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The Amber plugin for AiiDA aims to enable the capture and sharing of the full provenance of data when parameterising and running molecular dynamics simulations. This plugin is being developed as part of the Physical Sciences Data Infrastructure programme to improve the practices around data within the Physical Sciences remit area within the UK.

This package is currently a work in progress and we will be adding much more complete functionality to this plugin in the coming months.

The design pattern we are aiming for is to simply allow researchers to capture the full data provenance for their simulations by only switching on an AiiDA conda environment, along with modifying your command lines very slightly.

This means that you should gain access to powerful FAIR data practices without wholesale cultural or usage pattern shifts in your daily work.

Documentation

See here for documentation for users and developers.

License

MIT

Contact

About

An Amber plugin for AiiDA

aiida-amber.readthedocs.io

Topics

data-sciencedata-tools

Resources

Readme
MIT license

Contributing

Contributing
Activity
Custom properties

Stars

2 stars

Watchers

1 watching

Forks

3 forks
Report repository

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Used by

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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aiida-amber
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BuildBuild Status
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The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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aiida-amber
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BuildBuild Status
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PyPIPyPI - StatusPyPI versionPyPI - Python VersionPyPI - Total DownloadsPyPI - Monthly Downloads
AnacondaAnaconda.orgLast UpdatedPlatformsLicenseDownloads
QualityCoverage Status
The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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aiida-amber
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BuildBuild Status
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PyPIPyPI - StatusPyPI versionPyPI - Python VersionPyPI - Total DownloadsPyPI - Monthly Downloads
AnacondaAnaconda.orgLast UpdatedPlatformsLicenseDownloads
QualityCoverage Status
The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
Report repository
Releases
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Used by
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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aiida-amber
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BuildBuild Status
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PyPIPyPI - StatusPyPI versionPyPI - Python VersionPyPI - Total DownloadsPyPI - Monthly Downloads
AnacondaAnaconda.orgLast UpdatedPlatformsLicenseDownloads
QualityCoverage Status
The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
Report repository
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Used by
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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aiida-amber
CategoryBadges
BuildBuild Status
DocumentationDocs status
CitationDOI
PyPIPyPI - StatusPyPI versionPyPI - Python VersionPyPI - Total DownloadsPyPI - Monthly Downloads
AnacondaAnaconda.orgLast UpdatedPlatformsLicenseDownloads
QualityCoverage Status
The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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PyPIPyPI - StatusPyPI versionPyPI - Python VersionPyPI - Total DownloadsPyPI - Monthly Downloads
AnacondaAnaconda.orgLast UpdatedPlatformsLicenseDownloads
QualityCoverage Status
The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
Report repository
Releases
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Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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aiida-amber
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BuildBuild Status
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PyPIPyPI - StatusPyPI versionPyPI - Python VersionPyPI - Total DownloadsPyPI - Monthly Downloads
AnacondaAnaconda.orgLast UpdatedPlatformsLicenseDownloads
QualityCoverage Status
The Amber plugin for AiiDA aims to enable the capture and sharing of the full
provenance of data when parameterising and running molecular dynamics
simulations. This plugin is being developed as part of the Physical Sciences
Data Infrastructure programme to improve the practices around data within the
Physical Sciences remit area within the UK.
This package is currently a work in progress and we will be adding much more
complete functionality to this plugin in the coming months.
The design pattern we are aiming for is to simply allow researchers to capture
the full data provenance for their simulations by only switching on an AiiDA
conda environment, along with modifying your command lines very slightly.
This means that you should gain access to powerful FAIR data practices without
wholesale cultural or usage pattern shifts in your daily work.
Documentation
See here for documentation for users and developers.
License
MIT
Contact
About
An Amber plugin for AiiDA
aiida-amber.readthedocs.io
Topics
data-sciencedata-tools
Resources
Readme
MIT license
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
1 watching
Forks
3 forks
Report repository
Releases
Packages
Used by
Contributors
Languages