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--- exercise:mo_ethene [2014/03/27 16:21] – [3. Step] oschuett
+++ exercises:2014_ethz_mmm:mo_ethene [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 4: / Line 4: @@
  ==== 1. Step ====
 Run a calculation with the following (commented) input file. \\
-Note that the file contains explicit basis sets and potential for all-electron calculations. An explanation of the basis set formats is given here: [[exercise:basis_sets|Basis Sets]]
+Note that the file contains explicit basis sets and potential for all-electron calculations. An explanation of the basis set formats is given here: [[basis_sets|Basis Sets]]
 <code - ethene.inp >
@@ Line 163: / Line 163: @@
 ∗.cube files report the structure of a given MO and can be visualized with VMD:
-  * To run vmd: vmd ethene-WFN_00008_1-1_0.cub
+  * To run vmd: vmd ethene-WFN_00008_1-1_0.cube
-  * To visualize the moelcule (sometimes the default settings are not visible with VMD in Brutus):\\    Graphics > Representations > Draw style > Drawing Method: CPK
+  * To visualize the molecule (sometimes the default settings are not visible with VMD in Brutus):\\    Graphics > Representations > Draw style > Drawing Method: CPK
   * To visualize the MO structure in VMD:\\    Graphics > Representations > Draw style > Drawing Method: Isosurfaces
   * In  Isosurfaces, set Draw to "Wireframe" (other formats may not be visible with VMD in Brutus)
   * In Isosurfaces, set Isovalue to 0.1, 0.01 ...
+  * To visualize the positive and the negative part of an orbital simultaneously, add a second isosurface representation with isovalues -0.1, -0.01, ...
+  * To give the two representations different colors, set their "Coloring Method" to "ColorID" and choose different ids.
 What you get should look similar to this:
-{{ :exercise:ethene_pi_orbital.png |}}
+{{ ethene_pi_orbital.png |}}
 ==== Questions ====