Merge pull request #7 from gorges97/main

Added documenation of msreact mode for release of CREST 3.0

_data/keywords.yml

@@ -141,6 +141,15 @@ runtype:
       text: QCG keywords.
       link: /page/documentation/qcg.html
 
+  - cmd: --msreact 
+    type: MSREACT tool 
+    descript: >
+      Use the mass spectral fragment generator. 
+      MSREACT has several individual runtypes. See
+    url:
+      text: MSREACT keywords.
+      link: /page/documentation/msreact.html      
+
 
 leveloftheory:
 

_data/msreact.yml

@@ -0,0 +1,84 @@
+msreactkeywords:
+
+  - cmd: --msnbonds <int>
+    descript: >
+      maximum number of bonds between atoms pairs for applying a repulsive potential (default 3)
+
+  - cmd: --msnshifts <int>
+    descript: >
+      perform <i>int</i> optimizations with randomly shifted atom positions (default 0)
+
+  - cmd: --msnshifts2 <int>
+    descript: >
+      perform </i>int</i> optimizations with randomly shifted atom positions and a repulsive potential applied to atom pairs (default 0)
+
+  - cmd: ---msnoattrh
+    descript: >
+      deactivate attractive potential between hydrogen atoms and LMO centers.
+
+  - cmd: --msmolbar
+    descript: >
+      sort out topological duplicates by molbar codes (requires  sourced "molbar")
+
+  - cmd: --msinchi
+    descript: >
+      sort out topological duplicates by InChI codes (requires  sourced "obabel") 
+
+  - cmd: --mslargeprint
+    descript: >
+      do not remove temporary files and MSDIR with constrained optimizations and write
+      directories for isomers and fragmentpairs, as well as seperated fragment structures in 
+      individual directories. The nomenclature of the directories is `p<number of product>` for isomers and product pairs.
+      For fragments, it is `p<number of corresponding product pair>f<number of respective fragment>`.
+
+  - cmd: --chrg <int> 
+    descript: >
+      set the molecules´ charge (default 0, for EI-MS: 1, for DEA-MS: -1).    
+
+  - cmd: --ewin <real>
+    descript: >
+      set energy window in for sorting out fragments kcal/mol [default: 200.0 kcal/mol].  
+
+  - cmd: --msiso
+    descript: >
+      print only non-dissociated structures (isomers).
+
+  - cmd: --msnoiso 
+    descript: >
+      print only dissociated structures.
+       
+  - cmd: --msinput <file>
+    descript: >
+      read advanced settings from input file.
+
+
+
+msreactinputfilekeywords:
+
+    - cmd: fragdist <real>
+      descript: >
+        increase distance between fragments xyz structures (default 0 Angstrom). 
+        (Useful for input generation of automatic reaction pathfinder.)
+
+    - cmd: atomshift <real>
+      descript: >
+        shift of atoms in random atom displacement (default 0.75 Angstrom)
+
+    - cmd: distthr_attr <real>
+      descript: >
+        distance threshold in Angstrom for H-LMO attraction (default 4.0 Angstrom)
+
+    - cmd: fc_rep <real>
+      descript: >
+        force constant for repulsive potential between atom pairs (default 0.5)
+
+    - cmd: fc_attr <real>
+      descript: >
+        force constant for attractive potential between hydrogen and LMO centers (default -0.5)
+
+    - cmd: etemp <real>
+      descript: >
+        change electronic temperature in xTB optimizations       (default 5000 K)     
+
+        
+ 

page/documentation/keywords.md

@@ -135,3 +135,8 @@ The QCG keyword section can be found on the next page:
 
 [Go to Quantum Cluster Growth Keyword Documentation <i class="fa-solid fa-book"></i>](qcg.html){: .btn .btn-blue }
 
+## MSREACT mode Options
+
+Options for the MSREACT mode can be found here:
+
+[Go to MSREACT Keyword Documentation <i class="fa-solid fa-book"></i>](msreact.html){: .btn .btn-blue }

page/documentation/msreact_keywords.md

@@ -0,0 +1,52 @@
+---
+layout: default
+title: MSREACT Keywords
+parent: Command Line Keyword Documentation
+grand_parent: Documentation
+nav_order: 1
+summary: "The list of available command line arguments for MSREACT."
+permalink: /page/documentation/msreact.html
+---
+
+# {{page.title}}
+{: .no_toc }
+
+This page contains the documentation of available keywords for the MSREACT mode.
+Required arguments will be marked with `< >`, optional arguments are marked by brackets `[ ]`.
+
+## Table of contents
+{: .no_toc .text-delta }
+
+1. TOC
+{:toc}
+
+
+---
+
+{% include note.html content="Note that the MSREACT mode produces many topologically equivalent duplicates. To sort out duplicated structures you require the `molbar` program that can be obtained from the respective [*molbar* GitHub repository <i class='fa-brands fa-github'></i>](https://git.rwth-aachen.de/bannwarthlab/molbar) (recommended option). Alternatively, you can use InChI keys generated by the `obabel` program [*openbabel* GitHub repository <i class='fa-brands fa-github'></i>](https://github.com/openbabel). The programs have to be added to your path as `molbar` or `obabel`, respectively." %}
+
+The MSREACT extension of CREST can be invoked via the command line. 
+To activate MSREACT, use a command similar to
+
+```bash
+crest <INPUTFILE> -msreact [OPTIONS]
+```
+
+The input file coordinates have to be provided and can be in any format supported by CREST. 
+The general and technical command line options of CREST also apply to the MSREACT runtype 
+(see [**Keyword Documentation**]({{site.baseurl}}/page/documentation/keywords.html)).
+Take care to always set the number of cores with `--T <INT>`.
+The `[OPTIONS]` that can be used in conjunction with `-msreact` are documented below.
+{: .text-justify }
+
+## MSREACT Keywords
+
+{% include 2tab.html obj=site.data.msreact.msreactkeywords %}
+
+## MSREACT special settings specified in an input file
+
+Additional `[OPTIONS]` can be changed in an additional input file which is read via `-msinput <filename>`. The specific keywords are documented below. One should use only one `keyword <value>` pair per line.
+{: .text-justify }
+
+{% include 2tab.html obj=site.data.msreact.msreactinputfilekeywords %}
+