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| | | /* vim: set ts=4 sts=4 sw=4 noet : */ |
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| | | #include<stdlib.h> |
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| | | #include "general.h" |
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| | | #include "energy.h" |
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| | | #include "vertex.h" |
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| | | #include<math.h> |
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| | | #include<stdio.h> |
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| | | /** @brief Wrapper that calculates energy of every vertex in vesicle |
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| | | * |
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| | | * Function calculated energy of every vertex in vesicle. It can be used in |
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| | | * initialization procedure or in recalculation of the energy after non-MCsweep * operations. However, when random move of vertex or flip of random bond occur * call to this function is not necessary nor recommended. |
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| | | * @param *vesicle is a pointer to vesicle. |
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| | | * @returns TS_SUCCESS on success. |
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| | | */ |
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| | | ts_bool mean_curvature_and_energy(ts_vesicle *vesicle){ |
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| | | ts_uint i; |
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| | | return TS_SUCCESS; |
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| | | } |
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| | | |
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| | | /** @brief Calculate energy of a bond (in models where energy is bond related) |
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| | | * |
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| | | * This function is experimental and currently only used in polymeres calculation (PEGs or polymeres inside the vesicle). |
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| | | * |
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| | | * @param *bond is a pointer to a bond between two vertices in polymere |
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| | | * @param *poly is a pointer to polymere in which we calculate te energy of the bond |
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| | | * @returns TS_SUCCESS on successful calculation |
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| | | */ |
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| | | inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly){ |
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| | | //TODO: This value to be changed and implemented in data structure: |
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| | | ts_double d_relaxed=1.0; |
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| | | bond->energy=poly->k*pow(bond->bond_length-d_relaxed,2); |
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| | | return TS_SUCCESS; |
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| | | }; |
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| | | |
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| | | /** @brief Calculation of energy of the vertex |
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| | | * |
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| | | * Main function that calculates energy of the vertex \f$i\f$. Nearest neighbors (NN) must be ordered in counterclockwise direction for this function to work. |
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| | | * Firstly NNs that form two neighboring triangles are found (\f$j_m\f$, \f$j_p\f$ and common \f$j\f$). Later, the scalar product of vectors \f$x_1=(\mathbf{i}-\mathbf{j_p})\cdot (\mathbf{i}-\mathbf{j_p})(\mathbf{i}-\mathbf{j_p})\f$, \f$x_2=(\mathbf{j}-\mathbf{j_p})\cdot (\mathbf{j}-\mathbf{j_p})\f$ and \f$x_3=(\mathbf{j}-\mathbf{j_p})\cdot (\mathbf{i}-\mathbf{j_p})\f$ are calculated. From these three vectors the \f$c_{tp}=\frac{1}{\tan(\varphi_p)}\f$ is calculated, where \f$\varphi_p\f$ is the inner angle at vertex \f$j_p\f$. The procedure is repeated for \f$j_m\f$ instead of \f$j_p\f$ resulting in \f$c_{tn}\f$. |
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| | | * |
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| | | \begin{tikzpicture}{ |
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| | | \coordinate[label=below:$i$] (i) at (2,0); |
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| | | \coordinate[label=left:$j_m$] (jm) at (0,3.7); |
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| | | \coordinate[label=above:$j$] (j) at (2.5,6.4); |
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| | | \coordinate[label=right:$j_p$] (jp) at (4,2.7); |
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| | | |
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| | | \draw (i) -- (jm) -- (j) -- (jp) -- (i) -- (j); |
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| | | |
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| | | \begin{scope} |
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| | | \path[clip] (jm)--(i)--(j); |
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| | | \draw (jm) circle (0.8); |
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| | | \node[right] at (jm) {$\varphi_m$}; |
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| | | \end{scope} |
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| | | |
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| | | \begin{scope} |
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| | | \path[clip] (jp)--(i)--(j); |
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| | | \draw (jp) circle (0.8); |
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| | | \node[left] at (jp) {$\varphi_p$}; |
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| | | \end{scope} |
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| | | |
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| | | %%vertices |
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| | | \draw [fill=gray] (i) circle (0.1); |
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| | | \draw [fill=white] (j) circle (0.1); |
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| | | \draw [fill=white] (jp) circle (0.1); |
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| | | \draw [fill=white] (jm) circle (0.1); |
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| | | %\node[draw,circle,fill=white] at (i) {}; |
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| | | \end{tikzpicture} |
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| | | |
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| | | * The curvature is then calculated as \f$\mathbf{h}=\frac{1}{2}\Sigma_{k=0}^{\mathrm{neigh\_no}} c_{tp}^{(k)}+c_{tm}^{(k)} (\mathbf{j_k}-\mathbf{i})\f$, where \f$c_{tp}^{(k)}+c_{tm}^k=2\sigma^{(k)}\f$ (length in dual lattice?) and the previous equation can be written as \f$\mathbf{h}=\Sigma_{k=0}^{\mathrm{neigh\_no}}\sigma^{(k)}\cdot(\mathbf{j}-\mathbf{i})\f$ (See Kroll, p. 384, eq 70). |
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| | | * |
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| | | * From the curvature the enery is calculated by equation \f$E=\frac{1}{2}\mathbf{h}\cdot\mathbf{h}\f$. |
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| | | * @param *vtx is a pointer to vertex at which we want to calculate the energy |
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| | | * @returns TS_SUCCESS on successful calculation. |
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| | | */ |
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| | | inline ts_bool energy_vertex(ts_vertex *vtx){ |
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| | | // ts_vertex *vtx=&vlist->vertex[n]-1; // Caution! 0 Indexed value! |
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| | | // ts_triangle *tristar=vtx->tristar-1; |
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| | | //ts_vertex_data *data=vtx->data; |
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| | | ts_uint jj; |
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| | | ts_uint jjp,jjm; |
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| | | ts_vertex *j,*jp, *jm; |
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| | |
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| | | j=vtx->neigh[jj-1]; |
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| | | jp=vtx->neigh[jjp-1]; |
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| | | jm=vtx->neigh[jjm-1]; |
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| | | // printf("tristar_no=%u, neigh_no=%u, jj=%u\n",data->tristar_no,data->neigh_no,jj); |
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| | | jt=vtx->tristar[jj-1]; |
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| | | x1=vtx_distance_sq(vtx,jp); //shouldn't be zero! |
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| | | x2=vtx_distance_sq(j,jp); // shouldn't be zero! |
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| | |
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| | | vtx->curvature=-sqrtl(h); |
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| | | } |
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| | | #endif |
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| | | // What is vtx->c?????????????? Here it is 0! |
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| | | // c is forced curvature energy for each vertex. Should be set to zero for |
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| | | // normal circumstances. |
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| | | vtx->energy=0.5*s*(vtx->curvature/s-vtx->c)*(vtx->curvature/s-vtx->c); |
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