diff --git a/LoadCase/Case.py b/LoadCase/Case.py
new file mode 100644
index 0000000000000000000000000000000000000000..bc54c38ee8836e35cf566c4ad3b1249795ad3130
--- /dev/null
+++ b/LoadCase/Case.py
@@ -0,0 +1,21 @@
+from LoadCase import Step
+from LoadCase import Interaction
+from LoadCase import LoadsAndBCs
+from SpindleMesh import generate_mesh
+
+
+kwargs = {'x': 0, 'y': 0, 'index': 0, 'modelname': 'test', 'assembly': 0,
+ 'CentrosomeRadius': 0.06, 'CentrosomeLength': 0.1,
+ 'CentrosomeE': 1500000000.0, 'CentrosomeNu': 0.3, 'ipMTnumber': 6,
+ 'lengthInterval': [2, 6], 'r1': 0.015, 'r2': 0.025,
+ 'ElasticModulus': 1500000000.0, 'PoissonRatio': 0.3,
+ 'spindleLength': 10, 'Nconnectors': 5, 'connectorRadius': 0.005,
+ 'connectorE': 1500000000., 'connectorMu': 0.3, 'aMTnumber': 50,
+ 'aMTlength': 2, 'springStiffness': 10, 'StepName': 'Standard_Buckling',
+ 'CompressiveLoad': 1}
+kwargs, data = Interaction.create_interactions(**kwargs)
+Step.Step(**kwargs)
+LoadsAndBCs.create_load(data, **kwargs)
+LoadsAndBCs.create_bc(**kwargs)
+generate_mesh.standard_mesh(**kwargs)
+
diff --git a/LoadCase/__init__.py b/LoadCase/__init__.py
index bc8bca1b70c6f9df4e0fecfe176b9fccd89a9d87..ded8ee7c3e4a7bb8f41e67db9ecee2e1baf90e42 100644
--- a/LoadCase/__init__.py
+++ b/LoadCase/__init__.py
@@ -1,4 +1,4 @@
"""
-This module contains a set of functions that import and connect standard spindle parts into a
-structural assembly of the whole spindle
+This module contains functions that define interaction between various parts of the mitotic spindle,
+create compressive loads and specify boundary conditions as well as formulate the buckling step analysis.
"""
\ No newline at end of file
diff --git a/Parts/__init__.py b/Parts/__init__.py
index 93dbadf77244ffa1fc7670339572db8814c93dd5..aac01cbed6cfc9e656ba77c1a561ed72ebc7ad86 100644
--- a/Parts/__init__.py
+++ b/Parts/__init__.py
@@ -1,4 +1,4 @@
"""
-The 'standard_parts' module contains functions that generate geometry and mechanical properties
+This module contains functions that generate geometry and mechanical properties
of the standard elements of the mitotic spindle such as centromere, microtubule and interMT connectors
"""
\ No newline at end of file
diff --git a/Parts/standard_parts.py b/Parts/standard_parts.py
index b211a185038fc39dd948c4e5a5a67674ebf23037..ebcb77d5224d79e87cbe61a83994a57703c29206 100644
--- a/Parts/standard_parts.py
+++ b/Parts/standard_parts.py
@@ -88,8 +88,8 @@ def microtubule( type, l, i, **kwargs ):
gb.define_material('MT_material', ElasticModulus, PoissonRatio, **kwargs)
# Define pipe-like profile
- # d -> inner diameter of MT
- # D -> outer diameter of MT
+ # r1 -> inner radius of MT
+ # r2 -> outer radius of MT
modelname = kwargs['modelname']
r1 = kwargs['d']/2
@@ -137,7 +137,7 @@ def connector( i, length, connectorname, **kwargs ):
p = gb.create_connector_part(connectorname, length, **kwargs)
# Define circular profile and section
- '''
+ '''
r -> radius of a connector beam
E -> Elastic modulus of connector material
nu -> Poisson ratio of connector material
diff --git a/SpindleAssembly/__init__.py b/SpindleAssembly/__init__.py
index bc8bca1b70c6f9df4e0fecfe176b9fccd89a9d87..d4ff06ed5a80a1d0c1931f2a275c98a0eb286799 100644
--- a/SpindleAssembly/__init__.py
+++ b/SpindleAssembly/__init__.py
@@ -1,4 +1,4 @@
"""
-This module contains a set of functions that import and connect standard spindle parts into a
+This module contains functions that import and connect standard spindle parts into a
structural assembly of the whole spindle
"""
\ No newline at end of file
diff --git a/SpindleAssembly/assembly_random.py b/SpindleAssembly/assembly_random.py
index e3862680a204b5c145edaa2f95ab110a00cbdef3..031f4de0a9ed4afe6c07fca6a5ae6c3f5d8b7b94 100644
--- a/SpindleAssembly/assembly_random.py
+++ b/SpindleAssembly/assembly_random.py
@@ -1,6 +1,7 @@
from abaqus import *
from abaqusConstants import *
import sys
+from numpy import ones
from SpindleAssembly.PositionComponents import assign_aMT
from SpindleAssembly.PositionConnectors import attach_connectors
sys.path.append("J:\ECS Research\Public\VLC\Spindle")
diff --git a/SpindleMesh/__init__.py b/SpindleMesh/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0aa2beb30340e35f9e0d2b4610dec2dd429ee258 100644
--- a/SpindleMesh/__init__.py
+++ b/SpindleMesh/__init__.py
@@ -0,0 +1,3 @@
+"""
+This module contains functions that generate finite element mesh on each part of the mitotic spindle assembly
+"""
\ No newline at end of file
diff --git a/docs/build/doctrees/HowToRun.doctree b/docs/build/doctrees/HowToRun.doctree
index 7207ec8b4270e7e16b9d3ef3e437e4ca2266518c..d31f4f21d731669fcf9bb83ea8225524a311fc14 100644
Binary files a/docs/build/doctrees/HowToRun.doctree and b/docs/build/doctrees/HowToRun.doctree differ
diff --git a/docs/build/doctrees/LoadCase.doctree b/docs/build/doctrees/LoadCase.doctree
index 752aadae7da970853d113ab903ac005a60c52693..8f9e58c84d86d78e9ecbf2c3498562663f72ea1a 100644
Binary files a/docs/build/doctrees/LoadCase.doctree and b/docs/build/doctrees/LoadCase.doctree differ
diff --git a/docs/build/doctrees/Parts.doctree b/docs/build/doctrees/Parts.doctree
index 3f5b5aed81d4ff9d57708b5f15e3571a55e751d3..b14cd608b65fc1603b107291dc6901176ada7f22 100644
Binary files a/docs/build/doctrees/Parts.doctree and b/docs/build/doctrees/Parts.doctree differ
diff --git a/docs/build/doctrees/Project_idea.doctree b/docs/build/doctrees/Project_idea.doctree
index 1592bd618fa6ecf2afc37358176b321bfb3d5cab..707feb59be8424151a9410fa321cc28930d8bfcc 100644
Binary files a/docs/build/doctrees/Project_idea.doctree and b/docs/build/doctrees/Project_idea.doctree differ
diff --git a/docs/build/doctrees/SpindleAssembly.doctree b/docs/build/doctrees/SpindleAssembly.doctree
index 22bfa79cd26b08d971c49faeba7acf8cf71cc39d..f4bfd0f37f7cca7b6f78b2940b0bceb850ab47e1 100644
Binary files a/docs/build/doctrees/SpindleAssembly.doctree and b/docs/build/doctrees/SpindleAssembly.doctree differ
diff --git a/docs/build/doctrees/SpindleMesh.doctree b/docs/build/doctrees/SpindleMesh.doctree
index 797b0bc35c3f44fc4d3cf03dba630256a57e9827..f9c0552e0fa775e10e43061b9daea842123bfa81 100644
Binary files a/docs/build/doctrees/SpindleMesh.doctree and b/docs/build/doctrees/SpindleMesh.doctree differ
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index cd767a921b13685a36648508d321ef67b0d5e426..9df3952c46d5e63f3beafc8b10327c1208b192c9 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 14babe07fbffe5254c529fca7b7eb08f1ba4fea5..aebe8ee1636f986dc0cca168db200254c40663cc 100644
Binary files a/docs/build/doctrees/index.doctree and b/docs/build/doctrees/index.doctree differ
diff --git a/docs/build/doctrees/job.doctree b/docs/build/doctrees/job.doctree
index da5b8e1da191569f3c14fa1990d57ae06967e59a..2cecb1f006af3b939a1a80d359733daab8550f89 100644
Binary files a/docs/build/doctrees/job.doctree and b/docs/build/doctrees/job.doctree differ
diff --git a/docs/build/html/HowToRun.html b/docs/build/html/HowToRun.html
index 64e723ccce36acaf88b366ea7cc6969d4fc161b6..b1240f6b0a27eb9fdd903ee1c81713d259180b80 100644
--- a/docs/build/html/HowToRun.html
+++ b/docs/build/html/HowToRun.html
@@ -37,7 +37,7 @@
<link rel="search" title="Search" href="search.html"/>
<link rel="top" title="Spindle FEA 1.0.0 documentation" href="index.html"/>
<link rel="next" title="Objectives of this project" href="Project_idea.html"/>
- <link rel="prev" title="Spindle FEA application" href="index.html"/>
+ <link rel="prev" title="Welcome to the interactive documentation of the Spindle FEA application" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -176,14 +176,14 @@
<div class="section" id="how-to-use-spindle-fea">
<h1>How to use Spindle FEA<a class="headerlink" href="#how-to-use-spindle-fea" title="Permalink to this headline">¶</a></h1>
<p>Spindle FEA application is an easy to use tool that can be run either directly from the
-command line or from the Abaqus CAE gui interface. Here we discuss
+command line or from the Abaqus CAE GUI interface. Here we discuss
prerequisites and provide a step-by-step guide to running a simple analysis.</p>
<div class="section" id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
<p>1. The application relies on the third party finite element package <a class="reference external" href="https://www.3ds.com/products-services/simulia/products/abaqus/abaquscae/">Abaqus CAE</a>
by Dassault Systems. Abaqus CAE version 6.11+ should be installed in order to use this application.
No further requirements need to be satisfied for a simple use of the application without modifying
-its modules.</p>
+modules.</p>
<p>2. If, however, the internal modules need to be modified to add some new functionality or alter
the existing one it is recommended to install <a class="reference external" href="https://www.python.org/download/releases/2.7/">Python 2.7</a>
and <a class="reference external" href="https://www.anaconda.com/">Anaconda</a>
@@ -193,24 +193,25 @@ platform.</p>
<h2>Configure and run the analysis<a class="headerlink" href="#configure-and-run-the-analysis" title="Permalink to this headline">¶</a></h2>
<div class="section" id="run-executing-python-scripts-in-abaqus-cae-graphical-interface">
<h3>Run executing python scripts in Abaqus CAE graphical interface<a class="headerlink" href="#run-executing-python-scripts-in-abaqus-cae-graphical-interface" title="Permalink to this headline">¶</a></h3>
-<ol class="arabic">
-<li><p class="first">Lunch Abaqus CAE from command line or shortcut on your desktop and close the
-<code class="docutils literal notranslate"><span class="pre">Start</span> <span class="pre">Session</span></code> window.</p>
+<ol class="arabic simple">
+<li>Lunch Abaqus CAE from the command line or shortcut on your desktop and close the
+<code class="docutils literal notranslate"><span class="pre">Start</span> <span class="pre">Session</span></code> window.</li>
+</ol>
<div class="figure align-center">
<a class="reference external image-reference" href="../../source/images/GUIstp1.pdf"><img alt="_images/GUIstp1.pdf" src="_images/GUIstp1.pdf" /></a>
</div>
-</li>
-<li><p class="first">Go to <code class="docutils literal notranslate"><span class="pre">File</span></code> then to <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">Work</span> <span class="pre">Directory...</span></code></p>
+<ol class="arabic simple" start="2">
+<li>Go to <code class="docutils literal notranslate"><span class="pre">File</span></code> and to <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">Work</span> <span class="pre">Directory...</span></code></li>
+</ol>
<div class="figure align-center">
<a class="reference external image-reference" href="../../source/images/GUIstp2.pdf"><img alt="_images/GUIstp2.pdf" src="_images/GUIstp2.pdf" /></a>
</div>
-<p>and browse to the root directory of Spindle FEA called <code class="docutils literal notranslate"><span class="pre">Spindle</span></code>.</p>
-</li>
-<li><p class="first">Configure <code class="docutils literal notranslate"><span class="pre">job.py</span></code> file by providing all the essential modelling parameters.
+<ol class="arabic simple" start="3">
+<li>Configure <code class="docutils literal notranslate"><span class="pre">job.py</span></code> file by providing all the essential modelling parameters.
All the spindle geometric and physical parameters should be inserted into a
-dictionary <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p>
-</li>
-<li><p class="first">Modify execution parameters in <code class="docutils literal notranslate"><span class="pre">mdb.Job()</span></code> in <code class="docutils literal notranslate"><span class="pre">job.py</span></code> file.</p>
+dictionary <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</li>
+<li>Modify execution parameters in <code class="docutils literal notranslate"><span class="pre">mdb.Job()</span></code> in <code class="docutils literal notranslate"><span class="pre">job.py</span></code> file.</li>
+</ol>
<div class="highlight-python notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
@@ -227,13 +228,12 @@ dictionary <code class="docutils literal notranslate"><span class="pre">kwargs</
</pre></div>
</td></tr></table></div>
<p>Users may change queueing by changing <code class="docutils literal notranslate"><span class="pre">queue</span></code> parameter, memory allocation in % by changing <code class="docutils literal notranslate"><span class="pre">memory</span></code> parameter,
-precision of the computation in <code class="docutils literal notranslate"><span class="pre">explicitPrecision</span></code> and in <code class="docutils literal notranslate"><span class="pre">nodalOutputPrecision</span></code> and also request parallelisation of computations
+the precision of the computation in <code class="docutils literal notranslate"><span class="pre">explicitPrecision</span></code> and in <code class="docutils literal notranslate"><span class="pre">nodalOutputPrecision</span></code> and also request parallelisation of computations
by changing type of threading in <code class="docutils literal notranslate"><span class="pre">multiprocessingMode</span></code>, number of CPUs in <code class="docutils literal notranslate"><span class="pre">numCpus</span></code> and number of GPUs in <code class="docutils literal notranslate"><span class="pre">numGPUs</span></code>. It is highly
recommended that before changing any of the above parameters you closely read the Abaqus CAE documentation accessible from <code class="docutils literal notranslate"><span class="pre">Help</span></code> tab
in Abaqus CAE graphical interface.</p>
-</li>
-<li><p class="first">Run the analysis by going to <code class="docutils literal notranslate"><span class="pre">File</span></code> then <code class="docutils literal notranslate"><span class="pre">Run</span> <span class="pre">Script...</span></code> and selecting <code class="docutils literal notranslate"><span class="pre">job.py</span></code>.</p>
-</li>
+<ol class="arabic simple" start="5">
+<li>Run the analysis by going to <code class="docutils literal notranslate"><span class="pre">File</span></code> then <code class="docutils literal notranslate"><span class="pre">Run</span> <span class="pre">Script...</span></code> and selecting <code class="docutils literal notranslate"><span class="pre">job.py</span></code>.</li>
</ol>
<div class="figure align-center">
<a class="reference external image-reference" href="../../source/images/GUIstp3.pdf"><img alt="_images/GUIstp3.pdf" src="_images/GUIstp3.pdf" /></a>
@@ -247,17 +247,17 @@ The critical buckling loads will also be accessible from <code class="docutils l
<ol class="arabic simple">
<li>To run the job from the command line you should first navigate to <code class="docutils literal notranslate"><span class="pre">Spindle</span></code> directory using <code class="docutils literal notranslate"><span class="pre">cd</span></code> command.</li>
</ol>
-<p>2. Within <code class="docutils literal notranslate"><span class="pre">Spindle</span></code> directory you need to open <code class="docutils literal notranslate"><span class="pre">job.py</span></code> in your favourite code editing application if you want to
+<p>2. Within <code class="docutils literal notranslate"><span class="pre">Spindle</span></code> directory, you need to open <code class="docutils literal notranslate"><span class="pre">job.py</span></code> in your favourite code editing application if you want to
change some default parameters of the analysis.</p>
<ol class="arabic simple" start="3">
<li>When ready you need to type <code class="docutils literal notranslate"><span class="pre">abaqus</span> <span class="pre">cae</span> <span class="pre">noGUI=job.py</span></code> in the command line and hit enter to start the analysis.</li>
-<li>After analysis has finished you can open <code class="docutils literal notranslate"><span class="pre">Job-1.odb</span></code> in Abaqus GUI or access it via your own python scripts. Same for the <code class="docutils literal notranslate"><span class="pre">Job-1.dat</span></code> file.</li>
+<li>After the analysis has finished you can open <code class="docutils literal notranslate"><span class="pre">Job-1.odb</span></code> in Abaqus GUI or access it via your own python scripts. Same for the <code class="docutils literal notranslate"><span class="pre">Job-1.dat</span></code> file.</li>
</ol>
</div>
<div class="section" id="explanation-of-the-kwargs-parameters">
<h3>Explanation of the <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> parameters<a class="headerlink" href="#explanation-of-the-kwargs-parameters" title="Permalink to this headline">¶</a></h3>
-<p>The default <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> dictionary is presented in the code snippet blow. The defaults may be
-easily changed by replacing the values of <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> in <code class="docutils literal notranslate"><span class="pre">job.py</span></code> with the user defined ones.</p>
+<p>The default <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> dictionary is presented in the code snippet below. The defaults may be
+easily changed by replacing the values of <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> in <code class="docutils literal notranslate"><span class="pre">job.py</span></code> with the user-defined ones.</p>
<div class="highlight-python notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
2
3
@@ -296,16 +296,16 @@ easily changed by replacing the values of <code class="docutils literal notransl
<span class="s1">'index'</span> <span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
<span class="s1">'modelname'</span> <span class="p">:</span> <span class="s1">'test'</span><span class="p">,</span>
<span class="s1">'assembly'</span> <span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
- <span class="s1">'CentrosomeRadius'</span><span class="p">:</span> <span class="mf">0.24</span><span class="p">,</span>
- <span class="s1">'CentrosomeLength'</span><span class="p">:</span> <span class="mf">0.48</span><span class="p">,</span>
+ <span class="s1">'CentrosomeRadius'</span><span class="p">:</span> <span class="mf">0.12</span><span class="p">,</span>
+ <span class="s1">'CentrosomeLength'</span><span class="p">:</span> <span class="mf">0.24</span><span class="p">,</span>
<span class="s1">'CentrosomeE'</span> <span class="p">:</span> <span class="mf">1500000000.0</span><span class="p">,</span>
<span class="s1">'CentrosomeNu'</span> <span class="p">:</span> <span class="mf">0.3</span><span class="p">,</span>
<span class="s1">'ipMTnumber'</span> <span class="p">:</span> <span class="mi">6</span><span class="p">,</span>
<span class="s1">'lengthInterval'</span> <span class="p">:</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">],</span>
<span class="s1">'separation'</span> <span class="p">:</span> <span class="p">[</span><span class="mf">0.02876</span><span class="p">,</span> <span class="mf">0.0414</span><span class="p">],</span>
<span class="s1">'angle'</span> <span class="p">:</span> <span class="p">[</span><span class="mf">96.39</span><span class="p">,</span> <span class="mf">11.12</span><span class="p">],</span>
- <span class="s1">'d'</span> <span class="p">:</span> <span class="mf">0.015</span><span class="p">,</span>
- <span class="s1">'D'</span> <span class="p">:</span> <span class="mf">0.025</span><span class="p">,</span>
+ <span class="s1">'d'</span> <span class="p">:</span> <span class="mf">0.015</span><span class="p">,</span>
+ <span class="s1">'D'</span> <span class="p">:</span> <span class="mf">0.025</span><span class="p">,</span>
<span class="s1">'ElasticModulus'</span> <span class="p">:</span> <span class="mf">1500000000.0</span><span class="p">,</span>
<span class="s1">'PoissonRatio'</span> <span class="p">:</span> <span class="mf">0.3</span><span class="p">,</span>
<span class="s1">'spindleLength'</span> <span class="p">:</span> <span class="mi">10</span><span class="p">,</span>
@@ -318,7 +318,7 @@ easily changed by replacing the values of <code class="docutils literal notransl
<span class="s1">'aMTsSpring'</span> <span class="p">:</span> <span class="mi">10</span><span class="p">,</span>
<span class="s1">'groundSpring'</span> <span class="p">:</span> <span class="mi">10</span><span class="p">,</span>
<span class="s1">'StepName'</span> <span class="p">:</span> <span class="s1">'Standard_Buckling'</span><span class="p">,</span>
- <span class="s1">'NumberOfEigs'</span> <span class="p">:</span> <span class="mi">20</span><span class="p">,</span>
+ <span class="s1">'NumberOfEigs'</span> <span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
<span class="s1">'CompressiveLoad'</span> <span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
<span class="s1">'JobName'</span> <span class="p">:</span> <span class="s1">'Job-1'</span><span class="p">}</span>
</pre></div>
@@ -334,74 +334,71 @@ easily changed by replacing the values of <code class="docutils literal notransl
<div><div class="figure align-center" id="spindle">
<img alt="_images/spindle_html.pdf" src="_images/spindle_html.pdf" />
</div>
-<p>The inter-polar distance is the distance between the centrosomes <span class="math notranslate nohighlight">\(L_{p}\)</span> and the midzone length is the length <span class="math notranslate nohighlight">\(L_{m}\)</span> of the zone where MTs are coupled by interlinkers and protein motors as shown in <a class="reference internal" href="#spindle"><span class="std std-numref">Fig. 1</span></a>.</p>
+<p>The model of the whole spindle in anaphase B generated by Spindle FEA with the interpolar distance labelled <span class="math notranslate nohighlight">\(L_{p}\)</span> and the midzone length labelled <span class="math notranslate nohighlight">\(L_{m}\)</span>.</p>
</div></blockquote>
+<p>The inter-polar distance is the distance between the centrosomes <span class="math notranslate nohighlight">\(L_{p}\)</span> and the midzone length is the length <span class="math notranslate nohighlight">\(L_{m}\)</span> of the zone where MTs are coupled by cross-linkers and protein motors as shown in <a class="reference internal" href="#spindle"><span class="std std-numref">Fig. 1</span></a>.</p>
<p><code class="docutils literal notranslate"><span class="pre">separation</span></code> is the distance between two neighbouring MTs in the inter-polar bundle as shown on the cross-sectional view of the spindle in <a class="reference internal" href="#midzone"><span class="std std-numref">Fig. 2</span></a>.</p>
<blockquote>
<div><div class="figure align-center" id="midzone">
<img alt="_images/interlinked_zone.pdf" src="_images/interlinked_zone.pdf" />
</div>
-<p>It is generally random and by default is defined by the Gaussian distribution with <span class="math notranslate nohighlight">\(\mu_{s} = 0.02876 \mu m\)</span> and <span class="math notranslate nohighlight">\(\sigma_{s} = 0.0414 \mu m\)</span> that were calculated from the experimental data <a class="footnote-reference" href="#id2" id="id1">[1]</a>.</p>
-<table class="docutils footnote" frame="void" id="id2" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id3">2</a>, <a class="fn-backref" href="#id5">3</a>, <a class="fn-backref" href="#id8">4</a>, <a class="fn-backref" href="#id9">5</a>, <a class="fn-backref" href="#id10">6</a>)</em> J. J. Ward, H. Roque, C. Antony, and F. Nedelec.
-<cite>Mechanical design principles of a mitotic spindle.</cite>
-eLife, 2014.</td></tr>
-</tbody>
-</table>
+<p>The model of the inter-polar bundle of the mitotic spindle generated by Spindle FEA exhibiting right and left pole MTs, interlinked zone, connectors and protein motors as well as the separation distance between MTs in a bundle.</p>
</div></blockquote>
+<p>It is generally random and by default is defined by the Gaussian distribution with <span class="math notranslate nohighlight">\(\mu_{s} = 0.02876 \mu m\)</span> and <span class="math notranslate nohighlight">\(\sigma_{s} = 0.0414 \mu m\)</span> that were calculated from the experimental data <a class="footnote-reference" href="#id11" id="id1">[1]</a>.</p>
<p><code class="docutils literal notranslate"><span class="pre">angle</span></code> is the the orientation angle <span class="math notranslate nohighlight">\(\phi\)</span> of the microtubules within the inter-polar bundle as shown in <a class="reference internal" href="#mtangle"><span class="std std-numref">Fig. 3</span></a>.</p>
<blockquote>
<div><div class="figure align-center" id="mtangle">
<img alt="_images/MTangle.pdf" src="_images/MTangle.pdf" />
</div>
-<p>The MT angle is also a defined by a Gaussian distribution with mean and standard deviation taken from experimental data <a class="footnote-reference" href="#id2" id="id3">[1]</a>. The default values are <span class="math notranslate nohighlight">\(\mu_{\phi}=96.39^{\circ}\)</span> and <span class="math notranslate nohighlight">\(\sigma_{\phi}=11.12^{\circ}\)</span>.</p>
+<p>The schematic view of the cross-section of the inter-polar bundle of microtubules near-pole and in the mid-zone. The green MTs are growing from the left pole while the purple ones are growing from the right pole.</p>
</div></blockquote>
+<p>The MT angle is also defined by a Gaussian distribution with mean and standard deviation taken from experimental data <a class="footnote-reference" href="#id11" id="id2">[1]</a>. The default values are <span class="math notranslate nohighlight">\(\mu_{\phi}=96.39^{\circ}\)</span> and <span class="math notranslate nohighlight">\(\sigma_{\phi}=11.12^{\circ}\)</span>.</p>
<p><code class="docutils literal notranslate"><span class="pre">d</span></code> is the inner diameter of a microtubule as shown in <a class="reference internal" href="#mtangle"><span class="std std-numref">Fig. 3</span></a>. Default value is <span class="math notranslate nohighlight">\(d=0.015 \mu m\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">D</span></code> is the outer diameter of a microtubule as shown in <a class="reference internal" href="#mtangle"><span class="std std-numref">Fig. 3</span></a>. The value is <span class="math notranslate nohighlight">\(D=0.025 \mu m\)</span> according to Ward et al. <a class="footnote-reference" href="#id7" id="id4">[2]</a> and <span class="math notranslate nohighlight">\(D=0.018 \mu m\)</span> according to Pampaloni et al. <a class="footnote-reference" href="#id2" id="id5">[1]</a> The default value is <span class="math notranslate nohighlight">\(D=0.025 \mu m\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">ElasticModulus</span></code> is an elastic modulus of microtubule material. In the simplest case an isotropic model for microtubule is assumed and the default value is <span class="math notranslate nohighlight">\(E=1.5 \times 10^{9} \frac{pN}{\mu m^{2}}\)</span> <a class="footnote-reference" href="#id7" id="id6">[2]</a>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">D</span></code> is the outer diameter of a microtubule as shown in <a class="reference internal" href="#mtangle"><span class="std std-numref">Fig. 3</span></a>. The value is <span class="math notranslate nohighlight">\(D=0.025 \mu m\)</span> according to Ward et al. <a class="footnote-reference" href="#id12" id="id3">[2]</a> and <span class="math notranslate nohighlight">\(D=0.018 \mu m\)</span> according to Pampaloni et al. <a class="footnote-reference" href="#id11" id="id4">[1]</a> The default value is <span class="math notranslate nohighlight">\(D=0.025 \mu m\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">ElasticModulus</span></code> is an elastic modulus of microtubule material. In the simplest case of the isotropic model for microtubule is assumed and the default value is <span class="math notranslate nohighlight">\(E=1.5 \times 10^{9} \frac{pN}{\mu m^{2}}\)</span> <a class="footnote-reference" href="#id12" id="id5">[2]</a>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">PoissonRatio</span></code> is the Poisson ratio of microtubule material. Assumed to be <span class="math notranslate nohighlight">\(\nu=0.3\)</span> for the isotropic model.</p>
+<p><code class="docutils literal notranslate"><span class="pre">spindleLength</span></code> is the distance between poles of the spindle as shown in <a class="reference internal" href="#spindle"><span class="std std-numref">Fig. 1</span></a>. The default value for the late anaphase B is <span class="math notranslate nohighlight">\(L_{p}=10 \mu m\)</span> <a class="footnote-reference" href="#id11" id="id6">[1]</a>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">Nconnectors</span></code> is the number of cross-linkers and protein motors in the mid-zone (see <a class="reference internal" href="#midzone"><span class="std std-numref">Fig. 2</span></a>). The exact number of cross-linkers is hard to estimate from the experiments, therefore, it can become
+one of the governing parameters of the model. The default value is <span class="math notranslate nohighlight">\(10\)</span> per microtubule.</p>
+<p><code class="docutils literal notranslate"><span class="pre">connectorRadius</span></code> is the radius of the cross-link between MTs. The default value is <span class="math notranslate nohighlight">\(r=0.005 \mu m\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">connectorE</span></code> is the elastic modulus of the connector material. The default value is assumed the same as the one for the microtubule <span class="math notranslate nohighlight">\(E=1.5 \times 10^{9} \frac{pN}{\mu m^{2}}\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">connectorNu</span></code> Poisson ratio of the connector material. Assumed <span class="math notranslate nohighlight">\(\nu=0.3\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">aMTnumber</span></code> is the number of astral microtubules to be modelled in a spindle. The default is <span class="math notranslate nohighlight">\(20\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">aMTlength</span></code> is the length of astral MTs which is generally governed by the radius of the cell membrane and the length between cell tips. The default value is <span class="math notranslate nohighlight">\(L_{aMT}=2 \mu m\)</span> with cell radius <span class="math notranslate nohighlight">\(R_{cell}=1.6 \mu m\)</span> <a class="footnote-reference" href="#id11" id="id7">[1]</a> and the cell length <span class="math notranslate nohighlight">\(L_{cell}=14.3 \mu m\)</span> <a class="footnote-reference" href="#id11" id="id8">[1]</a>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">aMTsSpring</span></code> is the stiffness of the distributed spring that we employ to model astral microtubule embedding in the surrounding mesh of MT connectors <a class="footnote-reference" href="#id13" id="id9">[3]</a>. The default value is <span class="math notranslate nohighlight">\(k = 10 \frac{pN}{\mu m^{2}}\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">groundSpring</span></code> is the spring stiffness of the distributed spring that we employ to model inter-polar MT bundle embedding in the mesh of MT connectors <a class="footnote-reference" href="#id13" id="id10">[3]</a>. The default value is <span class="math notranslate nohighlight">\(k = 10 \frac{pN}{\mu m^{2}}\)</span>.</p>
+<p><code class="docutils literal notranslate"><span class="pre">StepName</span></code> is the name of the buckling analysis step.</p>
+<p><code class="docutils literal notranslate"><span class="pre">NumberOfEigs</span></code> is the number of the eigenvalues and, thus, critical buckling loads that need to be calculated. Notice, that as buckling analysis uses subspace algorithm for eigenvalue calculation the execution time will increase dramatically with the number of requested eigenvalues.
+The default is 5.</p>
+<p><code class="docutils literal notranslate"><span class="pre">CompressiveLoad</span></code> is the preload factor that will be used to multiply the eigenvalue to obtain the critical buckling load. It is recommended that this parameter is not changed.</p>
+<p><code class="docutils literal notranslate"><span class="pre">JobName</span></code> is the name of the job and will be included in all the names of all files produced by analysis. The default is <code class="docutils literal notranslate"><span class="pre">Job-1</span></code>.</p>
<blockquote>
-<div><table class="docutils footnote" frame="void" id="id7" rules="none">
+<div><table class="docutils footnote" frame="void" id="id11" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>, <a class="fn-backref" href="#id4">3</a>, <a class="fn-backref" href="#id6">4</a>, <a class="fn-backref" href="#id7">5</a>, <a class="fn-backref" href="#id8">6</a>)</em> J. J. Ward, H. Roque, C. Antony, and F. Nedelec.
+<cite>Mechanical design principles of a mitotic spindle.</cite>
+eLife, 2014.</td></tr>
+</tbody>
+</table>
+<table class="docutils footnote" frame="void" id="id12" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label">[2]</td><td><em>(<a class="fn-backref" href="#id4">1</a>, <a class="fn-backref" href="#id6">2</a>)</em> F. Pampaloni, G. Lattanzi, A. Jonas, T. Surrey, E. Frey, and E-L. Florin.
+<tr><td class="label">[2]</td><td><em>(<a class="fn-backref" href="#id3">1</a>, <a class="fn-backref" href="#id5">2</a>)</em> F. Pampaloni, G. Lattanzi, A. Jonas, T. Surrey, E. Frey, and E-L. Florin.
<cite>Thermal fluctuations of grafted microtubules provide evidence of a
length-dependent persistence length.</cite>
Proceedings of the National Academy of Sciences, 2006.</td></tr>
</tbody>
</table>
-</div></blockquote>
-<p><code class="docutils literal notranslate"><span class="pre">PoissonRatio</span></code> is the Poisson ratio of microtubule material. Assumed to be <span class="math notranslate nohighlight">\(\nu=0.3\)</span> for isotropic model.</p>
-<p><code class="docutils literal notranslate"><span class="pre">spindleLength</span></code> is the distance between poles of the spindle as shown in <a class="reference internal" href="#spindle"><span class="std std-numref">Fig. 1</span></a>. The default value for the late anaphase B is <span class="math notranslate nohighlight">\(L_{p}=10 \mu m\)</span> <a class="footnote-reference" href="#id2" id="id8">[1]</a>.</p>
-<dl class="docutils">
-<dt><code class="docutils literal notranslate"><span class="pre">Nconnectors</span></code> is the number of interlinkers and protein motors in the mid-zone (see <a class="reference internal" href="#midzone"><span class="std std-numref">Fig. 2</span></a>). The exact number of interlinkers is hard to estimate from the experiments therefore can become</dt>
-<dd>one of the governing parameters of the model. The default value is <span class="math notranslate nohighlight">\(10\)</span> per microtubule.</dd>
-</dl>
-<p><code class="docutils literal notranslate"><span class="pre">connectorRadius</span></code> is the radius of the cross-link between MTs. The default value is <span class="math notranslate nohighlight">\(r=0.005 \mu m\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">connectorE</span></code> is the elastic modulus of the connector material. The default value is assumed the same as the one for the microtubule <span class="math notranslate nohighlight">\(E=1.5 \times 10^{9} \frac{pN}{\mu m^{2}}\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">connectorNu</span></code> Poisson ratio of the connector material. Assumed <span class="math notranslate nohighlight">\(\nu=0.3\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">aMTnumber</span></code> is the number of astral microtubules to be modelled in a spindle. The default is <span class="math notranslate nohighlight">\(20\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">aMTlength</span></code> is the length of astral MTs which is generally governed by the radius of the cell membrane and the length between cell tips. The default value is <span class="math notranslate nohighlight">\(L_{aMT}=2 \mu m\)</span> with cell radius <span class="math notranslate nohighlight">\(R_{cell}=1.6 \mu m\)</span> <a class="footnote-reference" href="#id2" id="id9">[1]</a> and the cell length <span class="math notranslate nohighlight">\(L_{cell}=14.3 \mu m\)</span> <a class="footnote-reference" href="#id2" id="id10">[1]</a>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">aMTsSpring</span></code> is the stiffness of the distributed spring that we employ to model astral microtubule embedding in the surrounding mesh of MT connectors <a class="footnote-reference" href="#id12" id="id11">[3]</a>. The default value is <span class="math notranslate nohighlight">\(k = 10 \frac{pN}{\mu m^{2}}\)</span>.</p>
-<blockquote>
-<div><table class="docutils footnote" frame="void" id="id12" rules="none">
+<table class="docutils footnote" frame="void" id="id13" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label">[3]</td><td><em>(<a class="fn-backref" href="#id11">1</a>, <a class="fn-backref" href="#id13">2</a>)</em> F. M. Nixon, C. Gutierrez-Caballero, F. E. Hood, D. G. Booth, I. A. Prior,
+<tr><td class="label">[3]</td><td><em>(<a class="fn-backref" href="#id9">1</a>, <a class="fn-backref" href="#id10">2</a>)</em> F. M. Nixon, C. Gutierrez-Caballero, F. E. Hood, D. G. Booth, I. A. Prior,
and S. J. Royle. <cite>The mesh is a network of microtubule connectors that stabilizes
individual kinetochore fibers of the mitotic spindle.</cite> eLife, 2015.</td></tr>
</tbody>
</table>
</div></blockquote>
-<p><code class="docutils literal notranslate"><span class="pre">groundSpring</span></code> is the spring stiffness of the distributed spring that we employ to model inter-polar MT bundle embedding in the mesh of MT connectors <a class="footnote-reference" href="#id12" id="id13">[3]</a>. The default value is <span class="math notranslate nohighlight">\(k = 10 \frac{pN}{\mu m^{2}}\)</span>.</p>
-<p><code class="docutils literal notranslate"><span class="pre">StepName</span></code> is the name of the buckling analysis step.</p>
-<dl class="docutils">
-<dt><code class="docutils literal notranslate"><span class="pre">NumberOfEigs</span></code> is the number of the eigenvalues and, thus, critical buckling loads that need to be calculated. Notice, that as buckling analysis uses subspace algorithm for eigenvalue calculation the execution time will increase dramatically with the number of requested eigenvalues.</dt>
-<dd>The default is 5.</dd>
-</dl>
-<p><code class="docutils literal notranslate"><span class="pre">CompressiveLoad</span></code> is the preload factor that will be used to multiply the eigenvalue to obtain the critical buckling load. It is recommended that this parameter is not changed.</p>
-<p><code class="docutils literal notranslate"><span class="pre">JobName</span></code> is the name of the job and will be included in all the names of all files produced by analysis. Default is <code class="docutils literal notranslate"><span class="pre">Job-1</span></code>.</p>
</div>
</div>
</div>
@@ -419,7 +416,7 @@ individual kinetochore fibers of the mitotic spindle.</cite> eLife, 2015.</td></
<a href="Project_idea.html" class="btn btn-neutral float-right" title="Objectives of this project" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
- <a href="index.html" class="btn btn-neutral" title="Spindle FEA application" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+ <a href="index.html" class="btn btn-neutral" title="Welcome to the interactive documentation of the Spindle FEA application" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
diff --git a/docs/build/html/LoadCase.html b/docs/build/html/LoadCase.html
index 97414eb34bfe8f6768f27b692220df0f84ff97a1..f724f278de14c198d6902ceffcabc6f592f795d2 100644
--- a/docs/build/html/LoadCase.html
+++ b/docs/build/html/LoadCase.html
@@ -108,7 +108,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
@@ -514,8 +513,8 @@
</div>
<div class="section" id="module-LoadCase">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-LoadCase" title="Permalink to this headline">¶</a></h2>
-<p>This module contains a set of functions that import and connect standard spindle parts into a
-structural assembly of the whole spindle</p>
+<p>This module contains functions that define interaction between various parts of the mitotic spindle,
+create compressive loads and specify boundary conditions as well as formulate the buckling step analysis.</p>
</div>
</div>
diff --git a/docs/build/html/Parts.html b/docs/build/html/Parts.html
index 753e1ba937aab72d2f6823f8f2d4ab56962842dd..baa18179cb1b8a62e9399bc59b7575d947d1a26b 100644
--- a/docs/build/html/Parts.html
+++ b/docs/build/html/Parts.html
@@ -106,7 +106,6 @@
</li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
@@ -558,7 +557,7 @@ its module of elasticity and Poisson’s ratio</p>
</div>
<div class="section" id="module-Parts">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-Parts" title="Permalink to this headline">¶</a></h2>
-<p>The ‘standard_parts’ module contains functions that generate geometry and mechanical properties
+<p>This module contains functions that generate geometry and mechanical properties
of the standard elements of the mitotic spindle such as centromere, microtubule and interMT connectors</p>
</div>
</div>
diff --git a/docs/build/html/Project_idea.html b/docs/build/html/Project_idea.html
index 50550a83a04761b609244c506b77fd96455e2486..4054ddb12615005b1932d48f3b2aed2b77055328 100644
--- a/docs/build/html/Project_idea.html
+++ b/docs/build/html/Project_idea.html
@@ -166,9 +166,10 @@
<div class="section" id="objectives-of-this-project">
<h1>Objectives of this project<a class="headerlink" href="#objectives-of-this-project" title="Permalink to this headline">¶</a></h1>
-<div class="figure align-center" id="id1">
-<img alt="_images/Spindle_image.svg" src="_images/Spindle_image.svg" /><p class="caption"><span class="caption-number">Fig. 4 </span><span class="caption-text">3D Finite element model of the mitotic spindle</span></p>
-</div>
+<p>Fidelity of cell division is highly dependent on the ability of internal cell structure called mitotic spindle to preserve its structural functions and to generate forces under high compressive loading which results in spindles being prone to instabilities and buckling.</p>
+<p>Spindle FEA application is designed to employ continuous mechanics principles using the Abaqus CAE finite element code to study buckling of the mitotic spindle as a whole in various phases of mitosis.</p>
+<p>Spindle FEA has a modular structure which allows easy modification of any particular part of the analysis which is of particular importance considering that new data on cell division and spindle architecture is constantly emerging.</p>
+<p>Thanks to highly optimised finite element solver the application is particularly useful in multi-parameter large-scale modelling.</p>
</div>
diff --git a/docs/build/html/SpindleAssembly.html b/docs/build/html/SpindleAssembly.html
index dfb96188774a113012589911608b446d3e8999ec..b5fc54fb57e142e5bcc25720220dfa7749eba1d0 100644
--- a/docs/build/html/SpindleAssembly.html
+++ b/docs/build/html/SpindleAssembly.html
@@ -109,7 +109,6 @@
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
@@ -884,7 +883,7 @@ kwargs -> object</td>
</div>
<div class="section" id="module-SpindleAssembly">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-SpindleAssembly" title="Permalink to this headline">¶</a></h2>
-<p>This module contains a set of functions that import and connect standard spindle parts into a
+<p>This module contains functions that import and connect standard spindle parts into a
structural assembly of the whole spindle</p>
</div>
</div>
diff --git a/docs/build/html/SpindleMesh.html b/docs/build/html/SpindleMesh.html
index e7c165203d044a1609c13985b6864447110016c6..84848dd67f485023057edad3334cd70b08007a1a 100644
--- a/docs/build/html/SpindleMesh.html
+++ b/docs/build/html/SpindleMesh.html
@@ -36,7 +36,6 @@
href="genindex.html"/>
<link rel="search" title="Search" href="search.html"/>
<link rel="top" title="Spindle FEA 1.0.0 documentation" href="index.html"/>
- <link rel="next" title="job module" href="job.html"/>
<link rel="prev" title="SpindleAssembly package" href="SpindleAssembly.html"/>
@@ -105,7 +104,6 @@
<li class="toctree-l2"><a class="reference internal" href="#module-SpindleMesh">Module contents</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
@@ -184,6 +182,7 @@
</div>
<div class="section" id="module-SpindleMesh">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-SpindleMesh" title="Permalink to this headline">¶</a></h2>
+<p>This module contains functions that generate finite element mesh on each part of the mitotic spindle assembly</p>
</div>
</div>
@@ -197,8 +196,6 @@
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
- <a href="job.html" class="btn btn-neutral float-right" title="job module" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
-
<a href="SpindleAssembly.html" class="btn btn-neutral" title="SpindleAssembly package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
diff --git a/docs/build/html/_modules/LoadCase/Interaction.html b/docs/build/html/_modules/LoadCase/Interaction.html
index 97eff14bb64006d946e641c680f31b0818baf016..27c90afd786e71e5324abb7d1b30073a498db226 100644
--- a/docs/build/html/_modules/LoadCase/Interaction.html
+++ b/docs/build/html/_modules/LoadCase/Interaction.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/LoadCase/InteractionHelpers.html b/docs/build/html/_modules/LoadCase/InteractionHelpers.html
index 0d82a7bd24e0bf95e4be76b8dbca4ffee96fbc24..21c1f8151ff80a9ff5991da44da9ae7d7a4e0b5b 100644
--- a/docs/build/html/_modules/LoadCase/InteractionHelpers.html
+++ b/docs/build/html/_modules/LoadCase/InteractionHelpers.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/LoadCase/LoadsAndBCs.html b/docs/build/html/_modules/LoadCase/LoadsAndBCs.html
index f18f4dd47bb206d21a8c5247c61f89d86ff9d31d..9396452cbdc251d9e807b3e65ca54226e0ce3778 100644
--- a/docs/build/html/_modules/LoadCase/LoadsAndBCs.html
+++ b/docs/build/html/_modules/LoadCase/LoadsAndBCs.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/LoadCase/Step.html b/docs/build/html/_modules/LoadCase/Step.html
index 3253c2c5bdc9aa7e0c68861459ec7f88837a6835..d1f6b5b5f0b73b6018afa871a35539a31f3f7077 100644
--- a/docs/build/html/_modules/LoadCase/Step.html
+++ b/docs/build/html/_modules/LoadCase/Step.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/Parts/GeometryBuilder.html b/docs/build/html/_modules/Parts/GeometryBuilder.html
index b72f5ced45a034157f007e1c8356c240a85de272..11d96a4ae683554e3aa6dc2f170623ac71c6bbee 100644
--- a/docs/build/html/_modules/Parts/GeometryBuilder.html
+++ b/docs/build/html/_modules/Parts/GeometryBuilder.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/Parts/standard_parts.html b/docs/build/html/_modules/Parts/standard_parts.html
index f3bd8eb2efd808fd3e608723793cbb49a1707a9e..07fbd07ce442ce3c77a74f105cc0c507de1c9a26 100644
--- a/docs/build/html/_modules/Parts/standard_parts.html
+++ b/docs/build/html/_modules/Parts/standard_parts.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
@@ -254,8 +253,8 @@
<span class="n">gb</span><span class="o">.</span><span class="n">define_material</span><span class="p">(</span><span class="s1">'MT_material'</span><span class="p">,</span> <span class="n">ElasticModulus</span><span class="p">,</span> <span class="n">PoissonRatio</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="c1"># Define pipe-like profile</span>
- <span class="c1"># d -> inner diameter of MT</span>
- <span class="c1"># D -> outer diameter of MT</span>
+ <span class="c1"># r1 -> inner radius of MT</span>
+ <span class="c1"># r2 -> outer radius of MT</span>
<span class="n">modelname</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">'modelname'</span><span class="p">]</span>
<span class="n">r1</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">'d'</span><span class="p">]</span><span class="o">/</span><span class="mi">2</span>
@@ -303,7 +302,7 @@
<span class="n">p</span> <span class="o">=</span> <span class="n">gb</span><span class="o">.</span><span class="n">create_connector_part</span><span class="p">(</span><span class="n">connectorname</span><span class="p">,</span> <span class="n">length</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="c1"># Define circular profile and section</span>
- <span class="sd">''' </span>
+ <span class="sd">'''</span>
<span class="sd"> r -> radius of a connector beam</span>
<span class="sd"> E -> Elastic modulus of connector material</span>
<span class="sd"> nu -> Poisson ratio of connector material</span>
diff --git a/docs/build/html/_modules/SpindleAssembly/AddComponents.html b/docs/build/html/_modules/SpindleAssembly/AddComponents.html
index 7313e99fd862788b1ca9599c353c05e24f50d918..46c88ce491db5074c6ef227b26f6a0b7f0a20707 100644
--- a/docs/build/html/_modules/SpindleAssembly/AddComponents.html
+++ b/docs/build/html/_modules/SpindleAssembly/AddComponents.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/SpindleAssembly/PositionComponents.html b/docs/build/html/_modules/SpindleAssembly/PositionComponents.html
index be00bd587a716a7ae3a17e4a516afc6aafffe3f9..8291485818a74bf6a2f359dfa936762ef12bf8ba 100644
--- a/docs/build/html/_modules/SpindleAssembly/PositionComponents.html
+++ b/docs/build/html/_modules/SpindleAssembly/PositionComponents.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/SpindleAssembly/PositionConnectors.html b/docs/build/html/_modules/SpindleAssembly/PositionConnectors.html
index 4db78be8cc03e1071df98e6be61cc30d22f7aa76..fa2ca8342f4c5c876359d746265f6486f1d3b35f 100644
--- a/docs/build/html/_modules/SpindleAssembly/PositionConnectors.html
+++ b/docs/build/html/_modules/SpindleAssembly/PositionConnectors.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/SpindleAssembly/PositionIpMTs.html b/docs/build/html/_modules/SpindleAssembly/PositionIpMTs.html
index b8fba1332e08982ab5835ee44d74a1001d5f10b3..1fef3866d26ea3b8c64477f04e40e21ef4f246e8 100644
--- a/docs/build/html/_modules/SpindleAssembly/PositionIpMTs.html
+++ b/docs/build/html/_modules/SpindleAssembly/PositionIpMTs.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/SpindleAssembly/assembly_random.html b/docs/build/html/_modules/SpindleAssembly/assembly_random.html
index b4aea67e8cb634718416f8f5a3956b80cdff8a04..f42b24e25b999fa32890b32e473a869ff736f453 100644
--- a/docs/build/html/_modules/SpindleAssembly/assembly_random.html
+++ b/docs/build/html/_modules/SpindleAssembly/assembly_random.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
@@ -167,6 +166,7 @@
<span></span><span class="c1"># from abaqus import *</span>
<span class="c1"># from abaqusConstants import *</span>
<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">from</span> <span class="nn">numpy</span> <span class="k">import</span> <span class="n">ones</span>
<span class="kn">from</span> <span class="nn">SpindleAssembly.PositionComponents</span> <span class="k">import</span> <span class="n">assign_aMT</span>
<span class="kn">from</span> <span class="nn">SpindleAssembly.PositionConnectors</span> <span class="k">import</span> <span class="n">attach_connectors</span>
<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"J:\ECS Research\Public\VLC\Spindle"</span><span class="p">)</span>
diff --git a/docs/build/html/_modules/SpindleMesh/generate_mesh.html b/docs/build/html/_modules/SpindleMesh/generate_mesh.html
index ea39175747858c8b5ed3af48e6b8c7a14be189c5..25595268661e2a5c9528ba006568e959accd8b22 100644
--- a/docs/build/html/_modules/SpindleMesh/generate_mesh.html
+++ b/docs/build/html/_modules/SpindleMesh/generate_mesh.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="../../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
index 0b185bec4ec6b3de8a9026963af0adb90c2b4b62..e7d32dab500134e2ba0886df57775e1e836695bd 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -98,7 +98,6 @@
<li class="toctree-l1"><a class="reference internal" href="../Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="../SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/_sources/HowToRun.rst.txt b/docs/build/html/_sources/HowToRun.rst.txt
index 8f3a5857e1a742079119ea858954f97e69713972..6d3fe34cf644a4ba0ee28ca4331d8d04dbb864d2 100644
--- a/docs/build/html/_sources/HowToRun.rst.txt
+++ b/docs/build/html/_sources/HowToRun.rst.txt
@@ -1,7 +1,7 @@
How to use Spindle FEA
===============================
Spindle FEA application is an easy to use tool that can be run either directly from the
-command line or from the Abaqus CAE gui interface. Here we discuss
+command line or from the Abaqus CAE GUI interface. Here we discuss
prerequisites and provide a step-by-step guide to running a simple analysis.
Requirements
@@ -10,7 +10,7 @@ Requirements
<https://www.3ds.com/products-services/simulia/products/abaqus/abaquscae/>`_
by Dassault Systems. Abaqus CAE version 6.11+ should be installed in order to use this application.
No further requirements need to be satisfied for a simple use of the application without modifying
-its modules.
+modules.
2. If, however, the internal modules need to be modified to add some new functionality or alter
the existing one it is recommended to install `Python 2.7
@@ -23,18 +23,18 @@ Configure and run the analysis
-------------------------------
Run executing python scripts in Abaqus CAE graphical interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-1. Lunch Abaqus CAE from command line or shortcut on your desktop and close the
+1. Lunch Abaqus CAE from the command line or shortcut on your desktop and close the
``Start Session`` window.
- .. figure:: images/GUIstp1.pdf
- :target: ../../source/images/GUIstp1.pdf
- :align: center
+.. figure:: images/GUIstp1.pdf
+ :target: ../../source/images/GUIstp1.pdf
+ :align: center
-2. Go to ``File`` then to ``Set Work Directory...``
+2. Go to ``File`` and to ``Set Work Directory...``
- .. figure:: images/GUIstp2.pdf
- :target: ../../source/images/GUIstp2.pdf
- :align: center
+.. figure:: images/GUIstp2.pdf
+ :target: ../../source/images/GUIstp2.pdf
+ :align: center
and browse to the root directory of Spindle FEA called ``Spindle``.
@@ -44,22 +44,22 @@ Run executing python scripts in Abaqus CAE graphical interface
4. Modify execution parameters in ``mdb.Job()`` in ``job.py`` file.
- .. code-block:: python
- :linenos:
-
- mdb.Job(name=name, model=modelname, description='', type=ANALYSIS, atTime=None,
- waitMinutes=0, waitHours=0, queue=None, memory=90,
- memoryUnits=PERCENTAGE, getMemoryFromAnalysis=True,
- explicitPrecision=SINGLE, nodalOutputPrecision=SINGLE, echoPrint=OFF,
- modelPrint=OFF, contactPrint=OFF, historyPrint=OFF, userSubroutine='',
- scratch='', resultsFormat=ODB, multiprocessingMode=DEFAULT, numCpus=1,
- numGPUs=0)
-
- Users may change queueing by changing ``queue`` parameter, memory allocation in % by changing ``memory`` parameter,
- precision of the computation in ``explicitPrecision`` and in ``nodalOutputPrecision`` and also request parallelisation of computations
- by changing type of threading in ``multiprocessingMode``, number of CPUs in ``numCpus`` and number of GPUs in ``numGPUs``. It is highly
- recommended that before changing any of the above parameters you closely read the Abaqus CAE documentation accessible from ``Help`` tab
- in Abaqus CAE graphical interface.
+.. code-block:: python
+ :linenos:
+
+ mdb.Job(name=name, model=modelname, description='', type=ANALYSIS, atTime=None,
+ waitMinutes=0, waitHours=0, queue=None, memory=90,
+ memoryUnits=PERCENTAGE, getMemoryFromAnalysis=True,
+ explicitPrecision=SINGLE, nodalOutputPrecision=SINGLE, echoPrint=OFF,
+ modelPrint=OFF, contactPrint=OFF, historyPrint=OFF, userSubroutine='',
+ scratch='', resultsFormat=ODB, multiprocessingMode=DEFAULT, numCpus=1,
+ numGPUs=0)
+
+Users may change queueing by changing ``queue`` parameter, memory allocation in % by changing ``memory`` parameter,
+the precision of the computation in ``explicitPrecision`` and in ``nodalOutputPrecision`` and also request parallelisation of computations
+by changing type of threading in ``multiprocessingMode``, number of CPUs in ``numCpus`` and number of GPUs in ``numGPUs``. It is highly
+recommended that before changing any of the above parameters you closely read the Abaqus CAE documentation accessible from ``Help`` tab
+in Abaqus CAE graphical interface.
5. Run the analysis by going to ``File`` then ``Run Script...`` and selecting ``job.py``.
@@ -76,17 +76,17 @@ Run from Windows or Linux command line
1. To run the job from the command line you should first navigate to ``Spindle`` directory using ``cd`` command.
-2. Within ``Spindle`` directory you need to open ``job.py`` in your favourite code editing application if you want to
+2. Within ``Spindle`` directory, you need to open ``job.py`` in your favourite code editing application if you want to
change some default parameters of the analysis.
3. When ready you need to type ``abaqus cae noGUI=job.py`` in the command line and hit enter to start the analysis.
-4. After analysis has finished you can open ``Job-1.odb`` in Abaqus GUI or access it via your own python scripts. Same for the ``Job-1.dat`` file.
+4. After the analysis has finished you can open ``Job-1.odb`` in Abaqus GUI or access it via your own python scripts. Same for the ``Job-1.dat`` file.
Explanation of the ``kwargs`` parameters
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The default ``kwargs`` dictionary is presented in the code snippet blow. The defaults may be
-easily changed by replacing the values of ``kwargs`` in ``job.py`` with the user defined ones.
+The default ``kwargs`` dictionary is presented in the code snippet below. The defaults may be
+easily changed by replacing the values of ``kwargs`` in ``job.py`` with the user-defined ones.
.. code-block:: python
:linenos:
@@ -98,16 +98,16 @@ easily changed by replacing the values of ``kwargs`` in ``job.py`` with the user
'index' : 0,
'modelname' : 'test',
'assembly' : 0,
- 'CentrosomeRadius': 0.24,
- 'CentrosomeLength': 0.48,
+ 'CentrosomeRadius': 0.12,
+ 'CentrosomeLength': 0.24,
'CentrosomeE' : 1500000000.0,
'CentrosomeNu' : 0.3,
'ipMTnumber' : 6,
'lengthInterval' : [2, 5],
'separation' : [0.02876, 0.0414],
'angle' : [96.39, 11.12],
- 'd' : 0.015,
- 'D' : 0.025,
+ 'd' : 0.015,
+ 'D' : 0.025,
'ElasticModulus' : 1500000000.0,
'PoissonRatio' : 0.3,
'spindleLength' : 10,
@@ -120,7 +120,7 @@ easily changed by replacing the values of ``kwargs`` in ``job.py`` with the user
'aMTsSpring' : 10,
'groundSpring' : 10,
'StepName' : 'Standard_Buckling',
- 'NumberOfEigs' : 20,
+ 'NumberOfEigs' : 5,
'CompressiveLoad' : 1,
'JobName' : 'Job-1'}
@@ -143,9 +143,9 @@ Here ``modelname`` is the string representing the name of the model,
.. figure:: images/spindle_html.pdf
:align: center
- The model of the whole spindle in anaphase B generated by Spindle FEA with the interpolar distance labeled :math:`L_{p}` and the midzone length labeled :math:`L_{m}`.
+ The model of the whole spindle in anaphase B generated by Spindle FEA with the interpolar distance labelled :math:`L_{p}` and the midzone length labelled :math:`L_{m}`.
- The inter-polar distance is the distance between the centrosomes :math:`L_{p}` and the midzone length is the length :math:`L_{m}` of the zone where MTs are coupled by interlinkers and protein motors as shown in :numref:`spindle`.
+The inter-polar distance is the distance between the centrosomes :math:`L_{p}` and the midzone length is the length :math:`L_{m}` of the zone where MTs are coupled by cross-linkers and protein motors as shown in :numref:`spindle`.
``separation`` is the distance between two neighbouring MTs in the inter-polar bundle as shown on the cross-sectional view of the spindle in :numref:`midzone`.
@@ -153,13 +153,9 @@ Here ``modelname`` is the string representing the name of the model,
.. figure:: images/interlinked_zone.pdf
:align: center
- The model of the inter-polar bundle of the mitotic spindle generated by Spindle FEA exhibiting right and left pole MTs, interlinked zone, connectors and protein motors as well as separation distance between MTs in a bundle.
-
- It is generally random and by default is defined by the Gaussian distribution with :math:`\mu_{s} = 0.02876 \mu m` and :math:`\sigma_{s} = 0.0414 \mu m` that were calculated from the experimental data [1]_.
+ The model of the inter-polar bundle of the mitotic spindle generated by Spindle FEA exhibiting right and left pole MTs, interlinked zone, connectors and protein motors as well as the separation distance between MTs in a bundle.
- .. [1] J. J. Ward, H. Roque, C. Antony, and F. Nedelec.
- `Mechanical design principles of a mitotic spindle.`
- eLife, 2014.
+It is generally random and by default is defined by the Gaussian distribution with :math:`\mu_{s} = 0.02876 \mu m` and :math:`\sigma_{s} = 0.0414 \mu m` that were calculated from the experimental data [1]_.
``angle`` is the the orientation angle :math:`\phi` of the microtubules within the inter-polar bundle as shown in :numref:`MTangle`.
@@ -167,27 +163,22 @@ Here ``modelname`` is the string representing the name of the model,
.. figure:: images/MTangle.pdf
:align: center
- The schematic view of the cross-section of the inter-polar bundle of microtubules near pole and in the mid-zone. The green MTs are growing from the left pole while the purple ones are growing from the right pole.
+ The schematic view of the cross-section of the inter-polar bundle of microtubules near-pole and in the mid-zone. The green MTs are growing from the left pole while the purple ones are growing from the right pole.
- The MT angle is also a defined by a Gaussian distribution with mean and standard deviation taken from experimental data [1]_. The default values are :math:`\mu_{\phi}=96.39^{\circ}` and :math:`\sigma_{\phi}=11.12^{\circ}`.
+The MT angle is also defined by a Gaussian distribution with mean and standard deviation taken from experimental data [1]_. The default values are :math:`\mu_{\phi}=96.39^{\circ}` and :math:`\sigma_{\phi}=11.12^{\circ}`.
``d`` is the inner diameter of a microtubule as shown in :numref:`MTangle`. Default value is :math:`d=0.015 \mu m`.
``D`` is the outer diameter of a microtubule as shown in :numref:`MTangle`. The value is :math:`D=0.025 \mu m` according to Ward et al. [2]_ and :math:`D=0.018 \mu m` according to Pampaloni et al. [1]_ The default value is :math:`D=0.025 \mu m`.
-``ElasticModulus`` is an elastic modulus of microtubule material. In the simplest case an isotropic model for microtubule is assumed and the default value is :math:`E=1.5 \times 10^{9} \frac{pN}{\mu m^{2}}` [2]_.
-
- .. [2] F. Pampaloni, G. Lattanzi, A. Jonas, T. Surrey, E. Frey, and E-L. Florin.
- `Thermal fluctuations of grafted microtubules provide evidence of a
- length-dependent persistence length.`
- Proceedings of the National Academy of Sciences, 2006.
+``ElasticModulus`` is an elastic modulus of microtubule material. In the simplest case of the isotropic model for microtubule is assumed and the default value is :math:`E=1.5 \times 10^{9} \frac{pN}{\mu m^{2}}` [2]_.
-``PoissonRatio`` is the Poisson ratio of microtubule material. Assumed to be :math:`\nu=0.3` for isotropic model.
+``PoissonRatio`` is the Poisson ratio of microtubule material. Assumed to be :math:`\nu=0.3` for the isotropic model.
``spindleLength`` is the distance between poles of the spindle as shown in :numref:`spindle`. The default value for the late anaphase B is :math:`L_{p}=10 \mu m` [1]_.
-``Nconnectors`` is the number of interlinkers and protein motors in the mid-zone (see :numref:`midzone`). The exact number of interlinkers is hard to estimate from the experiments therefore can become
- one of the governing parameters of the model. The default value is :math:`10` per microtubule.
+``Nconnectors`` is the number of cross-linkers and protein motors in the mid-zone (see :numref:`midzone`). The exact number of cross-linkers is hard to estimate from the experiments, therefore, it can become
+one of the governing parameters of the model. The default value is :math:`10` per microtubule.
``connectorRadius`` is the radius of the cross-link between MTs. The default value is :math:`r=0.005 \mu m`.
@@ -201,20 +192,26 @@ Here ``modelname`` is the string representing the name of the model,
``aMTsSpring`` is the stiffness of the distributed spring that we employ to model astral microtubule embedding in the surrounding mesh of MT connectors [3]_. The default value is :math:`k = 10 \frac{pN}{\mu m^{2}}`.
- .. [3] F. M. Nixon, C. Gutierrez-Caballero, F. E. Hood, D. G. Booth, I. A. Prior,
- and S. J. Royle. `The mesh is a network of microtubule connectors that stabilizes
- individual kinetochore fibers of the mitotic spindle.` eLife, 2015.
-
``groundSpring`` is the spring stiffness of the distributed spring that we employ to model inter-polar MT bundle embedding in the mesh of MT connectors [3]_. The default value is :math:`k = 10 \frac{pN}{\mu m^{2}}`.
``StepName`` is the name of the buckling analysis step.
``NumberOfEigs`` is the number of the eigenvalues and, thus, critical buckling loads that need to be calculated. Notice, that as buckling analysis uses subspace algorithm for eigenvalue calculation the execution time will increase dramatically with the number of requested eigenvalues.
- The default is 5.
+The default is 5.
``CompressiveLoad`` is the preload factor that will be used to multiply the eigenvalue to obtain the critical buckling load. It is recommended that this parameter is not changed.
-``JobName`` is the name of the job and will be included in all the names of all files produced by analysis. Default is ``Job-1``.
+``JobName`` is the name of the job and will be included in all the names of all files produced by analysis. The default is ``Job-1``.
+ .. [1] J. J. Ward, H. Roque, C. Antony, and F. Nedelec.
+ `Mechanical design principles of a mitotic spindle.`
+ eLife, 2014.
+ .. [2] F. Pampaloni, G. Lattanzi, A. Jonas, T. Surrey, E. Frey, and E-L. Florin.
+ `Thermal fluctuations of grafted microtubules provide evidence of a
+ length-dependent persistence length.`
+ Proceedings of the National Academy of Sciences, 2006.
+ .. [3] F. M. Nixon, C. Gutierrez-Caballero, F. E. Hood, D. G. Booth, I. A. Prior,
+ and S. J. Royle. `The mesh is a network of microtubule connectors that stabilizes
+ individual kinetochore fibers of the mitotic spindle.` eLife, 2015.
diff --git a/docs/build/html/_sources/Project_idea.rst.txt b/docs/build/html/_sources/Project_idea.rst.txt
index 49e8daace4dabb46271c56f0f3441e75f4fe7c0f..fbec0c1bfdde804c0b2d76473e0c51447d951b49 100644
--- a/docs/build/html/_sources/Project_idea.rst.txt
+++ b/docs/build/html/_sources/Project_idea.rst.txt
@@ -1,7 +1,10 @@
Objectives of this project
===============================
-.. figure:: images/Spindle_image.svg
- :align: center
+Fidelity of cell division is highly dependent on the ability of internal cell structure called mitotic spindle to preserve its structural functions and to generate forces under high compressive loading which results in spindles being prone to instabilities and buckling.
- 3D Finite element model of the mitotic spindle
\ No newline at end of file
+Spindle FEA application is designed to employ continuous mechanics principles using the Abaqus CAE finite element code to study buckling of the mitotic spindle as a whole in various phases of mitosis.
+
+Spindle FEA has a modular structure which allows easy modification of any particular part of the analysis which is of particular importance considering that new data on cell division and spindle architecture is constantly emerging.
+
+Thanks to highly optimised finite element solver the application is particularly useful in multi-parameter large-scale modelling.
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
index 636e3283affb10249ee8ecae1d4bee01be29c1e8..d54470e078c5819a235e3da46997a18e0cec42a2 100644
--- a/docs/build/html/_sources/index.rst.txt
+++ b/docs/build/html/_sources/index.rst.txt
@@ -9,14 +9,14 @@ Welcome to the interactive documentation of the Spindle FEA application
.. figure:: images/Spindle_mode2.eps
:align: center
-This the interactive documentation to the application designed to perform parametric stability modelling of the
+This the interactive documentation of the application designed to perform parametric stability modelling of the
mitotic spindle structures within various cell types during mitosis. The application relies on `Abaqus CAE
<https://www.3ds.com/products-services/simulia/products/abaqus/abaquscae/>`_ finite
element code and allows users to design and execute mitotic spindle modelling provided the essential spindle parameter
-value are provided. The application is created ``Python 2.7`` and has a modular structure which allows easy modification
+value are provided. The application is created in `Python 2.7 <https://www.python.org/download/releases/2.7/>`_ and has a modular structure which allows easy modification
and extension of the current functionality.
-This documentation is a work in progress and is prone to changes and updates and so does the application itself.
+This documentation is a work in progress and is prone to changes and updates and so is the application itself.
.. toctree::
:maxdepth: 2
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 4897a0e330fd6cae342bbcca92ab188abdeeb103..ab528be13e745cd8759fa9ffed509d4549982998 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index b3fd9f3c12b83b610da001cb6a21d524bb843c96..68c0263b158f75d2154edad838f68b1a9258df8e 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -99,7 +99,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
@@ -168,12 +167,12 @@
<div class="figure align-center">
<img alt="_images/Spindle_mode2.eps" src="_images/Spindle_mode2.eps" />
</div>
-<p>This the interactive documentation to the application designed to perform parametric stability modelling of the
+<p>This the interactive documentation of the application designed to perform parametric stability modelling of the
mitotic spindle structures within various cell types during mitosis. The application relies on <a class="reference external" href="https://www.3ds.com/products-services/simulia/products/abaqus/abaquscae/">Abaqus CAE</a> finite
element code and allows users to design and execute mitotic spindle modelling provided the essential spindle parameter
-value are provided. The application is created <code class="docutils literal notranslate"><span class="pre">Python</span> <span class="pre">2.7</span></code> and has a modular structure which allows easy modification
+value are provided. The application is created in <a class="reference external" href="https://www.python.org/download/releases/2.7/">Python 2.7</a> and has a modular structure which allows easy modification
and extension of the current functionality.</p>
-<p>This documentation is a work in progress and is prone to changes and updates and so does the application itself.</p>
+<p>This documentation is a work in progress and is prone to changes and updates and so is the application itself.</p>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
@@ -220,7 +219,6 @@ and extension of the current functionality.</p>
<li class="toctree-l2"><a class="reference internal" href="SpindleMesh.html#module-SpindleMesh">Module contents</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
</div>
</div>
diff --git a/docs/build/html/modules.html b/docs/build/html/modules.html
index af818879676d8b4b13d6546d546bbbd03ea53b7e..6bc5a4e462756289a58dfbc63a9a761f5561566c 100644
--- a/docs/build/html/modules.html
+++ b/docs/build/html/modules.html
@@ -98,7 +98,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
@@ -198,7 +197,6 @@
<li class="toctree-l2"><a class="reference internal" href="SpindleMesh.html#module-SpindleMesh">Module contents</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
</div>
</div>
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index a3bc921388dac380bc18ab9272f2e2f4942e5b5f..ccdef65280c9e02423f686024bcdf6c4644d829b 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 38c5cae46d152cc85df16b64c82fa633cac9a6ac..565587dbd6d01ce574c86083c315c3d5b6f29c1e 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -101,7 +101,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 71743a7c267708bc25b047f432f2bebf45d20d11..bd3f43d1d186f9f91cb697ee6fb390af0a52af1a 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -98,7 +98,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index f8377e692722bacd6d4fff07807f4353f4f80cca..bd16424065879826498f0a76768250c480e78213 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["HowToRun","LoadCase","Parts","Project_idea","SpindleAssembly","SpindleMesh","index","job","modules"],envversion:53,filenames:["HowToRun.rst","LoadCase.rst","Parts.rst","Project_idea.rst","SpindleAssembly.rst","SpindleMesh.rst","index.rst","job.rst","modules.rst"],objects:{"":{LoadCase:[1,0,0,"-"],Parts:[2,0,0,"-"],SpindleAssembly:[4,0,0,"-"],SpindleMesh:[5,0,0,"-"]},"LoadCase.Interaction":{CoupleAMTs:[1,1,1,""],CoupleAMTsToCentrosomes:[1,1,1,""],CoupleIpMTsToCentrosomes:[1,1,1,""],CoupleIpMTsToSring:[1,1,1,""],create_interactions:[1,1,1,""]},"LoadCase.InteractionHelpers":{attach_spring:[1,1,1,""],couple_nearest_aMTs:[1,1,1,""],coupling_constraint:[1,1,1,""],create_RP:[1,1,1,""],find_nearest:[1,1,1,""],pick_region:[1,1,1,""],sum_regions:[1,1,1,""]},"LoadCase.LoadsAndBCs":{create_bc:[1,1,1,""],create_load:[1,1,1,""]},"LoadCase.Step":{Step:[1,1,1,""]},"Parts.GeometryBuilder":{assign_MT_section:[2,1,1,""],assign_MT_section_orientation:[2,1,1,""],assign_centrosome_section:[2,1,1,""],assign_connector_section:[2,1,1,""],create_MT_part:[2,1,1,""],create_centrosome_part:[2,1,1,""],create_centrosome_sketch:[2,1,1,""],create_connector_part:[2,1,1,""],create_mt_name:[2,1,1,""],create_section:[2,1,1,""],define_material:[2,1,1,""],model:[2,1,1,""]},"Parts.standard_parts":{centrosome:[2,1,1,""],connector:[2,1,1,""],microtubule:[2,1,1,""]},"SpindleAssembly.AddComponents":{add_centrosome:[4,1,1,""],add_connectors:[4,1,1,""],add_microtubule:[4,1,1,""],create_MT_instance:[4,1,1,""],generate_MT_length:[4,1,1,""],return_assembly:[4,1,1,""]},"SpindleAssembly.PositionComponents":{assign_aMT:[4,1,1,""],assign_ipMTs_left:[4,1,1,""],assign_ipMTs_right:[4,1,1,""],generate_aMT_position:[4,1,1,""],position_aMT:[4,1,1,""]},"SpindleAssembly.PositionConnectors":{attach_connectors:[4,1,1,""],generate_connector_positions:[4,1,1,""],generate_partition_points:[4,1,1,""],pick_vertices:[4,1,1,""],position_connectors:[4,1,1,""]},"SpindleAssembly.PositionIpMTs":{add_fifth_ipMT:[4,1,1,""],add_first_ipMT:[4,1,1,""],add_fourth_ipMT:[4,1,1,""],add_second_ipMT:[4,1,1,""],add_sixth_ipMT:[4,1,1,""],add_third_ipMT:[4,1,1,""],check_MT_within_centrosome:[4,1,1,""],condition_for_fourth_ipMT:[4,1,1,""],generate_separation:[4,1,1,""]},"SpindleAssembly.assembly_random":{add_and_position_astral_mts:[4,1,1,""],add_and_position_centrosomes:[4,1,1,""],add_and_position_interpolar_mts_and_connectors:[4,1,1,""],assign_ipMTs:[4,1,1,""],create_model_assembly:[4,1,1,""],generate_assembly:[4,1,1,""]},"SpindleMesh.generate_mesh":{standard_mesh:[5,1,1,""]},LoadCase:{Interaction:[1,0,0,"-"],InteractionHelpers:[1,0,0,"-"],LoadsAndBCs:[1,0,0,"-"],Step:[1,0,0,"-"]},Parts:{GeometryBuilder:[2,0,0,"-"],standard_parts:[2,0,0,"-"]},SpindleAssembly:{AddComponents:[4,0,0,"-"],PositionComponents:[4,0,0,"-"],PositionConnectors:[4,0,0,"-"],PositionIpMTs:[4,0,0,"-"],assembly_random:[4,0,0,"-"]},SpindleMesh:{generate_mesh:[5,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"3ds":[],"case":0,"default":0,"float":[2,4],"function":[0,1,2,4,6],"import":[1,4],"int":[1,2,4],"new":0,"null":[1,2,4],"return":[1,2,4],"true":[0,1,4],"while":[],MTs:0,The:[0,1,2,6],_abaqu:[],_cae:[],abaqu:[2,4,6],abaqusca:[],abov:0,academi:0,access:0,accord:0,add:[0,4],add_and_position_astral_mt:4,add_and_position_centrosom:4,add_and_position_interpolar_mts_and_connector:4,add_centrosom:4,add_connector:4,add_fifth_ipmt:4,add_first_ipmt:4,add_fourth_ipmt:4,add_microtubul:4,add_second_ipmt:4,add_sixth_ipmt:4,add_third_ipmt:4,addcompon:[6,8],added:4,after:0,algorithm:0,align:[],all:[0,1,4],alloc:0,allow:6,along:[2,4],alpha1:4,alpha2:4,alpha3:4,alpha4:4,alpha5:4,alpha:4,also:0,alter:0,amt:[1,2,4],amtlength:0,amtnam:4,amtnumb:0,amtsspr:0,anaconda:0,analysi:[1,6],anaphas:0,angl:[0,4],ani:0,antiparallel:4,antoni:0,appli:1,applic:0,argument:4,arrai:4,assembl:[0,1,4],assembly_random:[6,8],assign:[1,2],assign_amt:4,assign_centrosome_sect:2,assign_connector_sect:2,assign_ipmt:4,assign_ipmts_left:4,assign_ipmts_right:4,assign_mt_sect:2,assign_mt_section_orient:2,associ:[1,4],assum:0,astral:[0,1,4],attach:[1,4],attach_connector:4,attach_spr:1,attim:0,averag:[0,1],axi:2,base:[1,4],beam:2,becom:0,been:0,befor:0,belong:[1,4],below:[],between:[0,1,4],blow:0,booth:0,bound:4,brows:0,buckl:[0,1],build:2,bundl:0,caballero:0,cae:6,cae_:[],calcul:[0,4],call:[0,4],can:0,cartesian:4,cell:[0,6],center:[],centromer:2,centrosom:[0,1,2,4],centrosome:0,centrosomelength:0,centrosomenu:0,centrosomeradiu:0,centrosomesketch:2,chang:[0,6],check_mt_within_centrosom:4,circular:4,citward:[],close:0,closest:1,code:[0,6],collect:1,collectionnam:1,com:[],combin:1,combined_region:1,combined_region_left:1,combined_region_right:1,command:[],compress:1,compressiveload:0,comput:0,condit:4,condition_for_fourth_ipmt:4,configur:6,connect:[1,4],connector:[0,1,2,4],connectordata:4,connectornam:[2,4],connectornu:0,connectorradiu:0,constraint:1,contactprint:0,contain:[1,2,4],content:[6,8],coordin:[2,4],correspond:4,coupl:[0,1,4],couple_nearest_amt:1,coupleamt:1,coupleamtstocentrosom:1,coupleipmtstocentrosom:1,coupleipmtstosr:1,coupling_constraint:1,couplingtyp:1,cpu:0,creat:[1,2,4,6],create_bc:1,create_centrosome_part:2,create_centrosome_sketch:2,create_connector_part:2,create_interact:1,create_load:1,create_model_assembl:4,create_mt_inst:4,create_mt_nam:2,create_mt_part:2,create_rp:1,create_sect:2,critic:0,cross:[0,2,4],current:[4,6],cytoskeleton:[],dassault:0,dat:0,data:[0,1,4],defin:[0,1,2,4],define_materi:2,degre:4,depend:0,descript:0,design:[0,6],desktop:0,deviat:[0,4],diamet:0,dict:[1,2,4],dictionari:[0,4],differ:0,dimens:2,directli:0,directori:0,discuss:0,distanc:[0,4],distribut:[0,1,4],divis:[],document:0,doe:6,dof:1,download:[],dramat:0,dure:6,e03398:[],each:[1,2,4],easi:[0,6],easili:0,echoprint:0,edg:1,edit:0,eigenvalu:0,either:[0,1,2,4],elast:[0,1,2],elasticmodulu:0,elec:[],element:[0,2,3,6],elif:0,embed:0,emploi:0,end:[1,4],enter:0,entiti:1,essenti:[0,6],estim:0,evid:0,exact:0,exce:4,execut:6,exhibit:[],exist:0,experi:0,experienc:[],experiment:0,explicitprecis:0,extens:6,extern:[],factor:0,fals:4,favourit:0,fea:[],fiber:0,fifth:4,fig:0,figur:[],file:0,find:1,find_nearest:1,finish:0,finit:[0,3,6],first:[0,4],fit:[],fix:1,florin:0,fluctuat:0,fourth:4,free:4,frei:0,from:4,further:0,gaussian:[0,4],gener:[0,2,4],generate_amt_posit:4,generate_assembl:4,generate_connector_posit:4,generate_mesh:[6,8],generate_mt_length:4,generate_partition_point:4,generate_separ:4,geometr:0,geometri:2,geometrybuild:[6,8],getmemoryfromanalysi:0,given:4,global:4,going:0,govern:0,gpu:0,graft:0,green:[],ground:1,groundspr:0,grow:[1,4],gui:0,guid:0,guistp:[],gutierrez:0,hard:0,has:[0,6],have:[0,1],help:0,helper:2,here:0,highli:0,historyprint:0,hit:0,hood:0,how:6,howev:0,http:[],hyperlink:[],imag:[],includ:0,increas:0,index:[0,2,6],individu:[0,4],influenc:1,influenceradiu:1,inner:0,input:0,insert:0,instal:0,instanc:4,inter:0,interact:8,interactionhelp:[6,8],interfac:[],interlink:0,intermt:2,intern:0,interpolar:[1,4],introduct:[],ipmt:[1,2,4],ipmtnumb:0,isotrop:0,its:[0,2,4],itself:6,job:[0,6,8],jobnam:0,jona:0,keyword:4,kinetochor:0,know:[],kwarg:[1,2,4,5],label:[],late:0,lattanzi:0,left:[1,4],length:[0,2,4],lengthinterv:0,like:[],line:[],link:0,linux:[],list:[1,4],load:[0,1],loadcas:[6,8],loadsandbc:[6,8],local:[2,4],lunch:0,mai:0,maramet:4,master:1,materi:[0,2],math:[],mdb:0,mean:[0,4],mechan:[0,2],membran:[0,1],memori:0,memoryunit:0,mesh:0,method:1,mewalpha:4,micromet:[],microtubl:2,microtubul:[0,1,2,4],mid:0,middl:2,midzon:0,mitosi:6,mitot:[0,2,3,6],model:[0,1,2,3,4,6],modelnam:0,modelprint:0,modif:6,modifi:0,modul:[0,6,8],modular:6,modulu:0,more:[],motor:0,mt_materi:2,mtdata:4,mtname1:4,mtname2:4,mtname:[2,4],mttype:4,multipli:0,multiprocessingmod:0,name:[0,1,2,4],nation:0,navig:0,nconnector:0,nearest:1,nedelec:0,need:0,neighbour:0,network:0,newblock:[],nixon:0,nodaloutputprecis:0,nogui:0,none:[0,1,4],notic:0,number:[0,1,2,4],numberofeig:0,numcpu:0,numgpu:0,numpi:4,object:[1,2,4,6],obtain:0,odb:0,off:0,one:0,ones:0,opbject:1,open:0,order:0,org:[],orient:[0,2,4],outer:0,own:0,packag:[0,6,8],page:6,pair:[1,4],pampaloni:0,pamploni:[],parallel:4,parallelis:0,paramet:[1,2,4,6],parametr:6,part:[1,4,6,8],parti:0,partit:4,pdf:[],per:0,percentag:0,perform:6,persist:0,phase:[],phi:4,phrase:[],physic:0,pick:[1,4],pick_region:1,pick_vertic:4,plain:[],plane:2,platform:0,png:[],point:[1,4],poisson:[0,2],poissonratio:0,polar:0,pole:[0,1,4],pos1:4,pos2:4,pos3:4,pos4:4,pos5:4,pos:4,posit:[1,4],position_amt:4,position_connector:4,positioncompon:[6,8],positionconnector:[6,8],positionipmt:[6,8],precis:0,preload:0,prerequisit:0,present:0,previous:4,principl:0,prior:0,proceed:0,produc:0,product:[],profil:2,progress:6,project:6,prone:6,properti:[2,4],protein:0,provid:[0,6],purpl:[],pythagora:[],python:6,queue:0,radiu:[0,1,2,4],random:[0,4],ratio:[0,2],read:0,readi:0,recommend:0,refer:1,region1:1,region2:1,region:[1,2,4],regiontyp:1,releas:[],reli:[0,6],renam:0,replac:0,repres:[0,2],request:0,requir:6,respect:2,result:0,resultsformat:0,return_assembl:4,right:[1,4],root:0,roqu:0,royl:0,run:6,same:0,satisfi:0,schemat:[],scienc:0,scratch:0,search:6,second:4,section:[0,2,4],sectionmateri:2,sectionnam:2,sectionprofil:2,see:0,select:0,separ:[0,1,4],sequenti:[2,4],servic:[],session:0,set:[0,1,4],shortcut:0,should:[0,4],shown:0,sigma:[],simpl:0,simplest:0,simulia:[],sinc:[],singl:[0,1,2,4],sixth:4,sketch:2,slave:1,snippet:0,some:0,sourc:[1,2,4,5],specifi:[1,2,4],spheric:4,spindl:[1,2,3,4],spindleassembl:[6,8],spindlelength:0,spindlemesh:[6,8],split:1,spring:[0,1],springtyp:1,stabil:[0,6],standard:[0,1,2,4],standard_buckl:0,standard_mesh:5,standard_part:[6,8],start:[0,4],step:[0,6,8],stepnam:0,stiff:0,str:[1,2,4],string:[0,4],structur:[1,4,6],sub:1,submodul:[6,8],subregion:1,subspac:0,sum_region:1,surrei:0,surround:0,system:0,tab:0,taken:0,technic:6,test:0,text:[],thei:1,them:4,therefor:0,thermal:0,theta:4,thi:[0,1,4,6],third:[0,4],thread:0,throughout:1,thu:0,time:0,tip:0,tool:0,tupl:[1,4],two:[0,1,4],type:[0,1,2,4,6],typic:0,uniqu:2,updat:6,use:6,used:0,user:[0,6],usersubroutin:0,uses:0,using:0,valu:[0,6],variou:6,version:0,vertex:4,vertic:[1,4],verts_index:1,via:0,view:0,waithour:0,waitminut:0,want:0,ward:0,weightingmethod:1,well:[],were:0,when:0,where:[0,1],which:[0,1,2,4,6],whole:[1,4],window:[],wire:4,within:[0,1,4,6],without:0,work:[0,6],www:[],you:0,your:0,zbeginpo:4,zendpo:4,zone:0},titles:["How to use Spindle FEA","LoadCase package","Parts package","Objectives of this project","SpindleAssembly package","SpindleMesh package","Welcome to the interactive documentation of the Spindle FEA application","job module","Spindle"],titleterms:{abaqu:0,addcompon:4,analysi:0,applic:6,assembly_random:4,cae:0,cell:[],command:0,configur:0,content:[1,2,4,5],divis:[],document:6,execut:0,explan:0,fea:[0,6],from:0,generate_mesh:5,geometrybuild:2,graphic:0,how:0,indic:6,interact:[1,6],interactionhelp:1,interfac:0,job:7,kwarg:0,line:0,linux:0,loadcas:1,loadsandbc:1,mitot:[],modul:[1,2,4,5,7],object:3,packag:[1,2,4,5],paramet:0,part:2,phase:[],positioncompon:4,positionconnector:4,positionipmt:4,project:3,python:0,requir:0,run:0,script:0,spindl:[0,6,8],spindleassembl:4,spindlemesh:5,stabil:[],standard_part:2,step:1,submodul:[1,2,4,5],tabl:6,thi:3,use:0,variou:[],welcom:6,window:0}})
\ No newline at end of file
+Search.setIndex({docnames:["HowToRun","LoadCase","Parts","Project_idea","SpindleAssembly","SpindleMesh","index","modules"],envversion:53,filenames:["HowToRun.rst","LoadCase.rst","Parts.rst","Project_idea.rst","SpindleAssembly.rst","SpindleMesh.rst","index.rst","modules.rst"],objects:{"":{LoadCase:[1,0,0,"-"],Parts:[2,0,0,"-"],SpindleAssembly:[4,0,0,"-"],SpindleMesh:[5,0,0,"-"]},"LoadCase.Interaction":{CoupleAMTs:[1,1,1,""],CoupleAMTsToCentrosomes:[1,1,1,""],CoupleIpMTsToCentrosomes:[1,1,1,""],CoupleIpMTsToSring:[1,1,1,""],create_interactions:[1,1,1,""]},"LoadCase.InteractionHelpers":{attach_spring:[1,1,1,""],couple_nearest_aMTs:[1,1,1,""],coupling_constraint:[1,1,1,""],create_RP:[1,1,1,""],find_nearest:[1,1,1,""],pick_region:[1,1,1,""],sum_regions:[1,1,1,""]},"LoadCase.LoadsAndBCs":{create_bc:[1,1,1,""],create_load:[1,1,1,""]},"LoadCase.Step":{Step:[1,1,1,""]},"Parts.GeometryBuilder":{assign_MT_section:[2,1,1,""],assign_MT_section_orientation:[2,1,1,""],assign_centrosome_section:[2,1,1,""],assign_connector_section:[2,1,1,""],create_MT_part:[2,1,1,""],create_centrosome_part:[2,1,1,""],create_centrosome_sketch:[2,1,1,""],create_connector_part:[2,1,1,""],create_mt_name:[2,1,1,""],create_section:[2,1,1,""],define_material:[2,1,1,""],model:[2,1,1,""]},"Parts.standard_parts":{centrosome:[2,1,1,""],connector:[2,1,1,""],microtubule:[2,1,1,""]},"SpindleAssembly.AddComponents":{add_centrosome:[4,1,1,""],add_connectors:[4,1,1,""],add_microtubule:[4,1,1,""],create_MT_instance:[4,1,1,""],generate_MT_length:[4,1,1,""],return_assembly:[4,1,1,""]},"SpindleAssembly.PositionComponents":{assign_aMT:[4,1,1,""],assign_ipMTs_left:[4,1,1,""],assign_ipMTs_right:[4,1,1,""],generate_aMT_position:[4,1,1,""],position_aMT:[4,1,1,""]},"SpindleAssembly.PositionConnectors":{attach_connectors:[4,1,1,""],generate_connector_positions:[4,1,1,""],generate_partition_points:[4,1,1,""],pick_vertices:[4,1,1,""],position_connectors:[4,1,1,""]},"SpindleAssembly.PositionIpMTs":{add_fifth_ipMT:[4,1,1,""],add_first_ipMT:[4,1,1,""],add_fourth_ipMT:[4,1,1,""],add_second_ipMT:[4,1,1,""],add_sixth_ipMT:[4,1,1,""],add_third_ipMT:[4,1,1,""],check_MT_within_centrosome:[4,1,1,""],condition_for_fourth_ipMT:[4,1,1,""],generate_separation:[4,1,1,""]},"SpindleAssembly.assembly_random":{add_and_position_astral_mts:[4,1,1,""],add_and_position_centrosomes:[4,1,1,""],add_and_position_interpolar_mts_and_connectors:[4,1,1,""],assign_ipMTs:[4,1,1,""],create_model_assembly:[4,1,1,""],generate_assembly:[4,1,1,""]},"SpindleMesh.generate_mesh":{standard_mesh:[5,1,1,""]},LoadCase:{Interaction:[1,0,0,"-"],InteractionHelpers:[1,0,0,"-"],LoadsAndBCs:[1,0,0,"-"],Step:[1,0,0,"-"]},Parts:{GeometryBuilder:[2,0,0,"-"],standard_parts:[2,0,0,"-"]},SpindleAssembly:{AddComponents:[4,0,0,"-"],PositionComponents:[4,0,0,"-"],PositionConnectors:[4,0,0,"-"],PositionIpMTs:[4,0,0,"-"],assembly_random:[4,0,0,"-"]},SpindleMesh:{generate_mesh:[5,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"3ds":[],"case":0,"default":0,"float":[2,4],"function":[0,1,2,3,4,5,6],"import":[3,4],"int":[1,2,4],"new":[0,3],"null":[1,2,4],"return":[1,2,4],"true":[0,1,4],"while":0,MTs:0,The:[0,1,6],_abaqu:[],_cae:[],abaqu:[2,3,4,6],abaqusca:[],abil:3,abov:0,academi:0,access:0,accord:0,add:[0,4],add_and_position_astral_mt:4,add_and_position_centrosom:4,add_and_position_interpolar_mts_and_connector:4,add_centrosom:4,add_connector:4,add_fifth_ipmt:4,add_first_ipmt:4,add_fourth_ipmt:4,add_microtubul:4,add_second_ipmt:4,add_sixth_ipmt:4,add_third_ipmt:4,addcompon:[6,7],added:4,after:0,algorithm:0,align:[],all:[0,1,4],alloc:0,allow:[3,6],along:[2,4],alpha1:4,alpha2:4,alpha3:4,alpha4:4,alpha5:4,alpha:4,also:0,alter:0,amt:[1,2,4],amtlength:0,amtnam:4,amtnumb:0,amtsspr:0,anaconda:0,analysi:[1,3,6],anaphas:0,angl:[0,4],ani:[0,3],antiparallel:4,antoni:0,appli:1,applic:[0,3],architectur:3,argument:4,arrai:4,assembl:[0,4,5],assembly_random:[6,7],assign:[1,2],assign_amt:4,assign_centrosome_sect:2,assign_connector_sect:2,assign_ipmt:4,assign_ipmts_left:4,assign_ipmts_right:4,assign_mt_sect:2,assign_mt_section_orient:2,associ:[1,4],assum:0,astral:[0,1,4],attach:[1,4],attach_connector:4,attach_spr:1,attim:0,averag:[0,1],axi:2,base:[1,4],beam:2,becom:0,been:0,befor:0,being:3,belong:[1,4],below:0,between:[0,1,4],blow:[],booth:0,bound:4,boundari:1,brows:[],buckl:[0,1,3],build:2,bundl:0,caballero:0,cae:[3,6],cae_:[],calcul:[0,4],call:[3,4],can:0,cartesian:4,cell:[0,3,6],center:[],centromer:2,centrosom:[0,1,2,4],centrosome:0,centrosomelength:0,centrosomenu:0,centrosomeradiu:0,centrosomesketch:2,chang:[0,6],check_mt_within_centrosom:4,circular:4,citward:[],close:0,closest:1,code:[0,3,6],collect:1,collectionnam:1,com:[],combin:1,combined_region:1,combined_region_left:1,combined_region_right:1,command:[],compress:[1,3],compressiveload:0,comput:0,condit:[1,4],condition_for_fourth_ipmt:4,configur:6,connect:[1,4],connector:[0,1,2,4],connectordata:4,connectornam:[2,4],connectornu:0,connectorradiu:0,consid:3,constantli:3,constraint:1,contactprint:0,contain:[1,2,4,5],content:[6,7],continu:3,coordin:[2,4],correspond:4,coupl:[0,1,4],couple_nearest_amt:1,coupleamt:1,coupleamtstocentrosom:1,coupleipmtstocentrosom:1,coupleipmtstosr:1,coupling_constraint:1,couplingtyp:1,cpu:0,creat:[1,2,4,6],create_bc:1,create_centrosome_part:2,create_centrosome_sketch:2,create_connector_part:2,create_interact:1,create_load:1,create_model_assembl:4,create_mt_inst:4,create_mt_nam:2,create_mt_part:2,create_rp:1,create_sect:2,critic:0,cross:[0,2,4],current:[4,6],cytoskeleton:[],dassault:0,dat:0,data:[0,1,3,4],defin:[0,1,2,4],define_materi:2,degre:4,depend:[0,3],descript:0,design:[0,3,6],desktop:0,deviat:[0,4],diamet:0,dict:[1,2,4],dictionari:[0,4],differ:0,dimens:2,directli:0,directori:0,discuss:0,distanc:[0,4],distribut:[0,1,4],divis:3,document:0,doe:[],dof:1,download:[],dramat:0,dure:6,e03398:[],each:[1,2,4,5],easi:[0,3,6],easili:0,echoprint:0,edg:1,edit:0,eigenvalu:0,either:[0,1,2,4],elast:[0,1,2],elasticmodulu:0,elec:[],element:[0,2,3,5,6],elif:0,embed:0,emerg:3,emploi:[0,3],end:[1,4],enter:0,entiti:1,essenti:[0,6],estim:0,evid:0,exact:0,exce:4,execut:6,exhibit:0,exist:0,experi:0,experienc:[],experiment:0,explicitprecis:0,extens:6,extern:[],factor:0,fals:4,favourit:0,fea:3,fiber:0,fidel:3,fifth:4,fig:0,figur:[],file:0,find:1,find_nearest:1,finish:0,finit:[0,3,5,6],first:[0,4],fit:[],fix:1,florin:0,fluctuat:0,forc:3,formul:1,fourth:4,free:4,frei:0,from:4,further:0,gaussian:[0,4],gener:[0,2,3,4,5],generate_amt_posit:4,generate_assembl:4,generate_connector_posit:4,generate_mesh:[6,7],generate_mt_length:4,generate_partition_point:4,generate_separ:4,geometr:0,geometri:2,geometrybuild:[6,7],getmemoryfromanalysi:0,given:4,global:4,going:0,govern:0,gpu:0,graft:0,green:0,ground:1,groundspr:0,grow:[0,1,4],gui:0,guid:0,guistp:[],gutierrez:0,hard:0,has:[0,3,6],have:[0,1],help:0,helper:2,here:0,high:3,highli:[0,3],historyprint:0,hit:0,hood:0,how:6,howev:0,http:[],hyperlink:[],imag:[],includ:0,increas:0,index:[0,2,6],individu:[0,4],influenc:1,influenceradiu:1,inner:0,input:0,insert:0,instabl:3,instal:0,instanc:4,inter:0,interact:7,interactionhelp:[6,7],interfac:[],interlink:0,intermt:2,intern:[0,3],interpolar:[0,1,4],introduct:[],ipmt:[1,2,4],ipmtnumb:0,isotrop:0,its:[2,3,4],itself:6,job:0,jobnam:0,jona:0,keyword:4,kinetochor:0,know:[],kwarg:[1,2,4,5],label:0,larg:3,late:0,lattanzi:0,left:[0,1,4],length:[0,2,4],lengthinterv:0,like:[],line:[],link:0,linker:0,linux:[],list:[1,4],load:[0,1,3],loadcas:[6,7],loadsandbc:[6,7],local:[2,4],lunch:0,mai:0,maramet:4,master:1,materi:[0,2],math:[],mdb:0,mean:[0,4],mechan:[0,2,3],membran:[0,1],memori:0,memoryunit:0,mesh:[0,5],method:1,mewalpha:4,micromet:[],microtubl:2,microtubul:[0,1,2,4],mid:0,middl:2,midzon:0,mitosi:[3,6],mitot:[0,1,2,3,5,6],model:[0,1,2,3,4,6],modelnam:0,modelprint:0,modif:[3,6],modifi:0,modul:[0,6,7],modular:[3,6],modulu:0,more:[],motor:0,mt_materi:2,mtdata:4,mtname1:4,mtname2:4,mtname:[2,4],mttype:4,multi:3,multipli:0,multiprocessingmod:0,name:[0,1,2,4],nation:0,navig:0,nconnector:0,nearest:1,nedelec:0,need:0,neighbour:0,network:0,newblock:[],nixon:0,nodaloutputprecis:0,nogui:0,none:[0,1,4],notic:0,number:[0,1,2,4],numberofeig:0,numcpu:0,numgpu:0,numpi:4,object:[1,2,4,6],obtain:0,odb:0,off:0,one:0,ones:0,opbject:1,open:0,optimis:3,order:0,org:[],orient:[0,2,4],outer:0,own:0,packag:[0,6,7],page:6,pair:[1,4],pampaloni:0,pamploni:[],parallel:4,parallelis:0,paramet:[1,2,3,4,6],parametr:6,part:[1,3,4,5,6,7],parti:0,particular:3,particularli:3,partit:4,pdf:[],per:0,percentag:0,perform:6,persist:0,phase:3,phi:4,phrase:[],physic:0,pick:[1,4],pick_region:1,pick_vertic:4,plain:[],plane:2,platform:0,png:[],point:[1,4],poisson:[0,2],poissonratio:0,polar:0,pole:[0,1,4],pos1:4,pos2:4,pos3:4,pos4:4,pos5:4,pos:4,posit:[1,4],position_amt:4,position_connector:4,positioncompon:[6,7],positionconnector:[6,7],positionipmt:[6,7],precis:0,preload:0,prerequisit:0,present:0,preserv:3,previous:4,principl:[0,3],prior:0,proceed:0,produc:0,product:[],profil:2,progress:6,project:6,prone:[3,6],properti:[2,4],protein:0,provid:[0,6],purpl:0,pythagora:[],python:6,queue:0,radiu:[0,1,2,4],random:[0,4],ratio:[0,2],read:0,readi:0,recommend:0,refer:1,region1:1,region2:1,region:[1,2,4],regiontyp:1,releas:[],reli:[0,6],renam:0,replac:0,repres:[0,2],request:0,requir:6,respect:2,result:[0,3],resultsformat:0,return_assembl:4,right:[0,1,4],root:[],roqu:0,royl:0,run:6,same:0,satisfi:0,scale:3,schemat:0,scienc:0,scratch:0,search:6,second:4,section:[0,2,4],sectionmateri:2,sectionnam:2,sectionprofil:2,see:0,select:0,separ:[0,1,4],sequenti:[2,4],servic:[],session:0,set:0,shortcut:0,should:[0,4],shown:0,sigma:[],simpl:0,simplest:0,simulia:[],sinc:[],singl:[0,1,2,4],sixth:4,sketch:2,slave:1,snippet:0,solver:3,some:0,sourc:[1,2,4,5],specifi:[1,2,4],spheric:4,spindl:[1,2,3,4,5],spindleassembl:[6,7],spindlelength:0,spindlemesh:[6,7],split:1,spring:[0,1],springtyp:1,stabil:[0,6],standard:[0,2,4],standard_buckl:0,standard_mesh:5,standard_part:[6,7],start:[0,4],step:[0,6,7],stepnam:0,stiff:0,str:[1,2,4],string:[0,4],structur:[1,3,4,6],studi:3,sub:1,submodul:[6,7],subregion:1,subspac:0,sum_region:1,surrei:0,surround:0,system:0,tab:0,taken:0,technic:6,test:0,text:[],thank:3,thei:1,them:4,therefor:0,thermal:0,theta:4,thi:[0,1,2,4,5,6],third:[0,4],thread:0,throughout:1,thu:0,time:0,tip:0,tool:0,tupl:[1,4],two:[0,1,4],type:[0,1,2,4,6],typic:0,under:3,uniqu:2,updat:6,use:6,used:0,useful:3,user:[0,6],usersubroutin:0,uses:0,using:[0,3],valu:[0,6],variou:[1,3,6],version:0,vertex:4,vertic:[1,4],verts_index:1,via:0,view:0,waithour:0,waitminut:0,want:0,ward:0,weightingmethod:1,well:[0,1],were:0,when:0,where:[0,1],which:[0,1,2,3,4,6],whole:[0,3,4],window:[],wire:4,within:[0,1,4,6],without:0,work:[0,6],www:[],you:0,your:0,zbeginpo:4,zendpo:4,zone:0},titles:["How to use Spindle FEA","LoadCase package","Parts package","Objectives of this project","SpindleAssembly package","SpindleMesh package","Welcome to the interactive documentation of the Spindle FEA application","Spindle"],titleterms:{abaqu:0,addcompon:4,analysi:0,applic:6,assembly_random:4,cae:0,cell:[],command:0,configur:0,content:[1,2,4,5],divis:[],document:6,execut:0,explan:0,fea:[0,6],from:0,generate_mesh:5,geometrybuild:2,graphic:0,how:0,indic:6,interact:[1,6],interactionhelp:1,interfac:0,job:[],kwarg:0,line:0,linux:0,loadcas:1,loadsandbc:1,mitot:[],modul:[1,2,4,5],object:3,packag:[1,2,4,5],paramet:0,part:2,phase:[],positioncompon:4,positionconnector:4,positionipmt:4,project:3,python:0,requir:0,run:0,script:0,spindl:[0,6,7],spindleassembl:4,spindlemesh:5,stabil:[],standard_part:2,step:1,submodul:[1,2,4,5],tabl:6,thi:3,use:0,variou:[],welcom:6,window:0}})
\ No newline at end of file
diff --git a/job.py b/job.py
index c306c413b6c851e791f310ffc40c017ca1e66494..67f6dc307155d309e4044e206135d951b7a82551 100644
--- a/job.py
+++ b/job.py
@@ -1,3 +1,9 @@
+"""
+This is the main input file for the analysis. Provide all the geometric and physical properties of the mitotic
+spindle in the dictionary ```kwargs```. You can also adjust the solver parameters and request parallelization of
+computations by changing ```mdb.Job()``` parameters.
+"""
+
from abaqus import *
from abaqusConstants import *
import __main__
@@ -13,16 +19,16 @@ kwargs = {'x' : 0,
'index' : 0,
'modelname' : 'test',
'assembly' : 0,
- 'CentrosomeRadius': 0.24,
- 'CentrosomeLength': 0.48,
+ 'CentrosomeRadius': 0.12,
+ 'CentrosomeLength': 0.24,
'CentrosomeE' : 1500000000.0,
'CentrosomeNu' : 0.3,
'ipMTnumber' : 6,
- 'lengthInterval' : [2, 7],
+ 'lengthInterval' : [2, 5],
'separation' : [0.02876, 0.0414],
'angle' : [96.39, 11.12],
- 'd' : 0.015,
- 'D' : 0.025,
+ 'd' : 0.015,
+ 'D' : 0.025,
'ElasticModulus' : 1500000000.0,
'PoissonRatio' : 0.3,
'spindleLength' : 10,
@@ -35,7 +41,7 @@ kwargs = {'x' : 0,
'aMTsSpring' : 10,
'groundSpring' : 10,
'StepName' : 'Standard_Buckling',
- 'NumberOfEigs' : 20,
+ 'NumberOfEigs' : 5,
'CompressiveLoad' : 1,
'JobName' : 'Job-1'}