EI/VirtualLeaf Changeset - ec439fed4af8 · Centrum Wiskunde & Informatica (CWI)

Changeset - ec439fed4af8

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Michael Guravage - 15 years ago 2010-10-15 19:27:29
michael.guravage@cwi.nl

Synchronise leaf movie frame and cell export data timestep references.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed doc/v1.html
changed doc/v1.pdf
changed doc/v1.rst
changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.h

9 files changed with 915 insertions and 239 deletions:

doc/v1.html

doc/v1.pdf

717

223

doc/v1.rst

src/ChangeLog

src/VirtualLeaf.cpp

src/canvas.cpp

src/canvas.h

src/mainbase.h

src/mesh.h

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doc/v1.html

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@@ @@ -556,7 +556,7 @@ LanguageError: IOError: [Errno 2] No tra @@
 <li>make install</li>
 <li>cd ..</li>
 <li>wget <a class="reference external" href="http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz">http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz</a></li>
 <li>tar xzf PyQt-x11-gpl-4.7.7</li>
+<li>tar xzf PyQt-x11-gpl-4.7.7.tar.gz</li>
 <li>cd PyQt-x11-gpl-4.7.7</li>
 <li>python configure.py</li>
 <li>make</li>
@@ @@ -594,6 +594,80 @@ still be justified - though they become @@
 introduce the new schema changes.</p>
 </div>
 </div>
 <div class="section" id="wednesday-13-october-2010">
 <h1>Wednesday 13 October 2010</h1>
 <p>Tweaked <tt class="docutils literal">.bashrc</tt> and <tt class="docutils literal">virtualenvwrapper.sh</tt> to facilitate
 virtualenv and virtualenvwrapper - many unbound variables!</p>
 <p>Pushed recent changes to repository from where Roeland can retrieve
 and test them.</p>
 <p>OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.</p>
 </div>
 <div class="section" id="friday-15-october-2010">
 <h1>Friday 15 October 2010</h1>
 <div class="section" id="id1">
 <h2>Rhodecode</h2>
 <p>Installing RhodeCode locally on the nhypnos is a real pain. In
 addition to the previous list of dependencies, for the caterpie, add
 these for the nhypnos:</p>
 <ol class="arabic simple">
 <li>Python</li>
 <li>Bison (for sip)</li>
 <li>Flex (for sip)</li>
 <li>m4 (for Bison)</li>
 <li>Qt (for PyQt)</li>
 <li>GLIBCXX_3.4.9 (for Qt) - I draw the line at (re)installing GCC!</li>
 </ol>
 <p>OK. Forget sip bison, flex, m4, Qt and the rest. Let's install just
 the minimum.</p>
 <p>First, install sqlite; we'll see in a minute that Python requires
 it. The sources are available at: <a class="reference external" href="http://www.sqlite.org/download.html">http://www.sqlite.org/download.html</a>.</p>
 <p>Second, install Python. My initial attempt complained it was missing
 the following bits and pieces:</p>
 <pre class="literal-block">
 Python build finished, but the necessary bits to build these modules were not found:
 _bsddb             _sqlite3           _ssl
 _tkinter           bsddb185           dl
 imageop            readline           sunaudiodev
 To find the necessary bits, look in setup.py in detect_modules() for the module's name.
 </pre>
 <p>So install sqlite first. And, since Python's configure script doesn't
 have an option for it, I had to tweak <tt class="docutils literal">setup.py</tt> to enumerate the
 path where it would find sqlite;</p>
 <p>Third, install RhodeCode. I first installed it using easy_install, but
 while the result worked, the changelog view did not display the
 branch/merge graphics. I then cloned the code from its bitbucket repository:</p>
 <pre class="literal-block">
 clone https://litsol&#64;bitbucket.org/marcinkuzminski/rhodecode
 </pre>
 <p>Replacing the egg installed by easy_install by this code does display
 the branch/merge graphics.</p>
 <p>Fourth, setup and serve rhodecode. Following the instructions posted
 online at: <a class="reference external" href="http://packages.python.org/RhodeCode/setup.html#setup">http://packages.python.org/RhodeCode/setup.html#setup</a> works as advertised:</p>
 <pre class="literal-block">
 paster make-config RhodeCode production.ini
 paster setup-app production.ini
 paster serve production.ini
 </pre>
 <p>All that's left is an apache rewrite rule directing
 virtualleaf.project.cwi.nl/repository to port 5000, or whaterver we
 change it to, on the nhypnos.</p>
 </div>
 <div class="section" id="id2">
 <h2>The Virtual Leaf</h2>
 <p>Added <tt class="docutils literal">incrementIterations()</tt>, <tt class="docutils literal">getIterations()</tt> and <tt class="docutils literal">int
 iterations</tt> to mesh.h. <tt class="docutils literal">incrementIterations()</tt> is called in TIMESTEP in
 VirtualLeaf.cpp. The actual counter, <tt class="docutils literal">iterations</tt> is initalized to
 zero in the Mesh class constructor.</p>
 <p>The iterations are inquired in two places: for the frame count in
 <tt class="docutils literal"><span class="pre">MainBase::Plot</span></tt> in <tt class="docutils literal">VirtualLeaf.cpp` and for the export cell data
 interval in <span class="pre">``Main::TimeStepWrap</span></tt> in <tt class="docutils literal">canvas.cpp</tt>.</p>
 <p>The questions remain: Should we use this count, and if yes, where
 should it be incremented? The previous count was incremented in
 <tt class="docutils literal"><span class="pre">Main::TimeStepWrap</span></tt>. Or should we simply use
 <tt class="docutils literal">(int)mesh.getTime()</tt>? Since this is not an ordinal count, the
 results look strange.</p>
 </div>
 </div>
 </div>
 <div class="footer">
 <hr class="footer" />

doc/v1.pdf

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doc/v1.rst

➞

Show inline comments

@@ @@ -292,19 +292,19 @@ 6. python build.py prepare @@
 . python configure.py
 . make
 . make install
-. cd ..
+. cd \.\.
 . wget http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
 . tar xzf PyQt-x11-gpl-4.7.7
+. tar xzf PyQt-x11-gpl-4.7.7.tar.gz
 . cd PyQt-x11-gpl-4.7.7
 . python configure.py
 . make
 . make install
-. cd ..
+. cd \.\.
 . hg clone https://litsol@bitbucket.org/bfrog/cutehg
 . cd cutehg
 . python setup.py build
 . python setup.py install
-. cd ..
+. cd \.\.
 . easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2
@@ @@ -350,3 +350,81 @@ and test them. @@
 OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.
 Friday 15 October 2010
 ----------------------
 Rhodecode
 +++++++++
 Installing RhodeCode locally on the nhypnos is a real pain. In
 addition to the previous list of dependencies, for the caterpie, add
 these for the nhypnos:
 . Python
 . Bison (for sip)
 . Flex (for sip)
 . m4 (for Bison)
 . Qt (for PyQt)
 . GLIBCXX_3.4.9 (for Qt) - I draw the line at (re)installing GCC!
 OK. Forget sip bison, flex, m4, Qt and the rest. Let's install just
 the minimum.
 First, install sqlite; we'll see in a minute that Python requires
 it. The sources are available at: http://www.sqlite.org/download.html.
 Second, install Python. My initial attempt complained it was missing
 the following bits and pieces::
  Python build finished, but the necessary bits to build these modules were not found:
  _bsddb             _sqlite3           _ssl
  _tkinter           bsddb185           dl
  imageop            readline           sunaudiodev
  To find the necessary bits, look in setup.py in detect_modules() for the module's name.
 So install sqlite first. And, since Python's configure script doesn't
 have an option for it, I had to tweak ``setup.py`` to enumerate the
 path where it would find sqlite;
 Third, install RhodeCode. I first installed it using easy_install, but
 while the result worked, the changelog view did not display the
 branch/merge graphics. I then cloned the code from its bitbucket repository::
  clone https://litsol@bitbucket.org/marcinkuzminski/rhodecode
 Replacing the egg installed by easy_install by this code does display
 the branch/merge graphics.
 Fourth, setup and serve rhodecode. Following the instructions posted
 online at: http://packages.python.org/RhodeCode/setup.html#setup works as advertised::
  paster make-config RhodeCode production.ini
  paster setup-app production.ini
  paster serve production.ini
 All that's left is an apache rewrite rule directing
 virtualleaf.project.cwi.nl/repository to port 5000, or whaterver we
 change it to, on the nhypnos.
 The Virtual Leaf
 ++++++++++++++++
 Added ``incrementIterations()``, ``getIterations()`` and ``int
 iterations`` to mesh.h. ``incrementIterations()`` is called in TIMESTEP in
 VirtualLeaf.cpp. The actual counter, ``iterations`` is initalized to
 zero in the Mesh class constructor.
 The iterations are inquired in two places: for the frame count in
 ``MainBase::Plot`` in ``VirtualLeaf.cpp` and for the export cell data
 interval in ``Main::TimeStepWrap`` in ``canvas.cpp``.
 The questions remain: Should we use this count, and if yes, where
 should it be incremented? The previous count was incremented in
 ``Main::TimeStepWrap``. Or should we simply use
 ``(int)mesh.getTime()``? Since this is not an ordinal count, the
 results look strange.

src/ChangeLog

➞

Show inline comments

 -10-15    <guravage@caterpie.sen.cwi.nl>
 	* mesh.h (Mesh): Added iterations. incrementIterations() and
 	getIterations().
 	* VirtualLeaf.cpp (Plot): Replaced local frame counter with
 	mesh.incrementIterations().
 	* canvas.cpp (TimeStepWrap): Replaced local counter with
 	mesh.incrementIterations().
 -10-14    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Turned debug off to make all profiles must be
@@ @@ -14,10 +25,15 @@ 2010-10-14 <guravage@caterpie.sen.cwi @@
 -10-14    <merks@cwi.nl>
 	* mesh.cpp: In response to referees' comments, added new parameter "yield_threshold" instead of fixed parameter '4' for yield threshold.
 	* mesh.cpp: In response to referees' comments, added new parameter
 	"yield_threshold" instead of fixed parameter '4' for yield
 	threshold.
 	* wallitem.cpp: when clicking a wall, both the wall type was cycled and the transporterdialog popped up. Corrected this - for wall type cycling, hold the Control button while left clicking. TransporterDialog only pops up for left click. Also made sure the wall is redrawn after changing the transporter values.
 	* wallitem.cpp: when clicking a wall, both the wall type was
 	cycled and the transporterdialog popped up. Corrected this - for
 	wall type cycling, hold the Control button while left
 	clicking. TransporterDialog only pops up for left click. Also made
 	sure the wall is redrawn after changing the transporter values.
 	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

src/VirtualLeaf.cpp

➞

Show inline comments

@@ @@ -180,7 +180,7 @@ void MainBase::Plot(int resize_stride) @@
   if ( ( batch || MovieFramesP() )) {
     static int frame = 0;
+     static int frame = 0;
     // frame numbers are sequential for the most frequently written file type.
     // for the less frequently written file type they match the other type
     if (!(count%par.storage_stride) )  {
@@ @@ -192,7 +192,8 @@ void MainBase::Plot(int resize_stride) @@
       fname << frame << ".jpg";
       if (par.storage_stride <= par.xml_storage_stride) {
 	frame++;
 	//frame = (int)mesh.getTime();
 	frame = mesh.getIterations();
+      }
       // Write high-res JPG snapshot every plot step
@@ @@ -207,7 +208,8 @@ void MainBase::Plot(int resize_stride) @@
       fname << frame << ".xml";
       if (par.xml_storage_stride < par.storage_stride) {
 	frame++;
 	//frame = (int)mesh.getTime();
 	frame = mesh.getIterations();
+      }
       // Write XML file every ten plot steps
       mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
@@ @@ -282,6 +284,7 @@ TIMESTEP { @@
     Plot(par.resize_stride);
+  }
   i++;
   mesh.incrementIterations(); // WHERE SHOULD THIS GO?!
   return mesh.getTime();
+}

src/canvas.cpp

➞

Show inline comments

@@ @@ -584,6 +584,7 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
@@ @@ -1165,13 +1166,16 @@ void Main::print() @@
 void Main::TimeStepWrap(void)
+{
-  static int t=0;
   static int t;
   stringstream fname;
   TimeStep();
   t++;
   if ((par.export_interval > 0) && ((t % par.export_interval) == 0)){
   //mesh.incrementIterations();
   t = mesh.getIterations();
   //t = (int)mesh.getTime();
   if ((par.export_interval > 0) && !(t%par.export_interval)){
     fname << par.datadir << "/" << par.export_fn_prefix;
     fname.fill('0');
     fname.width(6);
@@ @@ -1180,7 +1184,7 @@ void Main::TimeStepWrap(void) @@
+  }
   // check number of timesteps
   if (t==par.nit) {
+  if (t == par.nit) {
     emit SimulationDone();
+  }
+}

src/canvas.h

➞

Show inline comments

@@ @@ -136,7 +136,6 @@ class Main : public Q3MainWindow, public @@
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
   public slots:
   void about();

src/mainbase.h

➞

Show inline comments

@@ @@ -108,10 +108,13 @@ class MainBase { @@
   Mesh &mesh;
   QTransform viewport;
  protected:
   QGraphicsScene &canvas;
   virtual xmlNode *XMLSettingsTree(void) const;
   virtual xmlNode *XMLViewportTree(QTransform &transform) const;
  protected:
   bool showcentersp;

src/mesh.h

➞

Show inline comments

@@ @@ -83,6 +83,7 @@ class Mesh { @@
     time = 0.;
     plugin = 0;
     boundary_polygon=0;
     iterations = 0;
   };
   ~Mesh(void) {
     if (boundary_polygon) {
@@ @@ -391,6 +392,10 @@ class Mesh { @@
   Node* findNextBoundaryNode(Node*);
   int iterations;
   int getIterations(){return this->iterations;}
   void incrementIterations(){this->iterations++;}
  private:
   // Data members

0 comments (0 inline, 0 general)