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Commit 7127da3b authored by Giovanni Bussi's avatar Giovanni Bussi
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Merge branch 'v2.3' into v2.4

parents 4ecf2091 98671c53
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...@@ -55,12 +55,13 @@ eRMSD measures the distance between structures by considering only the relative ...@@ -55,12 +55,13 @@ eRMSD measures the distance between structures by considering only the relative
2. Calculate all pairwise distance vectors \f$ \vec{r}_{i,j} \f$ among base centers. 2. Calculate all pairwise distance vectors \f$ \vec{r}_{i,j} \f$ among base centers.
3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where \f$ a=b=5 \AA, c= 3 \AA\f$. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions. 3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where a=b=5 \AA, c= 3 \AA. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
4. Calculate the G vectors 4. Calculate the G vectors
\f[ \f[
\vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times \Theta(\tilde{r}_{cutoff}-\tilde{r}) \vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times
\frac{\Theta(\tilde{r}_{cutoff}-\tilde{r})}{\gamma}
\f] \f]
Here, \f$ \gamma = \pi/\tilde{r}_{cutoff}\f$ and \f$ \Theta \f$ is the Heaviside step function. The default cutoff is set to 2.4. Here, \f$ \gamma = \pi/\tilde{r}_{cutoff}\f$ and \f$ \Theta \f$ is the Heaviside step function. The default cutoff is set to 2.4.
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