-C radial distribution functions compare quite well with these obtained by cascade amorphized and melt-quenched amorphous SiC using a modified Tersoff potential \cite{gao02}.
 
-The question of the formation of such an amoprhous phase, although experiments show crystalline 3C-SiC precipitates at prevailing temperatures remains.
-The answer is found in the short range and abrupt cut-off of the employed bond order potential.
-The abrupt cut-off, which ... to zero betwenn the first and second next neighbour distance, is responsible for overestimated and unphysical high forces of next neighboured atoms.
-Indeed it is not only the C-C bonds which seem to be unbreakable.
-Also the C-Si pairs, as observed in the low concentration simulations, are stuck.
-This can be seen from the almost horizontal progress of the total energy graph in the continuation step, even for the low concentartion simulation.
-Longer time scales might on the one hand be not sufficient enough and on the other hand not .
-Alternatively higher temperatures to speed up or actually make possible the precipitation simulation are needed.
+\subsection{Limitations of conventional MD and short order potentials}
 
-{\color{red}Todo: Read again about the accelerated dynamics methods and maybe explain a bit more here.}
+{\color{blue}
+Alternatively: Explain general problem of the slow propagation through phase space using conventional molecular dynamics and the accompanying difficulties for conformational search.
+Explain the methods available to overcome this limitation.
+Point out, that in this work, the sharp cut-off introduces unphysical and overestimated high forces between next neighboured atoms enhancing the problem of slow phase space propagation.
+}
+
+The formation of an amoprhous SiC-like phase although experiments show crystalline 3C-SiC precipitates at prevailing temperatures remains unexplained.
+The answer is found in the short range and sharp cut-off of the employed bond order potential.
+The cut-off funtion, which limits the interacting ions to the next neighboured atoms by gradually pushing the interaction force and energy to zero betwenn the first and second next neighbour distance, is responsible for overestimated and unphysical high forces of next neighboured atoms \cite{mattoni2007}.
+Indeed it is not only the strong C-C bond which is hard to break inhibiting carbon diffusion and further conformational changes.
+This is also true for the low concentration simulations dominated by C-Si dumbbells spread over the whole simulation volume.
+The bonds of these C-Si pairs are also affected by the cut-off artifact preventing carbon diffusion and agglomeration of the dumbbells.
+This can be seen from the almost horizontal progress of the total energy graph in the continuation step, even for the low concentration simulation.
+Thus, applying longer time scales in order to enable the system to undergo diffusion events, which become very unlikely to happen due to the overestimated bond strengthes, and in the end observe the agglomeration and precipitation might not be sufficient.
+On the other hand longer time scales are not accessible to simulation due to limited computational ressources.
+Alternatively the approach of using higher temperatures to speed up or actually make possible the steps involved in the precipitation mechanism is applied.
 
-Finally explain which methods will be applied in the following.
 
 \subsection{Increased temperature simulations}
 
-\subsection{Simulations at temperatures exceeding the silicon melting point}
-
-LL Cool J is hot as hell!
+{\color{red}Todo: We go for higher temepratures first due to the potential cut-off artifact discussed above.}
 
 \subsection{Constructed 3C-SiC precipitate in crystalline silicon}
 
+{\color{red}Todo: We want to know where we want to go ...}
+
 In the following a spherical 3C-SiC precipitate enclosed in a c-Si surrounding is constructed as it is expected from IBS experiments and from simulations that finally succeed simulating the precipitation event.
 On the one hand this sheds light on characteristic values like the radial distribution function or the total amount of energy for configurations that are aimed to be reproduced by simulation possibly enabling the prediction of conditions necessary for the simulation of the precipitation process.
 On the other hand, assuming a correct alignment of the precipitate with the c-Si matrix, investigations of the behaviour of such precipitates and the surrounding can be made.
@@ -305,3 +312,8 @@ PC and energy of that one.
 
 Now let's see, whether annealing will lead to some energetically more favorable configurations.
 
+Estimate surface energy ...
+
+\subsection{Simulations at temperatures exceeding the silicon melting point}
+
+LL Cool J is hot as hell!