Restructures the sites' source

Author: Philipp Pracht

_data/keywords.yml

@@ -75,15 +75,15 @@ runtype:
       Iterative version of the MTD-GC workflow, which is the [default] runtype of CREST.
     url:
       text: See here.
-      link: /docs/overview/workflows.html#imtd-gc-algorithm
+      link: /page/overview/workflows.html#imtd-gc-algorithm
 
   - cmd: --v4
     type: iMTD-sMTD sampling
     descript: >
       Iterative workflow making use of static metadynamics simulations.
     url:
       text: See here.
-      link: /docs/overview/workflows.html#conformational-entropy-calculations
+      link: /page/overview/workflows.html#conformational-entropy-calculations
 
   - cmd: --entropy 
     type: Confromational Entropy Algorithm 
@@ -92,15 +92,15 @@ runtype:
       used in the calculation of conformational entropy.
     url:
       text: See here.
-      link: /docs/overview/workflows.html#conformational-entropy-calculations
+      link: /page/overview/workflows.html#conformational-entropy-calculations
 
   - cmd: --protonate 
     type: Protonation site sampling 
     descript: >
       Workflow for sampling protonation sites. 
     url:
       link: See here.
-      link: /docs/overview/workflows.html#protonation-site-screening
+      link: /page/overview/workflows.html#protonation-site-screening
 
   - cmd: --deprotonate 
     type: Deprotonation site sampling 
@@ -121,7 +121,7 @@ runtype:
       trajectory into conformers and rotamers.
     url:
       text: See below. <i class="fa-solid fa-circle-down"></i>
-      link: /docs/documentation/keywords.html#ensemble-sorting-options
+      link: /page/documentation/keywords.html#ensemble-sorting-options
 
   - cmd: --qcg 
     type: QCG tool 
@@ -130,21 +130,22 @@ runtype:
       QCG has several individual runtypes. See
     url:
       text: QCG keywords.
-      link: /docs/documentation/qcg.html
+      link: /page/documentation/qcg.html
 
 
 leveloftheory:
 
   - subheader: "**GFN*n*-xTB method selection**"
 
   - cmd: --gfn1 
-    descript: Use GFN1-xTB.
+    descript: Use [GFN1-xTB](https://doi.org/10.1021/acs.jctc.7b00118)
 
   - cmd: --gfn2 
-    descript: Use GFN2-xTB.
+    descript: Use [GFN2-xTB](https://doi.org/10.1021/acs.jctc.8b01176)
 
   - comm: "`--gff`, `--gfnff`"
-    descript: Use GFN-FF.
+    descript: Use [GFN-FF](https://doi.org/10.1002/anie.202004239)
+
 
   - cmd: --gfn2//gfnff
     descript: >
@@ -175,8 +176,8 @@ leveloftheory:
     
   - cmd: --alpb <SOLVENT> 
     descript: >
-      Use the ALPB model, an improved version of GBSA. 
-      For available `<SOLVENT>` options see the 
+      Use the [ALPB model](https://doi.org/10.1021/acs.jctc.1c00471), an improved 
+      version of GBSA. For available `<SOLVENT>` options see the 
       [`xtb` documentation](https://xtb-docs.readthedocs.io/en/latest/gbsa.html#gbsa). 
       The solvent input is not case-sensitive.
     
@@ -296,13 +297,14 @@ confsettings:
       some settings are reduced in order to achieve lower computation times. See
     url:
        text: Example X.
-       link: /docs/examples/
+       link: /page/examples/
 
   - cmd: --wscal <REAL>
     descript: >
       Scale the ellipsoid potential axes generated by the `--nci` mode by factor`<REAL>`.
 
   - subheader: "<br>**Property appendix**"
+    anchor: propopt
 
   - cmd: --prop hess
     descript: >
@@ -327,7 +329,7 @@ confsettings:
       with the `--for` command,
     url:
       text: see below. <i class="fa-solid fa-circle-down"></i>
-      link: /docs/documentation/keywords.html#standalone-tools
+      link: /page/documentation/keywords.html#standalone-tools
 
   - subheader: "<br>**Technical settings**"
 
@@ -344,7 +346,7 @@ confsettings:
       Do not confuse with 
     url:
        text: "`--notopo` <i class='fa-solid fa-triangle-exclamation'></i>"
-       link: /docs/documentation/keywords.html#notopo
+       link: /page/documentation/keywords.html#notopo
 
 
 entropysettings:
@@ -388,7 +390,7 @@ entropysettings:
       <br>Also works with the `--thermo` option,
     url:
       text: see below. <i class="fa-solid fa-circle-down"></i>
-      link: /docs/documentation/keywords.html#standalone-tools
+      link: /page/documentation/keywords.html#standalone-tools
 
   - cmd: --sthr <REAL>
     descript: >
@@ -397,7 +399,7 @@ entropysettings:
       <br>Also works with the `--thermo` option,
     url:
       text: see below. <i class="fa-solid fa-circle-down"></i>
-      link: /docs/documentation/keywords.html#standalone-tools
+      link: /page/documentation/keywords.html#standalone-tools
 
   - cmd: --ithr <REAL>
     descript: >
@@ -406,7 +408,7 @@ entropysettings:
       <br>Also works with the `--thermo` option,
     url: 
       text: see below. <i class="fa-solid fa-circle-down"></i>
-      link: /docs/documentation/keywords.html#standalone-tools
+      link: /page/documentation/keywords.html#standalone-tools
 
 
 
@@ -469,7 +471,7 @@ sortingsettings:
       searches. See
     url:
       text: Example X.
-      link: /docs/examples/
+      link: /page/examples/
 
   - cmd: --notopo
     anchor: notopo
@@ -478,7 +480,7 @@ sortingsettings:
       Do not confuse with 
     url:
       text: "`--noreftopo` <i class='fa-solid fa-triangle-exclamation'></i>"
-      link: "/docs/documentation/keywords.html#noreftopo"
+      link: "/page/documentation/keywords.html#noreftopo"
 
 
 pcasettings:
@@ -497,7 +499,7 @@ pcasettings:
       See also
     url:
       text: Example X.
-      link: /docs/examples/
+      link: /page/examples/
 
   - cmd: --pccap <INT>
     descript: >
@@ -515,6 +517,131 @@ pcasettings:
       For the format of `<atomlist>` see
     url:
        text: this page.
-       link: /docs/documentation/coords.html#atomlists
+       link: /page/documentation/coords.html#atomlists
+
+
+
+
+standalonetools:
+
+  - cmd: --zsort
+    type: ZSORT z-matrix sorting
+    descript: >
+      The atom order of the given input file is sorted in order to yield a more 
+      consistent z-matrix, *i.e.*, atoms are grouped together according to the 
+      molecular structure (e.g. methyl groups).
+
+  - cmd: --mdopt <FILE>
+    type: MDOPT ensemble optimization
+    descript: >
+      Optimize each point on a given trajectory or ensemble file `<FILE>` with GFN*n*–xTB.
+
+  - cmd: --screen <FILE>
+    type: SCREEN ensemble optimization
+    descript: >
+      Optimize each point on a given trajectory or ensemble file `<FILE>` with GFNn–xTB.
+      The resulting ensemble is sorted using the CREGEN routine.
+
+  - cmd: --rrhoav <FILE>
+    type: Thermostatistical frequency contribution for ensembles
+    descript: >
+      Calculate the $$\overline{S}$$<sub>msRRHO</sub> contribution for a given ensemble
+      (similar to the `--mdopt` and `--screen` functions). The number of structures taken
+      from the ensemble for this calculation is determined dynamically based on their 
+      respective Boltzmann population. The calculation can be modified similar to the 
+      entropy mode, see
+    url:
+      test: entropy mode settings. <i class="fa-solid fa-circle-up"></i>
+      link: /page/documentation/keywords.html#entropy-mode-settings
+
+  - comm: "`--rmsd <FILE1> <FILE2>`, `--rmsdheavy <FILE1> <FILE2>`" 
+    type: Atomic RMSD calculation
+    descript: >
+      Calculate the RMSD or heavy atom RMSD between two given structures. 
+      Input format of the two structures can be any of the formats that can 
+      be read by CREST, output will always be the RMSD in Ångström.
+
+  - cmd: --testtopo <FILE>
+    type: Topology information
+    descript: >
+      Calculate the topology (neighbour lists) for a given input structure and 
+      print info (coordination numbers, neighbors for each atom) to screen.
+
+  - cmd: --thermo <FILE>
+    anchor: thermo
+    type: Thermostatistical calculations from frequencies
+    descript: >
+      Calculate thermo data for given structure. Also requires vibrational frequencies
+      in the Turbomole format, saved as file called `vibspectrum`. The calculation can
+      be modified by `--fscal`   and `--sthr`, see
+    url:
+      test: entropy mode settings. <i class="fa-solid fa-circle-up"></i>
+      link: /page/documentation/keywords.html#entropy-mode-settings
 
+  - comm: "`--for <FILE>`, `--forall <FILE>`" 
+    type: Ensemble processing
+    descript: >
+      Calculate some things for the ensemble specified as `<FILE>`. 
+      This option is to be used with the `--prop ...` option 
+      ([see above <i class="fa-solid fa-circle-up"></i>](#propopt)).
+      Also applicable for a standalone use of the 
+    url:
+      text: '`--cluster` option. <i class="fa-solid fa-circle-up"></i>'
+      link: /page/documentation/keywords.html#pca-clustering-options
+
+  - cmd: --splitfile <FILE> [from] [to]
+    type: Ensemble file splitting
+    descript: >
+      Split an ensemble from `<FILE>` into separate directories for each structure. 
+      `[from]` and `[to]` can optionally be used to select specific structures from 
+      the file or a range of structures. The new directories are collected in a 
+      directory called SPLIT.
+
+
+constrainment:
+
+  - cmd: --cinp <FILE>
+    descript: >
+      Specify a `<FILE>` with additional constraints in the xTB syntax.
+
+  - cmd: --constrain <atom list>
+    descript: >
+      Set up an example file in which the atoms in `<atom list>` shall be constrained. 
+      The file will be called `.xcontrol.sample`. No calculations will be performed and
+      the run is aborted after this sample is written. The written file can be read 
+      with the `--cinp` option. See
+
+  - cmd: --cbonds [REAL]
+    descript: >
+      Set up a constraint on all bonds (as detected in the input coordinates topology),
+      where `[REAL]` optionally can be used to set the force constant 
+      (default value 0.02 *E*<sub>h</sub>).
+
+  - cmd: --nocbonds
+    descript: >
+      Turn off `-cbonds` (mainly for GFN-FF)
+
+  - cmd: --cmetal [REAL]
+    descript: >
+      Set up a constraint on all M-X bonds (as detected in the input coordinates, 
+      M = transition metal atom), where `[REAL]` optionally can be used to set the 
+      force constant (default value 0.02 *E*<sub>h</sub>)
+
+  - cmd: --cheavy [REAL]
+    descript: >
+      Set up a constraint on all heavy atom bonds (*i.e.*, X-H bonds will be 
+      not constrained), where `[REAL]` optionally can be used to set the 
+      force constant (default value 0.02 *E*<sub>h</sub>)
+
+  - cmd: --clight [REAL]
+    descript: >
+      Set up a constraint on all X-H bonds (as detected in the input 
+      coordinates), where `[REAL]` optionally can be used to set the
+      force constant (default value 0.02 *E*<sub>h</sub>)
+
+  - cmd: --fc <REAL>
+    descript: >
+      Specify a force constant for the applied constraints (default
+      value 0.02 *E*<sub>h</sub>). 
+      Note: Only one force constant is applied for all constraints!