Documentation update with CREST 3.0 info

_data/keywords.yml

@@ -54,29 +54,49 @@ general:
 
   - cmd: "--input <INPUTFILE>"
     descript: >
-      <span class='label label-green'>CREST 3.0 preview</span>
+      <span class='label label-green'>CREST 3.0</span>
       Specify a CREST input file from which the calculation settings are read.
       For more information see the
       [**Input File Documentation** <i class='fa-solid fa-book'></i>](./inputfiles.html
       'Documentation / Input File Documentation').
 
-
+  - cmd: "--legacy"
+    descript: >
+      <span class='label label-green'>CREST 3.0</span>
+      Attempt (where possible) to switch the program behavior back to previous
+      program versions (<3.0).
 
 
 runtype:
 
+  - comm: "`--sp`"
+    type: Singlepoint energy and gradient evaluation
+    descript: >
+      <span class='label label-green'>CREST 3.0</span>
+      Standalone energy and gradient evaluation of the given input structure.
+
+
+  - comm: "`--opt [level]`,<br> `--ancopt [level]`"
+    type: Geometry optimization
+    descript: >
+      <span class='label label-green'>CREST 3.0</span>
+      Standalone geometry optimization of the given input structure via the ANCOPT algorithm.
+      The optional `[level]` argument can be used to select predefined convergence criteria
+      (see Table IV in [https://doi.org/10.1063/5.0197592](https://doi.org/10.1063/5.0197592)).
+
   - cmd: --v1 
     type: MF-MD-GC sampling (outdated) 
     descript: >
       First generation of the GFN*n*-xTB driven conformational search algorithm,
       consisting out of mode following, molecular dynamics sampling and genetic 
-      structure crossing. This workflow is deprecated.
+      structure crossing. This workflow is **deprecated**.
     
   - cmd: --v2 
     type: MTD-GC sampling (outdated) 
     descript: >
       Second generation of the GFN*n*-xTB driven conformational search algorithm,
-      consisting out of a metadynamics approach and genetic structure crossing.
+      consisting out of a metadynamics approach and genetic structure crossing. 
+      This workflow is **deprecated**.
     
   - comm: "`--v2i`, `--v3`"
     type: iMTD-GC sampling
@@ -144,6 +164,7 @@ runtype:
   - cmd: --msreact 
     type: MSREACT tool 
     descript: >
+      <span class='label label-green'>CREST 3.0</span>
       Use the mass spectral fragment generator. 
       MSREACT has several individual runtypes. See
     url:
@@ -201,12 +222,13 @@ leveloftheory:
     
   - subheader: <br>**Geometry optimization**
 
-  - cmd: --opt <LEVEL> 
+  - cmd: --optlev <LEVEL> 
     descript: >
-      Set the optimization accuracy for GFN*n*–xTB optimizations. 
+      Set the optimization accuracy for ANCOPT optimizations. 
       In CREST's multilevel approach, only the *final* geometry optimization 
       is affected by this setting. For available `<LEVEL>` see the 
       [`xtb` documentation](https://xtb-docs.readthedocs.io/en/latest/optimization.html#geometry-optimization). The [default] is `<LEVEL>`=*vtight*.
+       
 
 
 mdsettings:
@@ -370,8 +392,10 @@ confsettings:
     descript: >
       Turn of automatic pre-optimization of the input geometry at the beinning of a run.
 
-
-
+  - comm: "`--wall`,`--wallxl`,`--wallxxl`"
+    descript: >
+      Automatically set up a wall potential (3 different sizes are available) for the
+      calculation, independent of any NCI mode.
 
 entropysettings:
 
@@ -509,10 +533,10 @@ sortingsettings:
       text: "`--noreftopo` <i class='fa-solid fa-triangle-exclamation'></i>"
       link: "/page/documentation/keywords.html#noreftopo"
 
-  - comm: "`--wall`,`--wallxl`,`--wallxxl`"
-    descript: >
-      Automatically set up a wall potential (3 different sizes are available) for the
-      calculation, independent of any NCI mode.
+
+
+
+
 
 
 

_posts/2024-03-21-new-crest-release.md

@@ -0,0 +1,11 @@
+---
+layout: post
+title: "Release of CREST 3.0"
+date: 2024-03-21
+categories: blog
+---
+
+Version 3.0 of the CREST code was released. 
+Read the new publication in the *Journal of Chemical Physics* special issue "Modular and Interoperable Software for Chemical Physics":
+- *CREST — A program for the exploration of low-energy molecular chemical space*, Pracht, P.; Grimme, S.; Bannwarth, C.; Bohle, F.; Ehlert, S.; Feldmann, G.; Gorges, J.; Müller, M.; Neudecker, T.; Plett, C.; Spicher, S.; Steinbach, P.; Wesołowski, P.A.; Zeller, F.; [*J. Chem. Phys.*, **2024**, *160*, 114110. DOI: 10.1063/5.0197592](https://doi.org/10.1063/5.0197592)
+<br>

index.md

@@ -18,8 +18,7 @@ Welcome to the documentation site of {% include tooltip.html tool="CREST" tip=si
 CREST was developed as a utility and driver program for the semiempirical quantum chemistry package [`xtb`{{ site.data.icons.github }}](https://github.com/grimme-lab/xtb).
 The programs name originated as an abbreviation for *Conformer–Rotamer Ensemble Sampling Tool* as it was developed as a program for conformational sampling at the extended tight-binding level GFN-xTB.
 Since then several functionalities have been added to the code.
-In its current state, the program provides a variety of sampling procedures, for example for improved thermochemistry, or solvation.
-Generally, CREST functions as an IO-based scheduler for the `xtb` program and as tool for analyzing structure ensembles.
+In its current state, the program provides a variety of sampling procedures, for example for improved thermochemistry, or explicit solvation.
 {: .text-justify }
 
 This documentation aims to provide a practical [installation guide](./page/installation) and a series of [example applications](./page/examples).
@@ -72,4 +71,10 @@ Quick links to different sections of the documentation can be found below.
 ---
 ## News
 
+{% for post in site.posts %}
+  <h2><a href="{{ site.baseurl }}{{ post.url }}">{{ post.title }}</a></h2>
+  <p>{{ post.excerpt }}</p>
+{% endfor %}
+
+
 {% include twitter.html %}

page/about/literature.md

@@ -24,6 +24,8 @@ This is a collection of various works that focus on CREST and `xtb`.
 
 - **CREST:** Pracht, P.; Bohle, F.; Grimme, S.; *Automated exploration of the low-energy chemical space with fast quantum chemical methods*, *Phys. Chem. Chem. Phys.*, **2020**, *22*, 7169-7192. [DOI: 10.1039/C9CP06869D](https://doi.org/10.1039/C9CP06869D)
 
+- **CREST 3.0:** Pracht, P.; Grimme, S.; Bannwarth, C.; Bohle, F.; Ehlert, S.; Feldmann, G.; Gorges, J.; Müller, M.; Neudecker, T.; Plett, C.; Spicher, S.; Steinbach, P.; Wesołowski, P.A.; Zeller, F.; *CREST — A program for the exploration of low-energy molecular chemical space*, *J. Chem. Phys.*, **2024**, *160*, 114110. [DOI: 10.1063/5.0197592](https://doi.org/10.1063/5.0197592)
+
 - **Conformational Entropy:** Pracht, P.; Grimme, S.; *Calculation of absolute molecular entropies and heat capacities made simple*, *Chem. Sci.*, **2021**, *12*, 6551-6568. [DOI: 10.1039/D1SC00621E](https://doi.org/10.1039/D1SC00621E)
 
 - **Meta-Dynamics Simulations:** Grimme, S.; *Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations*, *J. Chem. Theory Comput.*, **2019**, *15 (5)*, 2847-2862. [DOI: 10.1021/acs.jctc.9b00143](https://doi.org/10.1021/acs.jctc.9b00143)
@@ -34,7 +36,7 @@ This is a collection of various works that focus on CREST and `xtb`.
 
 - **Minimum Energy Crossing Point (MECP) sampling:** Pracht, P.; Bannwarth, C.; *Fast Screening of Minimum Energy Crossing Points with Semiempirical Tight-Binding Methods*, *J. Chem. Theory Comput.*, **2022**, *18 (10)*, 6370-6385. [DOI: 10.1021/acs.jctc.2c00578](https://doi.org/10.1021/acs.jctc.2c00578).
 
-
+- **MC-ONIOM*n*:** Wesołowski, P.A.; Wales, D.J.; Pracht, P.; *Multilevel Framework for Analysis of Protein Folding Involving Disulfide Bond Formation*, *J. Phys. Chem. B*, **2024**, *128*, 3145–3156. [DOI: 10.1021/acs.jpcb.4c00104](https://doi.org/10.1021/acs.jpcb.4c00104)
 
 ---
 

page/about/news.md

@@ -13,4 +13,10 @@ permalink: /page/about/news.html
 
 ---
 
+{% for post in site.posts %}
+  <h2><a href="{{ site.baseurl }}{{ post.url }}">{{ post.title }}</a></h2>
+  <p>{{ post.excerpt }}</p>
+{% endfor %}
+
+
 {% include twitter.html %}

page/documentation/documentation.md

@@ -28,12 +28,15 @@ Usually, either must be present.
 The different command line `[OPTIONS]` can be found in the [**Keyword Documentation** {{site.data.icons.book}}]({{site.baseurl}}/page/documentation/keywords.html).
 {: .text-justify }
 
----
-<span class="label label-green">CREST 3.0 Preview</span>
 
-***Alternatively***, [CREST 3]({{site.baseurl}}/page/releases/release_preview.html) instructions can be defined entriely in a separate input file and passed via
+**As of, [CREST 3.0]({{site.baseurl}}/page/releases/release_current.html) instructions can be defined entriely in a separate input file in the TOML format.**
+The `*.toml` input file can be given as the `[INPUT]` argument or passed explicitly via
 ```bash
 crest --input <INPUTFILE>
 ```
 For more information see the [**Input File Documentation** {{site.data.icons.book}}]({{site.baseurl}}/page/documentation/inputfiles.html) section,
-or [some selected **examples**]({{site.baseurl}}/page/examples/mecp).
+or [some **input examples**]({{site.baseurl}}/page/documentation/inputfiles_examples).
+
+
+{% include note.html content="Command line arguments and options read from the TOML input file are usually compatible. As a rule-of-thumb, command line arguments have a higher parsing priority and will overwrite options from the input file at runtime." %}
+

page/documentation/inputfiles.md

@@ -3,6 +3,7 @@ layout: default
 title: Input File Documentation
 parent: Documentation
 nav_order: 2
+has_children: true
 toc: false
 summary: "A guide to CREST input files (program versions >3.0)."
 permalink: /page/documentation/inputfiles.html
@@ -14,46 +15,53 @@ permalink: /page/documentation/inputfiles.html
 This page contains a guide to CREST input files that can be used with program versions >3.0.
 {: .fs-6 .fw-300 }
 
-<div class="label label-green">CREST 3.0 preview</div>
+<div class="label label-green">CREST 3.0</div>
 
 ---
 
 CREST program instructions via the various [command line arguments](./documentation.html) can become quite lengthy and tedious.
 Therefore, following version 3.0 of CREST, input files will be available.
-Currently, the input files are *loosely* based on the [**TOML format** {{site.data.icons.ext}}](https://toml.io/en/ "https://toml.io") and are parsed using [**TOML-F**](https://github.com/toml-f/toml-f).
+Currently, the input files are based on the [**TOML format** {{site.data.icons.ext}}](https://toml.io/en/ "https://toml.io") and are parsed using [**TOML-F**](https://github.com/toml-f/toml-f).
 {: .text-justify }
 
 CREST input files can be loaded with the `--input` command
 ```bash
-crest --input input.toml
+crest struc.xyz --input input.toml
+```
+or simply be given as the first argument (the file extension `.toml` is mandatory)
+```bash
+crest input.toml
 ```
 where the `input.toml` would look something like this
 
 {% capture infile %}
-input = "struc.xyz"
+# CREST 3 input file
+input = "struc.xyz"   
 runtype="ancopt"
 threads = 9
 
 [calculation]
-type = 1 
-eprint = true
 elog="energies.log"
 
 [[calculation.level]]
-method = "xtb"
-binary = "xtb-6.5.0"
+method = "gfn2"
 uhf = 0
-flags = "--gfn 2 --grad"
-dir = "s0"
+chrg = 0
+
 {% endcapture %}
 {% include codecell.html content=infile style="font-size:12px" %}
 
 As can be seen from this example, the file is hierarchically structured.
 At the top level, things like the input coord file name, runtype, and parallelization are specified.
 The calculation group (defined by `[ ]`) includes some settings about the internal calculation
- settings and printouts, while its level subgroup (defined by `[[ ]]`) provides the actual method and `xtb` binary.
+ settings and printouts, while its level subgroup (defined by `[[ ]]`) provides the actual method and calculation information.
 {: .text-justify }
 
+Some more input file example can be found here:
+
+[Go to Example Input Files <i class="fa-solid fa-book"></i>](inputfiles_examples.html){: .btn .btn-blue }
+
+
 The documentation of blocks and keywords can be found in the following.
 
 {% include note.html content="Command line arguments that can be found in the [**Keyword Documentation** <i class='fa-solid fa-book'></i>](./keywords.html) will ***overwrite*** the     settings read from CREST input files." %}
@@ -67,7 +75,7 @@ The documentation of blocks and keywords can be found in the following.
 {:toc}
 
 
-{% include important.html content="The following lists are incomplete and will be expanded over time until the actual release of CREST 3.0" %}
+{% include important.html content="The following lists not extensive and will be expanded over time." %}
 
 ---
 
@@ -93,12 +101,6 @@ the used programs, and system specific data such as the molecular charge or numb
 {% include kv.html obj=site.data.inputkv.calclevel %}
 
 
----
-### `[[calculation.mecp]]` sub-blocks
-A special type of the `[[calculation.level]]` sub-block that is used *only* for the MECP screening workflow.
-Instead of setting up a single calculations, this block will set up *two* identical calculations that differ only with regards to their multiplicities (`uhf` parameter).
-Input arguments are identical to the [`[[calculation.level]]` options {{site.data.icons.aup}}](#calculationlevel-sub-blocks) but should *not* include any `uhf` or directory specifications.
-
 ---
 ### `[[calculation.constraints]]` sub-blocks
 The `[[calculation.constraints]]` sub-blocks are used to introduce constraints.