diff --git a/docs/.DS_Store b/docs/.DS_Store new file mode 100644 index 0000000..d50adf6 Binary files /dev/null and b/docs/.DS_Store differ diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle index bf201cd..1545d0f 100644 Binary files a/docs/build/doctrees/environment.pickle and b/docs/build/doctrees/environment.pickle differ diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree index 92f56cc..dfb2e3f 100644 Binary files a/docs/build/doctrees/index.doctree and b/docs/build/doctrees/index.doctree differ diff --git a/docs/build/doctrees/modules.doctree b/docs/build/doctrees/modules.doctree index 614127a..6c93083 100644 Binary files a/docs/build/doctrees/modules.doctree and b/docs/build/doctrees/modules.doctree differ diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo index eae5db8..42691c2 100644 --- a/docs/build/html/.buildinfo +++ b/docs/build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: af1005e6b5cb943e75ffafa7a50014fd +config: 3e24725cde270cd0e889a75e43e9746b tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html index 5e00664..eba95e4 100644 --- a/docs/build/html/_modules/index.html +++ b/docs/build/html/_modules/index.html @@ -4,13 +4,21 @@ - Overview: module code — pylj 0.0.6a documentation - + @@ -23,7 +31,8 @@ - + +
@@ -73,14 +82,12 @@

Related Topics

@@ -91,7 +98,7 @@

Quick search

©2018, Andrew R. McCluskey. | - Powered by Sphinx 1.7.4 + Powered by Sphinx 1.6.3 & Alabaster 0.7.10 diff --git a/docs/build/html/_modules/pylj/examples.html b/docs/build/html/_modules/pylj/examples.html index 12aeff0..f3276a5 100644 --- a/docs/build/html/_modules/pylj/examples.html +++ b/docs/build/html/_modules/pylj/examples.html @@ -4,13 +4,21 @@ - pylj.examples — pylj 0.0.6a documentation - + @@ -23,7 +31,8 @@ - + +
@@ -70,8 +79,8 @@

Source code for pylj.examples

         system.step += 1
         if system.step % sample_frequency == 0:
             sample_system.update(system)
-    return system
-
+ return system
+
[docs]def md_nve(number_of_particles, temperature, box_length, number_of_steps, sample_frequency): """This is an example NVE (constant number of particles, system volume and system energy) simulation. @@ -107,8 +116,36 @@

Source code for pylj.examples

         system.step += 1
         if system.step % sample_frequency == 0:
             sample_system.update(system)
-    return system
-
+ return system + + +
[docs]def periodic_boundary(number_of_steps, temperature): + """This is a piece of exemplary code to show a single particle traveling across the periodic boundary. + + Parameters + ---------- + number_of_steps: int + Number of step in simulation. + temperature: float + Temperature of simulation. + """ + number_of_particles = 1 + sample_freq = 10 + system = md.initialise(number_of_particles, temperature, 50, 'square') + sampling = sample.JustCell(system) + system.time = 0 + for i in range(0, number_of_steps): + system.particles, system.distances, system.forces = comp.compute_forces(system.particles, + system.distances, + system.forces, system.box_length) + system.particles = md.velocity_verlet(system.particles, system.timestep_length, system.box_length) + system = md.sample(system.particles, system.box_length, system.initial_particles, system) + system.particles = comp.heat_bath(system.particles, system.temperature_sample, temperature) + system.time += system.timestep_length + system.step += 1 + if system.step % sample_freq == 0: + sampling.update(system)
+ @@ -146,14 +183,12 @@

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@@ -164,7 +199,7 @@

Quick search

©2018, Andrew R. McCluskey. | - Powered by Sphinx 1.7.4 + Powered by Sphinx 1.6.3 & Alabaster 0.7.10 diff --git a/docs/build/html/_modules/pylj/md.html b/docs/build/html/_modules/pylj/md.html index 37b018d..c7e2056 100644 --- a/docs/build/html/_modules/pylj/md.html +++ b/docs/build/html/_modules/pylj/md.html @@ -4,13 +4,21 @@ - pylj.md — pylj 0.0.6a documentation - + @@ -23,7 +31,8 @@ - + +
@@ -185,7 +194,6 @@

Source code for pylj.md

     velocities[0] += 0.5 * accelerations[0] * timestep_length
     velocities[1] += 0.5 * accelerations[1] * timestep_length
     return [velocities[0], velocities[1]]
-
@@ -224,14 +232,12 @@

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@@ -242,7 +248,7 @@

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©2018, Andrew R. McCluskey. | - Powered by Sphinx 1.7.4 + Powered by Sphinx 1.6.3 & Alabaster 0.7.10 diff --git a/docs/build/html/_modules/pylj/sample.html b/docs/build/html/_modules/pylj/sample.html index d6fa173..367b4c7 100644 --- a/docs/build/html/_modules/pylj/sample.html +++ b/docs/build/html/_modules/pylj/sample.html @@ -4,13 +4,21 @@ - pylj.sample — pylj 0.0.6a documentation - + @@ -23,7 +31,8 @@ - + +
@@ -92,8 +101,8 @@

Source code for pylj.sample

         line = self.ax[1, 1].lines[0]
         line.set_ydata(iq)
         line.set_xdata(x)
-        self.ax[1, 1].set_ylim([np.amin(iq) - np.amax(iq) * 0.05, np.amax(iq) + np.amax(iq) * 0.05])
-        self.ax[1, 1].set_xlim([np.amin(x), np.amax(x)])
+ self.ax[1, 1].set_ylim([0, np.amax(iq) + np.amax(iq) * 0.05]) + self.ax[1, 1].set_xlim([0, np.amax(x)])
[docs]class Interactions(object): @@ -110,9 +119,9 @@

Source code for pylj.sample

         fig, ax = environment(4)
 
         setup_cellview(ax[0, 0], system)
-        setup_forceview(ax[0, 1])
+        setup_forceview(ax[1, 1])
         setup_pressureview(ax[1, 0])
-        setup_tempview(ax[1, 1])
+        setup_tempview(ax[0, 1])
 
         plt.tight_layout()
         self.ax = ax
@@ -128,8 +137,8 @@ 
Source code for pylj.sample
             The whole system information.
         """
         update_cellview(self.ax[0, 0], system)
-        update_forceview(self.ax[0, 1], system)
-        update_tempview(self.ax[1, 1], system)
+        update_forceview(self.ax[1, 1], system)
+        update_tempview(self.ax[0, 1], system)
         update_pressureview(self.ax[1, 0], system)
 
         self.fig.canvas.draw()
@@ -232,7 +241,6 @@

Source code for pylj.sample

         The axes related to each of the panes. For panes=1 this is a single object, for panes=2 it is a 1-D array and
         for panes=4 it is a 2-D array.
     """
-    fig, ax = plt.subplot()
     if panes == 1:
         fig, ax = plt.subplots(figsize=(4, 4))
     elif panes == 2:
@@ -305,7 +313,7 @@ 
Source code for pylj.sample
     ax.plot([0], color='#34a5daff')
     ax.set_yticks([])
     ax.set_ylabel('log(I[q])', fontsize=16)
-    ax.set_xlabel('log(q)/Å$^{-1}$', fontsize=16)

+    ax.set_xlabel('q/Å$^{-1}$', fontsize=16)
[docs]def setup_pressureview(ax): @@ -392,18 +400,21 @@

Source code for pylj.sample

     q: array_like
         The scattering profile's q for each timestep, to later be averaged.
     """
-    hist, bin_edges = np.histogram(system.distances, bins=np.linspace(0, system.box_length/2 + 0.5, 100))
-    gr = hist / (system.number_of_particles * (system.number_of_particles / system.box_length ** 2) * np.pi *
-                 (bin_edges[:-1] + 0.5 / 2.) * 0.5)
-    x2 = np.log(np.fft.rfftfreq(len(gr))[5:])
-    y2 = np.log(np.fft.rfft(gr)[5:])
+    qw = np.linspace(2 * np.pi /(system.box_length/2)*4, system.box_length/10, 100)
+    i = np.zeros_like(qw)
+    for j in range(0, len(qw)):
+        i[j] = np.sum(3.644 * (np.sin(qw[j] * system.distances))/(qw[j] * system.distances))
+        if i[j] < 0:
+            i[j] = 0
+    x2 = qw
+    y2 = i
     average_diff.append(y2)
     q.append(x2)
     line1 = ax.lines[0]
     line1.set_xdata(x2)
     line1.set_ydata(y2)
-    ax.set_ylim([np.amin(y2) - np.amax(y2) * 0.05, np.amax(y2) + np.amax(y2) * 0.05])
-    ax.set_xlim([np.amin(x2), np.amax(x2)])
+ ax.set_ylim([0, np.amax(y2) + np.amax(y2) * 0.05]) + ax.set_xlim(0, np.amax(x2))
[docs]def update_forceview(ax, system): @@ -453,11 +464,11 @@

Source code for pylj.sample

         The whole system information.
     """
     line = ax.lines[0]
-    line.set_ydata(system.pressure_sample * 1e10)
+    line.set_ydata(system.pressure_sample)
     line.set_xdata(np.arange(0, system.step) * system.timestep_length)
     ax.set_xlim(0, system.step * system.timestep_length)
-    ax.set_ylim(np.amin(system.pressure_sample * 1e10) - np.amax(system.pressure_sample * 1e10) * 0.05,
-                np.amax(system.pressure_sample * 1e10) + np.amax(system.pressure_sample * 1e10) * 0.05)
+ ax.set_ylim(np.amin(system.pressure_sample) - np.amax(system.pressure_sample) * 0.05, + np.amax(system.pressure_sample) + np.amax(system.pressure_sample) * 0.05)
[docs]def setup_msdview(ax): @@ -527,14 +538,12 @@

Related Topics

@@ -545,7 +554,7 @@

Quick search

©2018, Andrew R. McCluskey. | - Powered by Sphinx 1.7.4 + Powered by Sphinx 1.6.3 & Alabaster 0.7.10 diff --git a/docs/build/html/_modules/pylj/util.html b/docs/build/html/_modules/pylj/util.html index 7f87513..da75162 100644 --- a/docs/build/html/_modules/pylj/util.html +++ b/docs/build/html/_modules/pylj/util.html @@ -4,13 +4,21 @@ - pylj.util — pylj 0.0.6a documentation - + @@ -23,7 +31,8 @@ - + +
@@ -234,14 +243,12 @@

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@@ -252,7 +259,7 @@

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©2018, Andrew R. McCluskey. | - Powered by Sphinx 1.7.4 + Powered by Sphinx 1.6.3 & Alabaster 0.7.10 diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css index 19ced10..6df76b0 100644 --- a/docs/build/html/_static/basic.css +++ b/docs/build/html/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -82,21 +82,9 @@ div.sphinxsidebar input { } div.sphinxsidebar #searchbox input[type="text"] { - float: left; - width: 80%; - padding: 0.25em; - box-sizing: border-box; -} - -div.sphinxsidebar #searchbox input[type="submit"] { - float: left; - width: 20%; - border-left: none; - padding: 0.25em; - box-sizing: border-box; + width: 170px; } - img { border: 0; max-width: 100%; @@ -211,11 +199,6 @@ table.modindextable td { /* -- general body styles --------------------------------------------------- */ -div.body { - min-width: 450px; - max-width: 800px; -} - div.body p, div.body dd, div.body li, div.body blockquote { -moz-hyphens: auto; -ms-hyphens: auto; @@ -349,11 +332,6 @@ table.docutils { border-collapse: collapse; } -table.align-center { - margin-left: auto; - margin-right: auto; -} - table caption span.caption-number { font-style: italic; } @@ -467,14 +445,10 @@ dd { margin-left: 30px; } -dt:target, span.highlighted { +dt:target, .highlighted { background-color: #fbe54e; } -rect.highlighted { - fill: #fbe54e; -} - dl.glossary dt { font-weight: bold; font-size: 1.1em; diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js index d892892..5654977 100644 --- a/docs/build/html/_static/doctools.js +++ b/docs/build/html/_static/doctools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for all documentation. * - * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -45,7 +45,7 @@ jQuery.urlencode = encodeURIComponent; * it will always return arrays of strings for the value parts. */ jQuery.getQueryParameters = function(s) { - if (typeof s === 'undefined') + if (typeof s == 'undefined') s = document.location.search; var parts = s.substr(s.indexOf('?') + 1).split('&'); var result = {}; @@ -66,55 +66,29 @@ jQuery.getQueryParameters = function(s) { * span elements with the given class name. */ jQuery.fn.highlightText = function(text, className) { - function highlight(node, addItems) { - if (node.nodeType === 3) { + function highlight(node) { + if (node.nodeType == 3) { var val = node.nodeValue; var pos = val.toLowerCase().indexOf(text); - if (pos >= 0 && - !jQuery(node.parentNode).hasClass(className) && - !jQuery(node.parentNode).hasClass("nohighlight")) { - var span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } + if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) { + var span = document.createElement("span"); + span.className = className; span.appendChild(document.createTextNode(val.substr(pos, text.length))); node.parentNode.insertBefore(span, node.parentNode.insertBefore( document.createTextNode(val.substr(pos + text.length)), node.nextSibling)); node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var bbox = span.getBBox(); - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - var parentOfText = node.parentNode.parentNode; - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } } } else if (!jQuery(node).is("button, select, textarea")) { jQuery.each(node.childNodes, function() { - highlight(this, addItems); + highlight(this); }); } } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); + return this.each(function() { + highlight(this); }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; }; /* @@ -157,21 +131,21 @@ var Documentation = { * i18n support */ TRANSLATIONS : {}, - PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; }, + PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; }, LOCALE : 'unknown', // gettext and ngettext don't access this so that the functions // can safely bound to a different name (_ = Documentation.gettext) gettext : function(string) { var translated = Documentation.TRANSLATIONS[string]; - if (typeof translated === 'undefined') + if (typeof translated == 'undefined') return string; - return (typeof translated === 'string') ? translated : translated[0]; + return (typeof translated == 'string') ? translated : translated[0]; }, ngettext : function(singular, plural, n) { var translated = Documentation.TRANSLATIONS[singular]; - if (typeof translated === 'undefined') + if (typeof translated == 'undefined') return (n == 1) ? singular : plural; return translated[Documentation.PLURALEXPR(n)]; }, @@ -206,7 +180,7 @@ var Documentation = { * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075 */ fixFirefoxAnchorBug : function() { - if (document.location.hash && $.browser.mozilla) + if (document.location.hash) window.setTimeout(function() { document.location.href += ''; }, 10); @@ -242,7 +216,7 @@ var Documentation = { var src = $(this).attr('src'); var idnum = $(this).attr('id').substr(7); $('tr.cg-' + idnum).toggle(); - if (src.substr(-9) === 'minus.png') + if (src.substr(-9) == 'minus.png') $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); else $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); @@ -274,7 +248,7 @@ var Documentation = { var path = document.location.pathname; var parts = path.split(/\//); $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { - if (this === '..') + if (this == '..') parts.pop(); }); var url = parts.join('/'); diff --git a/docs/build/html/_static/jquery.js b/docs/build/html/_static/jquery.js index 644d35e..f6a6a99 100644 --- a/docs/build/html/_static/jquery.js +++ b/docs/build/html/_static/jquery.js @@ -1,4 +1,4 @@ -/*! jQuery v3.2.1 | (c) JS Foundation and other contributors | jquery.org/license */ -!function(a,b){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){"use strict";var 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Generally these are functions required by pylj which involve a pair-wise comparison of particles. These are written in C++, the source of which can be found in the src/comp.cpp_ file. + +.. _comp.cpp: https://github.com/arm61/pylj/blob/master/src/comp.cpp + .. automodule:: pylj.comp :members: :undoc-members: diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 4fa2631..5c5a56d 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -1,6 +1,8 @@ pylj\.examples ============== +Some examples of uses of pylj. + .. automodule:: pylj.examples :members: :undoc-members: diff --git a/docs/source/md.rst b/docs/source/md.rst index 7c20d71..a8de369 100644 --- a/docs/source/md.rst +++ b/docs/source/md.rst @@ -1,6 +1,8 @@ pylj\.md ======== +Functions related to the molecular dynamics components of pylj. + .. automodule:: pylj.md :members: :undoc-members: diff --git a/docs/source/sample.rst b/docs/source/sample.rst index d9b472a..8f6d9e8 100644 --- a/docs/source/sample.rst +++ b/docs/source/sample.rst @@ -1,6 +1,10 @@ pylj\.sample ============ +This module is dedicated visualisation of the pylj output. More details of how to implement custom visualisation see :doc:`visualisation`. + +.. _here: + .. automodule:: pylj.sample :members: :undoc-members: diff --git a/docs/source/visualisation.rst b/docs/source/visualisation.rst index 3aae858..1d968c5 100644 --- a/docs/source/visualisation.rst +++ b/docs/source/visualisation.rst @@ -11,9 +11,7 @@ pylj comes with four different methods for visualising the simulation that is ta - Scattering - Interactions -Full information about the existing classes can be found in the sample_ class documentation. - -.. _sample: /en/latest/sample.html +Full information about the existing classes can be found in the :doc:`sample` class documentation. building your own class -----------------------