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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).

, '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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README.md

Python Examples

This software was written in 2016/17 by Michael P. Allen m.p.allen@warwick.ac.uk/m.p.allen@bristol.ac.uk and Dominic J. Tildesley d.tildesley7@gmail.com ("the authors"), to accompany the book Computer Simulation of Liquids, second edition, 2017 ("the text"), published by Oxford University Press ("the publishers").

Licence

Creative Commons CC0 Public Domain Dedication. To the extent possible under law, the authors have dedicated all copyright and related and neighboring rights to this software to the PUBLIC domain worldwide. This software is distributed without any warranty. You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

Disclaimer

The authors and publishers make no warranties about the software, and disclaim liability for all uses of the software, to the fullest extent permitted by applicable law. The authors and publishers do not recommend use of this software for any purpose. It is made freely available, solely to clarify points made in the text. When using or citing the software, you should not imply endorsement by the authors or publishers.

Language

The programs contain some explanatory comments, and are written in Python3 using the NumPy and SciPy libraries. The User Guide contains some comments on the Python language, some notes to assist in running the programs, and some typical results. The Python versions do not require building, they are simply run through the Python interpreter. They have been tested with Python 3.14.3 and NumPy 2.4.3 (and previously, Python versions back to 3.6.0, with compatible versions of NumPy v1 and v2).