Recent changes to Plotting

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Jun 2019 13:13:29 -0000

--- v13
+++ v14
@@ -27,6 +27,31 @@
 ![frag_decomp.png](https://sourceforge.net/p/theodore-qc/wiki/Plotting/attachment/frag_decomp.png)

 ### Fragment decomposition (Omega matrices)
-An interactive script plot_Om_bars.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py
+An interactive script plot_Om_bars.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py. The script proceeds by asking for different components, which are each in turn composed of several donor/acceptor pairs. To define, for example, the MLCT states in a complex with three ligands, proceed like this:
+
+~~~~
+Name of component 1
+Choice: MLCT
+
+Color for plotting
+Choice: blue
+
+ *** Fragment pairs belonging to MLCT ***
+  Enter two indices between 1 and 4, separated by spaces
+  Leave empty to finish
+
+Hole/electron indices for pair 1
+Choice: 1 2
+
+Hole/electron indices for pair 2
+Choice: 1 3
+
+Hole/electron indices for pair 3
+Choice: 1 4
+
+Hole/electron indices for pair 4
+Choice: 
+ ... switching to next component.
+~~~~

 ![Om_bars.png](https://sourceforge.net/p/theodore-qc/wiki/Plotting/attachment/Om_bars.png)

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Jun 2019 13:09:30 -0000

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Jun 2019 13:08:26 -0000

--- v11
+++ v12
@@ -27,4 +27,6 @@
 ![frag_decomp.png](https://sourceforge.net/p/theodore-qc/wiki/Plotting/attachment/frag_decomp.png)

 ### Fragment decomposition (Omega matrices)
-An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py
+An interactive script plot_Om_bars.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py
+
+![Om_bars.png](https://sourceforge.net/p/theodore-qc/wiki/Plotting/attachment/Om_bars.png)

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Jun 2019 13:00:47 -0000

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Jun 2019 12:58:17 -0000

--- v9
+++ v10
@@ -24,7 +24,7 @@
 ### Fragment decomposition (e/h populations)
 An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py

-![](http://!)
+![frag_decomp.png](https://sourceforge.net/p/theodore-qc/wiki/Plotting/attachment/frag_decomp.png)

 ### Fragment decomposition (Omega matrices)
 An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Jun 2019 12:54:51 -0000

--- v8
+++ v9
@@ -21,5 +21,10 @@

 It is also possible to compute the density of states (no weighting by oscillator strengths) and to add restrictions with respect to the states chosen (e.g. only states with CT > 0.5).

-### Fragment decomposition
-An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py
+### Fragment decomposition (e/h populations)
+An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py
+
+![](http://!)
+
+### Fragment decomposition (Omega matrices)
+An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the electron and hole populations of the excited states. To be called after analyze_tden.py

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Apr 2017 11:34:26 -0000

--- v7
+++ v8
@@ -12,14 +12,14 @@

 For parsing [Newton-X](http://www.newtonx.org/) trajectories, a specialized script plot_graph_nx.py exists.

-### Fragment decomposition
-An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py
-
-### Spectrum
-Create a convoluted spectrum from the energies and oscillator strengths parsed by analyze_tden.py.
+### Absorption spectrum
+Create a convoluted absorption spectrum from the energies and oscillator strengths parsed by analyze_tden.py.

 ~~~~
 spectrum.py <tden_summ1> [<tden_summ2> ...]
 ~~~~

 It is also possible to compute the density of states (no weighting by oscillator strengths) and to add restrictions with respect to the states chosen (e.g. only states with CT > 0.5).
+
+### Fragment decomposition
+An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Apr 2017 11:33:40 -0000

--- v6
+++ v7
@@ -10,16 +10,12 @@

 The graphs are collected in a file graphs.html ([Example](http://theodore-qc.sourceforge.net/images/graphs.html)).

-### plot_graph.py
-Interactive script that allows to create graphs from a set of computations in different directories, e.g. from a potential curve.
+For parsing [Newton-X](http://www.newtonx.org/) trajectories, a specialized script plot_graph_nx.py exists.

-### plot_graph_nx.py
-Interactive script that allows to create graphs from [Newton-X](http://www.newtonx.org/) trajectories.
+### Fragment decomposition
+An interactive script plot_frag_decomp.py can be used for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py

-### plot_frag_decomp.py
-Interactive script for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py
-
-### spectrum.py
+### Spectrum
 Create a convoluted spectrum from the energies and oscillator strengths parsed by analyze_tden.py.

 ~~~~

Plotting modified by Felix Plasser

Felix Plasser — Wed, 26 Apr 2017 11:31:10 -0000

--- v5
+++ v6
@@ -1,3 +1,5 @@
+[TOC]
+
 ### Electron-hole correlation plots
 *Electron-hole* correlation plots can be created with the plot_OmFrag.py utility. You are asked about the output options directly by this script. To view the output, simply open the file OmFrag.html in a web browser ([Example](http://theodore-qc.sourceforge.net/images/OmFrag.html)).

@@ -7,3 +9,21 @@
 Call plot_graph.py and follow the instructions on the screen.

 The graphs are collected in a file graphs.html ([Example](http://theodore-qc.sourceforge.net/images/graphs.html)).
+
+### plot_graph.py
+Interactive script that allows to create graphs from a set of computations in different directories, e.g. from a potential curve.
+
+### plot_graph_nx.py
+Interactive script that allows to create graphs from [Newton-X](http://www.newtonx.org/) trajectories.
+
+### plot_frag_decomp.py
+Interactive script for plotting the fragment decomposition of the excited states. To be called after analyze_tden.py
+
+### spectrum.py
+Create a convoluted spectrum from the energies and oscillator strengths parsed by analyze_tden.py.
+
+~~~~
+spectrum.py <tden_summ1> [<tden_summ2> ...]
+~~~~
+
+It is also possible to compute the density of states (no weighting by oscillator strengths) and to add restrictions with respect to the states chosen (e.g. only states with CT > 0.5).

Plotting modified by Felix Plasser

Felix Plasser — Wed, 10 Dec 2014 15:51:24 -0000

--- v4
+++ v5
@@ -6,4 +6,4 @@

 Call plot_graph.py and follow the instructions on the screen.

-The graphs are collected in a file graphs.html (TODO: Example).
+The graphs are collected in a file graphs.html ([Example](http://theodore-qc.sourceforge.net/images/graphs.html)).