Recent changes to Input

Input modified by Felix Plasser

Felix Plasser — Wed, 08 May 2019 10:54:00 -0000

--- v12
+++ v13
@@ -20,7 +20,7 @@

 Mode 2 is a special utility for automatic fragment definition. If the system of interest is composed of different molecules, these are detected automatically. Further customization can be performed by exporting the molecule in .mol format and changing the bond definitions by using for example [Avogadro](http://avogadro.cc/).

-Mode 3 is a shortcut version of mode 2 that specifically works for transition metal complexes, see [Coord. Chem. Rev., **2018**, 361, 74](http://dx.doi.org/10.1016/j.ccr.2018.01.019). You simply have to add the atom of the transition metal and the system is automatically separated into the transition metal and the different ligands.
+Mode 3 is a shortcut version of mode 2 that specifically works for transition metal complexes, see [*Coord. Chem. Rev.*, **361**, 74 (2018)](http://dx.doi.org/10.1016/j.ccr.2018.01.019). You simply have to add the atom of the transition metal and the system is automatically separated into the transition metal and the different ligands.

 Mode 4 automatically separates the list by elements.

Input modified by Felix Plasser

Felix Plasser — Wed, 08 May 2019 10:52:28 -0000

--- v11
+++ v12
@@ -5,21 +5,26 @@
 ### Molecular fragment definition
 A key input quantity for the charge transfer number analysis in TheoDORE is the molecular fragment definition. First, the user has to decide on how to separate the system under study into fragments. There is no unique way to do so, and it may be necessary to try out different fragmentation schemes to produce the most meaningful results.

-There are three different ways of specifying the fragment information in theoinp.
+There are five different ways of specifying the fragment information in theoinp.

 ~~~~
 Mode for specifying molecular fragments (at_lists):
   [ 1] Manual input
-  [ 2] Automatic generation from coordinate file (using python-openbabel)
-  [ 3] Leave empty and fill out later
-Choice: 
+  [ 2] Automatic generation by fragment (using python-openbabel)
+  [ 3] Automatic generation for transition metal complexes (using python-openbabel)
+  [ 4] Automatic generation by element (using python-openbabel)
+  [ 5] Leave empty and fill out later
 ~~~~

 In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments successively.

 Mode 2 is a special utility for automatic fragment definition. If the system of interest is composed of different molecules, these are detected automatically. Further customization can be performed by exporting the molecule in .mol format and changing the bond definitions by using for example [Avogadro](http://avogadro.cc/).

-For mode 3 the dens_ana.in file has to be edited manually. For example, the input
+Mode 3 is a shortcut version of mode 2 that specifically works for transition metal complexes, see [Coord. Chem. Rev., **2018**, 361, 74](http://dx.doi.org/10.1016/j.ccr.2018.01.019). You simply have to add the atom of the transition metal and the system is automatically separated into the transition metal and the different ligands.
+
+Mode 4 automatically separates the list by elements.
+
+For mode 5 the dens_ana.in file has to be edited manually. For example, the input

 ~~~~
 at_lists = [ [1,3,4], [2,5,6] ]

Input modified by Felix Plasser

Felix Plasser — Wed, 13 Jan 2016 11:18:44 -0000

--- v10
+++ v11
@@ -3,7 +3,9 @@
 The theoinp utility allows quick generation of the input information needed by TheoDORE. When running theoinp, the relevant options are suggested by default and only minimal input by the user is needed. It is however advised to take a look at the [program specific information](Program specific information) for the different interfaced quantum chemistry codes. After running theoinp a list of [keywords](Keywords) is written to the file dens_ana.in.

 ### Molecular fragment definition
-A key input quantity for excited state analysis in TheoDORE is the molecular fragment definition. For this purpose, it is necessary to specify which atoms belong to any given fragment. There are three different options for specifying this information in theoinp.
+A key input quantity for the charge transfer number analysis in TheoDORE is the molecular fragment definition. First, the user has to decide on how to separate the system under study into fragments. There is no unique way to do so, and it may be necessary to try out different fragmentation schemes to produce the most meaningful results.
+
+There are three different ways of specifying the fragment information in theoinp.

 ~~~~
 Mode for specifying molecular fragments (at_lists):

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:26:11 -0000

--- v9
+++ v10
@@ -15,9 +15,9 @@

 In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments successively.

-Mode 2 is a special utility for automatic fragment definition. If the system of interest is already composed of different molecules, these can be detected automatically. Further customization can be performed by exporting the molecule in .mol format and changing the bond definitions by using for example [Avogadro](http://avogadro.cc/).
+Mode 2 is a special utility for automatic fragment definition. If the system of interest is composed of different molecules, these are detected automatically. Further customization can be performed by exporting the molecule in .mol format and changing the bond definitions by using for example [Avogadro](http://avogadro.cc/).

-For mode 3 you can edit the dens_ana.in file later. For example, the input
+For mode 3 the dens_ana.in file has to be edited manually. For example, the input

 ~~~~
 at_lists = [ [1,3,4], [2,5,6] ]

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:25:04 -0000

--- v8
+++ v9
@@ -15,7 +15,7 @@

 In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments successively.

-Mode 2 is a special utility available to allow for automatic fragment definition for the computation of [charge transfer numbers](Transition density matrix analysis). To customize the fragment definition you may export the coordinate file in .mol format and set custom bond definitions by using for example [Avogadro](http://avogadro.cc/).
+Mode 2 is a special utility for automatic fragment definition. If the system of interest is already composed of different molecules, these can be detected automatically. Further customization can be performed by exporting the molecule in .mol format and changing the bond definitions by using for example [Avogadro](http://avogadro.cc/).

 For mode 3 you can edit the dens_ana.in file later. For example, the input

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:23:24 -0000

--- v7
+++ v8
@@ -13,7 +13,7 @@
 Choice: 
 ~~~~

-In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments.
+In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments successively.

 Mode 2 is a special utility available to allow for automatic fragment definition for the computation of [charge transfer numbers](Transition density matrix analysis). To customize the fragment definition you may export the coordinate file in .mol format and set custom bond definitions by using for example [Avogadro](http://avogadro.cc/).

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:22:16 -0000

--- v6
+++ v7
@@ -3,7 +3,7 @@
 The theoinp utility allows quick generation of the input information needed by TheoDORE. When running theoinp, the relevant options are suggested by default and only minimal input by the user is needed. It is however advised to take a look at the [program specific information](Program specific information) for the different interfaced quantum chemistry codes. After running theoinp a list of [keywords](Keywords) is written to the file dens_ana.in.

 ### Molecular fragment definition
-A key input quantity for excited state analysis in TheoDORE is concerned with the molecular fragment definition. For this purpose, it is necessary to specify which atoms belong to any given fragment. There are three different options for specifying this information in theoinp.
+A key input quantity for excited state analysis in TheoDORE is the molecular fragment definition. For this purpose, it is necessary to specify which atoms belong to any given fragment. There are three different options for specifying this information in theoinp.

 ~~~~
 Mode for specifying molecular fragments (at_lists):

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:22:04 -0000

--- v5
+++ v6
@@ -3,7 +3,7 @@
 The theoinp utility allows quick generation of the input information needed by TheoDORE. When running theoinp, the relevant options are suggested by default and only minimal input by the user is needed. It is however advised to take a look at the [program specific information](Program specific information) for the different interfaced quantum chemistry codes. After running theoinp a list of [keywords](Keywords) is written to the file dens_ana.in.

 ### Molecular fragment definition
-A key input quantity related to excited state analysis in TheoDORE is concerned with the molecular fragment definition. For this purpose, it is necessary to specify which atoms belong to any given fragment. There are three different options for specifying this information in theoinp.
+A key input quantity for excited state analysis in TheoDORE is concerned with the molecular fragment definition. For this purpose, it is necessary to specify which atoms belong to any given fragment. There are three different options for specifying this information in theoinp.

 ~~~~
 Mode for specifying molecular fragments (at_lists):

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:21:51 -0000

--- v4
+++ v5
@@ -17,7 +17,7 @@

 Mode 2 is a special utility available to allow for automatic fragment definition for the computation of [charge transfer numbers](Transition density matrix analysis). To customize the fragment definition you may export the coordinate file in .mol format and set custom bond definitions by using for example [Avogadro](http://avogadro.cc/).

-For mode [3] you can edit the dens_ana.in file later. For example, the input
+For mode 3 you can edit the dens_ana.in file later. For example, the input

 ~~~~
 at_lists = [ [1,3,4], [2,5,6] ]

Input modified by Felix Plasser

Felix Plasser — Tue, 18 Aug 2015 12:21:31 -0000

--- v3
+++ v4
@@ -10,10 +10,17 @@
   [ 1] Manual input
   [ 2] Automatic generation from coordinate file (using python-openbabel)
   [ 3] Leave empty and fill out later
-Choice: 2
+Choice: 
 ~~~~

+In mode 1 you will be asked to enter the indices of the atoms that belong to the different fragments.

-A special utility is available to allow for automatic fragment definition for the computation of [charge transfer numbers](Transition density matrix analysis). This utility is accessed by specifying
+Mode 2 is a special utility available to allow for automatic fragment definition for the computation of [charge transfer numbers](Transition density matrix analysis). To customize the fragment definition you may export the coordinate file in .mol format and set custom bond definitions by using for example [Avogadro](http://avogadro.cc/).

-To customize the fragment definition you may export the coordinate file in .mol format and set custom bond definitions by using for example [Avogadro](http://avogadro.cc/). 
+For mode [3] you can edit the dens_ana.in file later. For example, the input
+
+~~~~
+at_lists = [ [1,3,4], [2,5,6] ]
+~~~~
+
+means that there are two molecular fragments. The first contains atoms 1, 3, and 4, the second 2, 5, and 6.