fix: truncate time in plumed output to 1 fs (#484)

and update examples from tests fix: copy plumed.dat input file to setup --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
graeter-group · Sep 12, 2024 · b73104a · b73104a
1 parent 505c823
commit b73104a
Show file tree

Hide file tree

Showing 59 changed files with 5,896 additions and 845 deletions.
diff --git a/_reference/parsing.qmd b/_reference/parsing.qmd
@@ -58,6 +58,13 @@ Used for topology like files that use ';' for comments.
 
 Read a distances.dat plumed output file.
 
+A typical file looks like this:
+
+```
+#! FIELDS time d0 d1 d2 d3 d4 d5 d6  ...
+0.000000 0.153211 0.157662 0.139923 ...
+```
+
 ### read_edissoc { #kimmdy.parsing.read_edissoc }
 
 `parsing.read_edissoc(path)`

diff --git a/docs/_reference/analysis.html b/docs/_reference/analysis.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/cmd.html b/docs/_reference/cmd.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/config.html b/docs/_reference/config.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/constants.html b/docs/_reference/constants.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/coordinates.html b/docs/_reference/coordinates.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/dummyreaction.reaction.DummyReaction.html b/docs/_reference/dummyreaction.reaction.DummyReaction.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/hat_naive.reaction.NaiveHAT.html b/docs/_reference/hat_naive.reaction.NaiveHAT.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/homolysis.reaction.Homolysis.html b/docs/_reference/homolysis.reaction.Homolysis.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/index.html b/docs/_reference/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/kmc.html b/docs/_reference/kmc.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/parsing.TopologyDict.html b/docs/_reference/parsing.TopologyDict.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/parsing.html b/docs/_reference/parsing.html
diff --git a/docs/_reference/plugins.html b/docs/_reference/plugins.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/recipe.html b/docs/_reference/recipe.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/runmanager.html b/docs/_reference/runmanager.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/schema.html b/docs/_reference/schema.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/tasks.html b/docs/_reference/tasks.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/tools.html b/docs/_reference/tools.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/topology.atomic.html b/docs/_reference/topology.atomic.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/topology.ff.html b/docs/_reference/topology.ff.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/topology.topology.html b/docs/_reference/topology.topology.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/topology.utils.html b/docs/_reference/topology.utils.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/_reference/utils.html b/docs/_reference/utils.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/explanation/components.html b/docs/guide/explanation/components.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -586,15 +586,15 @@ <h1 class="title">Explanations</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1726061984173" data-listing-reading-time-sort="20" data-listing-word-count-sort="3838" data-listing-title-sort="Components of KIMMDY" data-listing-filename-sort="components.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="20" data-listing-word-count-sort="3838" data-listing-title-sort="Components of KIMMDY" data-listing-filename-sort="components.qmd">
 <td>
 <a href="../../guide/explanation/components.html" class="title listing-title">Components of KIMMDY</a>
 </td>
 <td>
 <span class="listing-author">Kai Riedmiller</span>
 </td>
 </tr>
-<tr data-index="1" data-listing-file-modified-sort="1726061984173" data-listing-reading-time-sort="1" data-listing-word-count-sort="188" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
+<tr data-index="1" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="1" data-listing-word-count-sort="188" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
 <td>
 <a href="../../guide/explanation/topology.html" class="title listing-title">Visualize Topologies</a>
 </td>

diff --git a/docs/guide/explanation/topology.html b/docs/guide/explanation/topology.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/how-to/analyze.html b/docs/guide/how-to/analyze.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -1141,7 +1141,7 @@ <h2 class="anchored" data-anchor-id="runtimes">Runtimes</h2>
   </div>
 </nav>
 </div> <!-- /content -->
-<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/graeter-group/kimmdy/edit/main/guide/how-to/analyze.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/graeter-group/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer><script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom","openEffect":"zoom"});
+<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/graeter-group/kimmdy/edit/main/guide/how-to/analyze.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/graeter-group/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer><script>var lightboxQuarto = GLightbox({"loop":false,"closeEffect":"zoom","openEffect":"zoom","selector":".lightbox","descPosition":"bottom"});
 (function() {
   let previousOnload = window.onload;
   window.onload = () => {

diff --git a/docs/guide/how-to/contribute.html b/docs/guide/how-to/contribute.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/how-to/examples.html b/docs/guide/how-to/examples.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/how-to/hcp.html b/docs/guide/how-to/hcp.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -586,47 +586,47 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1726061984177" data-listing-reading-time-sort="2" data-listing-word-count-sort="390" data-listing-title-sort="Analyze a KIMMDY run" data-listing-filename-sort="analyze.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="2" data-listing-word-count-sort="390" data-listing-title-sort="Analyze a KIMMDY run" data-listing-filename-sort="analyze.qmd">
 <td>
 <a href="../../guide/how-to/analyze.html" class="title listing-title">Analyze a KIMMDY run</a>
 </td>
 <td>
 <span class="listing-author">Kai Riedmiller</span>
 </td>
 </tr>
-<tr data-index="1" data-listing-file-modified-sort="1726061984177" data-listing-reading-time-sort="2" data-listing-word-count-sort="266" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
+<tr data-index="1" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="2" data-listing-word-count-sort="266" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
 <td>
 <a href="../../guide/how-to/contribute.html" class="title listing-title">Contribute</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="2" data-listing-file-modified-sort="1726061984177" data-listing-reading-time-sort="1" data-listing-word-count-sort="105" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
+<tr data-index="2" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="1" data-listing-word-count-sort="105" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
 <td>
 <a href="../../guide/how-to/examples.html" class="title listing-title">Examples</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="3" data-listing-file-modified-sort="1726061984177" data-listing-reading-time-sort="1" data-listing-word-count-sort="87" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
+<tr data-index="3" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="1" data-listing-word-count-sort="87" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
 <td>
 <a href="../../guide/how-to/hcp.html" class="title listing-title">High Performance Computing</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="4" data-listing-file-modified-sort="1726061984177" data-listing-reading-time-sort="1" data-listing-word-count-sort="152" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
+<tr data-index="4" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="1" data-listing-word-count-sort="152" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
 <td>
 <a href="../../guide/how-to/install-ml-plugins.html" class="title listing-title">Install Machine Learning Plugins</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="5" data-listing-file-modified-sort="1726061984177" data-listing-reading-time-sort="1" data-listing-word-count-sort="165" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
+<tr data-index="5" data-listing-file-modified-sort="1724675456000" data-listing-reading-time-sort="1" data-listing-word-count-sort="165" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
 <td>
 <a href="../../guide/how-to/reaction_only.html" class="title listing-title">Reaction only</a>
 </td>

diff --git a/docs/guide/how-to/install-ml-plugins.html b/docs/guide/how-to/install-ml-plugins.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/how-to/reaction_only.html b/docs/guide/how-to/reaction_only.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/docs/guide/references/cmd_ref.html b/docs/guide/references/cmd_ref.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.53">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">