Changeset 25d9d9 for doc

Timestamp:

Jun 12, 2016, 8:48:21 AM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Fix_BoundInBox_CenterInBox_MoleculeActions

Parents:

996ef1

git-author:

Frederik Heber <heber@…> (06/11/16 16:43:54)

git-committer:

Frederik Heber <heber@…> (06/12/16 08:48:21)

Message:

FIX: CenterInBox and BoundInBox are actions acting on molecules, not world.

• just stumbled over this when realizing that center-in-box does not center all selected atoms within the box but each of the currently present molecules individually.
• this is also changed to act only on selected molecules.
• TEST: extended regression test to only test centering and bounding of some molecules (and not only all).
• TESTFIX: needed to change regression tests on all molecules to prepend action with select-all-molecules.
• Needed to renamed python action in boxmaker.py.in.
• DOCU: Corrected description in userguide.

File:

• doc/userguide/userguide.xml (modified) (1 diff)

doc/userguide/userguide.xml

@@ -1154 +1154 @@
         </section>
         <section xml:id="domain.bound-in-box">
-          <title xml:id="domain.bound-in-box.title">Bound atoms inside box </title>
+          <title xml:id="domain.bound-in-box.title">Bound selected molecules inside box </title>
           <para>The following applies the current boundary conditions to the
-          atoms. In case of periodic or wrapped boundary conditions the atoms
-          will be periodically translated to be inside the domain
-          again.</para>
-          <programlisting>... --bound-in-box</programlisting>
+          atoms of all currently selected molecules. In case of periodic or 
+          wrapped boundary conditions the atoms will be periodically translated
+          to be inside the domain again.</para>
+          <programlisting>... --select-all-molecules --bound-in-box</programlisting>
         </section>
         <section xml:id="domain.center-in-box">
-          <title xml:id="domain.center-in-box.title">Center atoms inside the domain</title>
-          <para>This is a combination of changing the box and bounding the
-          atoms inside it.</para>
-          <programlisting>... --center-in-box &quot;20,0,20,0,0,20&quot;</programlisting>
+          <title xml:id="domain.center-in-box.title">Center each selected molecule inside the domain</title>
+          <para>This takes each molecule in turn, calculates its center and shifts all 
+          associated atoms in such a way that its center coincides with that of the
+          domain.</para>
+          <programlisting>... --select-molecule-by-order -1 
+          --center-in-box &quot;20,0,20,0,0,20&quot;</programlisting>
         </section>
         <section xml:id="domain.center-edge">