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- new option "-orthogonal-cell" allows to find a suitable equivalent …
…orthorhombic cell for any type of system. - updated doc and CHANGELOG.
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Pierre Hirel
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Feb 15, 2018
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<!DOCTYPE html> | ||
<html lang="en" > | ||
<head> | ||
<title>Option orthogonal-cell - Atomsk - Pierre Hirel</title> | ||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | ||
<link rel="stylesheet" media="screen" type="text/css" title="Default" href="./default.css" /> | ||
<link rel="icon" href="../img/atomsk_logo.png" type="image/png" /> | ||
</head> | ||
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<body> | ||
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<p><a href="./index.html">Back to main menu</a></p> | ||
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<h2>Option: orthogonal-cell</h2> | ||
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<h4>Syntax</h4> | ||
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<p><code>-orthogonal-cell</code></p> | ||
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<h4>Description</h4> | ||
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<p>This option finds the optimal orthorhombic cell that corresponds to the system. This can be useful when working with complex lattices, that one needs to rotate</p> | ||
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<p>The system may have any arbitrary vectors H1, H2, H3. This option searches for linear combinations m*H1+n*H2+o*H3 (with m,n,o integers) that produce vectors aligned with the Cartesian directions X, Y, Z. Then, atom positions are duplicated using the translation vectors H1, H2, H3, so as to fill this new orthogonal cell. Finally, the initial cell vectors are replaced by the vectors of the orthorhombic cell. Since the new cell vectors are linear combinations of the initial cell vectors, they respect the lattice periodicity.</p> | ||
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<p>If shells (in the sense of an ionic core-shell model) and/or auxiliary properties are present, then they are also duplicated.</p> | ||
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<p>Note that, after this option is applied, the total number of atoms may differ from that of the initial system.</p> | ||
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<h4>Default</h4> | ||
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<p>By default, Atomsk preserves the cell vectors and does not try to find an equivalent orthogonal cell.</p> | ||
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<h4>Examples</h4> | ||
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<ul> | ||
<li><code class="command">atomsk initial.cfg -rotate 45 z -orthocell final.cfg</code> | ||
<p>The initial system (<code>initial.cfg</code>) is rotated by 45° around the Z axis. Then, a suitable equivalent orthogonal cell is found, and atoms are duplicated to fill the new orthogonal cell. The final result will be output to <code>final.cfg</code>.</p></li> | ||
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</ul> | ||
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<p><a href="./index.html">Back to main menu</a></p> | ||
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</body> | ||
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</html> |
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<!DOCTYPE html> | ||
<html lang="fr" > | ||
<head> | ||
<title>Option orthogonal-cell - Atomsk - Pierre Hirel</title> | ||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | ||
<link rel="stylesheet" media="screen" type="text/css" title="Default" href="./default.css" /> | ||
<link rel="icon" href="../img/atomsk_logo.png" type="image/png" /> | ||
</head> | ||
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<body> | ||
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<p><a href="./index.html">Back to main menu</a></p> | ||
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<h2>Option : orthogonal-cell</h2> | ||
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<h4>Syntaxe</h4> | ||
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<p><code>-orthogonal-cell</code></p> | ||
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<h4>Description</h4> | ||
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<p>Cette option cherche une boîte orthogonale optimale qui convienne au système.</p> | ||
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<p>Le système peut être défini par des vecteurs de boîtes arbitraires H1, H2, H3. Cette option recherche les combinaisons linéaires de ces vecteurs, m*H1+n*H2+o*H3 (où m,n,o sont des entiers) qui produisent des vecteurs de boîte alignés avec les axes Cartésiens X, Y, Z. Puis, les positions des atomes sont dupliquées en utilisant les vecteurs de translation H1, H2, H3, afin de remplir la boîte orthorombique. Finalement, les vecteurs de boîte initiaux sont remplacés par les vecteurs de la boîte orthogonale. Puisque ces nouveaux vecteurs de boîte sont une combinaison linéaire des anciens, la périodicité de la maille est préservée.</p> | ||
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<p>Si des coquilles (dans le cadre d'un modèle ionique cœur-coquille) et/ou des propriétés auxiliaires existent dans le système, alors elles sont aussi dupliquées.</p> | ||
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<p>Notez que, après l'application de cette option, le nombre total d'atomes peut être différent du nombre initial.</p> | ||
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<h4>Défaut</h4> | ||
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<p>Par défaut, Atomsk préserve les vecteurs de boîte et n'essaye pas de trouver une boîte orthogonale équivalente.</p> | ||
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<h4>Exemples</h4> | ||
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<ul> | ||
<li><code class="command">atomsk initial.cfg -rotate 45 z -orthocell final.cfg</code> | ||
<p>Le système initial (<code>initial.cfg</code>) est tourné de 45° autour de l'axe Z. Puis, une boîte orthogonale équivalente est trouvée, et les atomes sont dupliqués afin de remplir cette boîte. Le résultat final est écrit dans le fichier <code>final.cfg</code>.</p></li> | ||
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</ul> | ||
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<p><a href="./index.html">Back to main menu</a></p> | ||
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</body> | ||
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</html> |
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