packages feed

simgi (empty) → 0.1.1

raw patch · 37 files changed

+3834/−0 lines, 37 filesdep +basedep +containersdep +haskell98setup-changedbinary-added

Dependencies added: base, containers, haskell98, mtl, parsec, random

Files

+ .gitignore view
@@ -0,0 +1,11 @@+syntax: glob+src/*.o+src/*.hi+src/simgi+src/*.swp+test/*.o+test/*.hi+test/*.swp+average+RpnStackTest+check_deviation
+ AUTHORS view
@@ -0,0 +1,1 @@+Markus Dittrich <haskelladdict@users.sourceforge.net>
+ COPYING view
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+ ChangeLog view
@@ -0,0 +1,8 @@+2009-06-02 Markus Dittrich <haskelladdict@users.sourceforge.net>++      * 0.1.1 release (identical to 0.1 with only a few minor+	changes needed for uploading to Hackage).++2009-05-30 Markus Dittrich <haskelladdict@users.sourceforge.net>++      * initial commit
+ INSTALL view
@@ -0,0 +1,16 @@+COMPILATION+-----------+Compilaton of simgi requires ++- >=ghc-6.10+- >=gmp-4.3++To compile the documentation (not required), you will also need++- >=docutils-0.5 +- latex, e.g., tetex or texlive++Building of simgi can be done either via ++- the standard ``make, make check, make install``+- or via cabal
+ Makefile view
@@ -0,0 +1,55 @@+# Copyright 2009 Markus Dittrich <haskelladdict@users.sourceforge.net>+# Distributed under the terms of the GNU General Public License v3++VERSION=0.1.1+DESTDIR=+prefix=/usr+mandir=$(DESTDIR)$(prefix)/share/man/man1+docdir=$(DESTDIR)$(prefix)/share/doc/simgi-$(VERSION)+htmldir=$(docdir)/html+bindir=$(DESTDIR)$(prefix)/bin++GHC_FLAGS_DEVEL = -O -Wall -fwarn-simple-patterns -fwarn-tabs -fwarn-incomplete-record-updates -fwarn-monomorphism-restriction -fwarn-implicit-prelude -fno-warn-orphans+GHC_FLAGS_RELEASE = -O2++OBJECTS = src/simgi.hs src/CommandLine.hs src/Engine.hs  \+	  src/GenericModel.hs src/InputCheck.hs src/InputParser.hs \+	  src/PrettyPrint.hs src/RpnParser.hs src/RpnCalc.hs \+	  src/RpnData.hs src/TokenParser.hs ++all: simgi++simgi: $(OBJECTS) +	ghc -i./Models -i./src $(GHC_FLAGS_RELEASE) --make src/simgi.hs++++debug: $(OBJECTS) +	ghc -i./Models -i./src $(GHC_FLAGS_DEVEL) --make src/simgi.hs++++check: $(OBJECTS) all+	make -C test++++install: simgi+	install -d $(docdir)+	install -d $(bindir)+	install -d $(htmldir)+	install -m 0755 src/simgi $(bindir)/+	install -m 0644 ChangeLog COPYING AUTHORS $(docdir)/+	install -m 0644 doc/*.pdf doc/*.rst $(docdir)/+	install -m 0644 doc/*.html $(htmldir)/+++.PHONY: clean doc++doc:+	make -C doc++clean:+	rm -f src/*.o src/*.hi src/simgi +	make -C test clean	+	make -C doc clean
+ Models/brusselator.sgl view
@@ -0,0 +1,26 @@+{-----------------------------------------------------++  this is the input deck for the brusselator model +  (C) 2009 Markus Dittrich++------------------------------------------------------}++def parameters+  time       = 50.0+  outputIter = 50000+  outputFreq = 200+  systemVol  = nil  -- interpret rates as propensities+  outputFile = "brusselator_output.dat"+end++def molecules+  x 1000+  y 2000+end++def reactions+  nil    -> x         { 5000    }+  x      -> y         { 50.0    }+  2x + y -> 3x        { 0.00005 }+  x      -> nil       { 5.0     }+end
+ Models/oregonator.sgl view
@@ -0,0 +1,28 @@+{-----------------------------------------------------++  this is the input deck for the oregonator model +  (C) 2009 Markus Dittrich++------------------------------------------------------}++def parameters+  time       = 50.0+  outputIter = 50000+  outputFreq = 500+  systemVol  = nil  -- interpret rates as propensities+  outputFile = "oregonator_output.dat"+end++def molecules+  x 500+  y 1000+  z 2000  +end++def reactions+  y      -> x         { 2.0   }+  x + y  -> nil       { 0.1   }+  x      -> 2x + z    { 104.0 }+  2x     -> nil       { 0.016 }+  z      -> y         { 26.0  }+end
+ Models/volterra.sgl view
@@ -0,0 +1,26 @@+{-----------------------------------------------------++  this is the input deck for the lotka-volterra model +  (C) 2009 Markus Dittrich++------------------------------------------------------}++def parameters+  time       = 50.0+  outputIter = 50000+  outputFreq = 200+  systemVol  = nil  -- interpret rates as propensities+  outputFile = "volterra_output.dat"+end++def molecules+  x 1000+  y 2000+end++def reactions+  x      -> 2x       { 10.0 }+  x + y  -> 2y       { 0.01 }+  y      -> nil      { 10.0 }+end +
+ README view
@@ -0,0 +1,13 @@+DESCRIPTION:+------------++simgi is a stochastic simulator using the Gillespie algorithm [1,2].+simgi is released under the GPL v3.++(C) 2009 Markus Dittrich++See doc/simgi.html for more information.+++[1] D.T. Gillespie, J. Comput. Phys., 22, 403 (1976)+[2] D.T. Gillespie, J. Phys. Chem., 81, 2340 (1977)
+ Setup.hs view
@@ -0,0 +1,3 @@+#!/usr/bin/env runhaskell+import Distribution.Simple+main = defaultMain
+ doc/Makefile view
@@ -0,0 +1,31 @@++RST_FILES = simgi.rst++default: doc+++doc: clean_old build_html build_pdf+++build_html: $(RST_FILES)+	rst2html.py $< > $(<:.rst=.html)++build_pdf: $(RST_FILES)+	rst2latex.py $< > $(<:.rst=.tex)++	# fix indentation+	sed -i "17 s:^\(.*\):\\\setlength{\\\parindent}{0in}\n\1:" \+		$(<:.rst=.tex)+	pdflatex $(<:.rst=.tex)+	rm -f *.aux *.log *.out *.tex+++clean_old:+	rm -f *.html *.pdf+++.PHONY: clean++clean:+	+
+ doc/simgi.html view
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}++ul.auto-toc {+  list-style-type: none }++</style>+</head>+<body>+<div class="document" id="simgi-a-stochastic-gillespie-simulator-for-molecular-systems">+<h1 class="title">simgi - A Stochastic Gillespie Simulator for Molecular Systems</h1>+<table class="docinfo" frame="void" rules="none">+<col class="docinfo-name" />+<col class="docinfo-content" />+<tbody valign="top">+<tr><th class="docinfo-name">Author:</th>+<td>Markus Dittrich</td></tr>+<tr class="field"><th class="docinfo-name">email:</th><td class="field-body">haskelladdict at users dot sourceforge dot net</td>+</tr>+<tr><th class="docinfo-name">Version:</th>+<td>0.1.1 (06/02/2009)</td></tr>+</tbody>+</table>+<div class="section" id="contents">+<h1>Contents</h1>+<ol class="arabic simple">+<li><a class="reference internal" href="#introduction">Introduction</a></li>+<li><a class="reference internal" href="#status">Status</a></li>+<li><a class="reference internal" href="#download">Download</a></li>+<li><a class="reference internal" href="#compilation">Compilation</a></li>+<li><a class="reference internal" href="#simgi-model-generation-language-sgl">Simgi Model Generation Language (SGL)</a></li>+<li><a class="reference internal" href="#example-input-files">Example Input Files</a></li>+<li><a class="reference internal" href="#bugs">Bugs</a></li>+<li><a class="reference internal" href="#references">References</a></li>+</ol>+</div>+<div class="section" id="introduction">+<h1>Introduction</h1>+<p><strong>simgi</strong> is a fairly simple and straightforward stochastic simulator+based on Gillspie's <a class="footnote-reference" href="#id7" id="id1">[1]</a> direct method. <strong>simgi</strong> is implemented in+pure Haskell, command line driven and comes with a flexible simulation+description language called <a class="reference internal" href="#simgi-model-generation-language-sgl">Simgi Model Generation Language (SGL)</a>.+More information is available from the <a class="reference external" href="http://sourceforge.net/projects/simgi">project summary page</a>.</p>+</div>+<div class="section" id="status">+<h1>Status</h1>+<p>The 0.1 release of <strong>simgi</strong> provides a fully functional simulator+but should still be treated as an alpha version since several parts+of the code are currently not fully optimal. This is particularly+true for the random number generator which presently leverages the+StdGen instance of RandomGen <a class="footnote-reference" href="#id8" id="id2">[2]</a> and is probably not sufficient for+large simulations in terms of random number quality. Later revisions+of simgi will have a more sophisticated random number generator.+Nevertheless, for small systems (such as the examples in the+<em>Models/</em> directory) the current implementation should be sufficient.</p>+</div>+<div class="section" id="download">+<h1>Download</h1>+<p>The current release of simgi can be downloaded <a class="reference external" href="http://sourceforge.net/project/platformdownload.php?group_id=260550">here</a>.</p>+</div>+<div class="section" id="compilation">+<h1>Compilation</h1>+<p>Compilaton of <strong>simgi</strong> requires</p>+<ul class="simple">+<li><a class="reference external" href="http://haskell.org/ghc/">&gt;=ghc-6.10</a></li>+<li><a class="reference external" href="http://gmplib.org/">&gt;=gmp-4.3</a></li>+</ul>+<p>To compile the documentation (not required), you will also need</p>+<ul class="simple">+<li><a class="reference external" href="http://docutils.sourceforge.net/">&gt;=docutils-0.5</a></li>+<li>latex, e.g., tetex or texlive</li>+</ul>+<p>Building of <strong>simgi</strong> can be done either via</p>+<ul class="simple">+<li>the standard <tt class="docutils literal"><span class="pre">make,</span> <span class="pre">make</span> <span class="pre">check,</span> <span class="pre">make</span> <span class="pre">install</span></tt></li>+<li>or via cabal</li>+</ul>+</div>+<div class="section" id="simgi-model-generation-language-sgl">+<h1>Simgi Model Generation Language (SGL)</h1>+<p>simgi simulations are described via <a class="reference internal" href="#simgi-model-generation-language-sgl">Simgi Model Generation Language+(SGL)</a>. The corresponding simulation files typically have an <em>.sgl</em>+extension, but this is not enforced by the <strong>simgi</strong> simulation engine.</p>+<p>A SGL file consists of zero or more descriptor blocks of the form</p>+<pre class="literal-block">+def &lt;block name&gt;++  &lt;block content&gt;++end+</pre>+<p>The (but see <a class="footnote-reference" href="#id9" id="id3">[3]</a>) formatting of the input files is very flexible. In+particular, neither newlines <a class="footnote-reference" href="#id10" id="id4">[4]</a> nor extraneous whitespace matter.+Hence, the above SDL block could also be written on a single line.+However, it is strongly recommended to stick to a consistent and+&quot;visually simple&quot; layout to aid in &quot;comprehending&quot; the underlying+model.</p>+<p><strong>Comments</strong> can be added to the SGL file and are parsed according to+the Haskell language specs</p>+<ul class="simple">+<li>simple line comments begin with a <tt class="docutils literal"><span class="pre">--</span></tt> token and treat everything+until the next newline as a comment, including valid SDL commands.+Hence, SDL blocks containing line comments need to be separated by+newlines in order to be parsed correctly.</li>+<li>block comments begin with a <tt class="docutils literal"><span class="pre">{-</span></tt> token and end with a <tt class="docutils literal"><span class="pre">-}</span></tt>+token. Everything within a comment block is ignored by the parser+and block comments can be nested.</li>+</ul>+<p>Currently, the SDL specs define the following block types with their+respective block commands and block content:</p>+<p><strong>parameter block:</strong> <em>&lt;block name&gt; = parameters</em></p>+<blockquote>+<p>The purpose of the parameter block is to describe the global+simulation parameters. The following parameters are currently+supported:</p>+<dl class="docutils">+<dt><em>time = &lt;double&gt;</em></dt>+<dd>Maximum simulation time in seconds. Default is 0.0 s.</dd>+<dt><em>outputIter = &lt;Integer&gt;</em></dt>+<dd><p class="first">Output will be kept in memory and written to the output file and+stdout every <em>outputIter</em> iterations. Larger values should result+in faster simulations but require more system memory.+Default is to write output every 10000 iterations.</p>+<p class="last">Note: <em>outputIter</em> only affects how often output is written to+the output file, not how much is being accumulated during a+simulation (see outputFreq parameter).</p>+</dd>+<dt><em>outputFreq = &lt;Integer&gt;</em></dt>+<dd>Frequency with which output is generated. Default is 1000.</dd>+<dt><em>systemVol = &lt;double&gt;</em></dt>+<dd>Volume of the simulation system in liters. This is needed to+properly compute the reaction rates in molar units. If rates+should rather be interpreted as reaction propensities (like+in <a class="footnote-reference" href="#id7" id="id5">[1]</a>) please set <em>systemVol = nil</em>. Default is a system+volume of 1.0 liter.</dd>+<dt><em>outputFile = &lt;quoted string&gt;</em>:</dt>+<dd>Name of the output file. This is the only required parameter+in the parameter section. If not given, the simulation will+terminate.</dd>+</dl>+</blockquote>+<p><strong>molecule block:</strong> <em>&lt;block name&gt; = molecules</em></p>+<blockquote>+<p>This block consist of a list of pairs of the form</p>+<pre class="literal-block">+&lt;String&gt; &lt;Integer&gt;+</pre>+<p>giving the name of each molecule and the number of molecules+present initially. For example, the following molecule definition+block defines molecules <tt class="docutils literal"><span class="pre">A</span></tt> and <tt class="docutils literal"><span class="pre">B</span></tt> with initial numbers of+100 and 200, respectively</p>+<pre class="literal-block">+def molecules+  A 100+  B 200+end+</pre>+</blockquote>+<p><strong>reaction block</strong>: <em>&lt;block name&gt; = reactions</em></p>+<blockquote>+<p>This block describes the reactions between molecules defined in+the molecule block. Reactions are specified via</p>+<pre class="literal-block">+reactants -&gt; product { rate expression }+</pre>+<p>Here, <tt class="docutils literal"><span class="pre">reactants</span></tt> and <tt class="docutils literal"><span class="pre">products</span></tt> are of the form</p>+<pre class="literal-block">+&lt;Integer&gt; &lt;String&gt; + &lt;Integer&gt; &lt;String&gt; + .....+</pre>+<p>In this expression, <tt class="docutils literal"><span class="pre">&lt;String&gt;</span></tt> is the reactant or product name+as defined in the molecule block and <tt class="docutils literal"><span class="pre">&lt;Integer&gt;</span></tt> an optional+integer specifying the stoichiometry. If <tt class="docutils literal"><span class="pre">&lt;Integer&gt;</span></tt> is not+explicitly given, it is assumed to be 1.</p>+<p>The reaction rate can either be a fixed value of type <tt class="docutils literal"><span class="pre">&lt;Double&gt;</span></tt>+or else an mathematical expression involving <tt class="docutils literal"><span class="pre">&lt;Double&gt;</span></tt>,+molecule names, and the current simulation time. Hence, <strong>simgi</strong>+rate expressions can be arbitrary complex functions of the+instantaneous simulation time and the instantaneous numbers of any+molecule in the model. The parser will interpret any string in the+rate expression as a molecule name in a case sensitive fashion,+a mathematical operator or function (see <a class="footnote-reference" href="#id11" id="id6">[5]</a> for supported+functions), or the special variable TIME which refers to the+current simulation time. Hence, do <strong>not</strong> use any of the+mathematical keywords as a molecule name; this leads to undefined+behavior.</p>+<p>Here is an example reaction block for the two molecules <tt class="docutils literal"><span class="pre">A</span></tt> and+<tt class="docutils literal"><span class="pre">B</span></tt> defined above:</p>+<pre class="literal-block">+define reactions+  2A + B -&gt; A  { 10.0e-5 }+  B      -&gt; A  { 2.0e-5 * A * exp(-0.5*TIME) }+end+</pre>+<p>In the first reaction, 2 <tt class="docutils literal"><span class="pre">A</span></tt> molecules react with one <tt class="docutils literal"><span class="pre">B</span></tt> to+yield another <tt class="docutils literal"><span class="pre">A</span></tt> at a rate of 10.0e-5 1/(Mol s). The second+reaction describes a decay of <tt class="docutils literal"><span class="pre">B</span></tt> back to <tt class="docutils literal"><span class="pre">A</span></tt> at a rate+that is computed based on the instantaneous number of <tt class="docutils literal"><span class="pre">A</span></tt>+molecules present and which decays exponentially with simulation+time.</p>+<p>Internally, rate expressions are converted into a compute stack+in RPN format which is evaluated at run-time. Even though this+procedure is fairly efficient, there is some numerical overhead+incurred at each iteration and the use of complicated rate+expressions should therefore be avoided if possible.</p>+</blockquote>+</div>+<div class="section" id="example-input-files">+<h1>Example Input Files</h1>+<p>Below are several example input files detailing the use of SGL:</p>+<ul class="simple">+<li><a class="reference external" href="model_files/volterra.sgl">Lotka-Volterra Model</a></li>+<li><a class="reference external" href="model_files/brusselator.sgl">Brusselator Model</a></li>+<li><a class="reference external" href="model_files/oregonator.sgl">Oregonator Model</a></li>+</ul>+<p>These are also available in the <em>Models/</em> sub-directory in the source tree.</p>+</div>+<div class="section" id="bugs">+<h1>Bugs</h1>+<p>Please report all bugs and feature requests to+&lt;haskelladdict at users dot sourceforge dot net&gt;.</p>+</div>+<div class="section" id="references">+<h1>References</h1>+<table class="docutils footnote" frame="void" id="id7" 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="#id5">2</a>)</em> Daniel T. Gillespie (1977). &quot;Exact Stochastic Simulation of Coupled Chemical Reactions&quot;. The Journal of Physical Chemistry 81 (25): 2340-2361</td></tr>+</tbody>+</table>+<table class="docutils footnote" frame="void" id="id8" rules="none">+<colgroup><col class="label" /><col /></colgroup>+<tbody valign="top">+<tr><td class="label"><a class="fn-backref" href="#id2">[2]</a></td><td><a class="reference external" href="http://hackage.haskell.org/packages/archive/random/1.0.0.1/doc/html/System-Random#globalrng.html">http://hackage.haskell.org/packages/archive/random/1.0.0.1/doc/html/System-Random#globalrng.html</a></td></tr>+</tbody>+</table>+<table class="docutils footnote" frame="void" id="id9" rules="none">+<colgroup><col class="label" /><col /></colgroup>+<tbody valign="top">+<tr><td class="label"><a class="fn-backref" href="#id3">[3]</a></td><td>Since <strong>simgi</strong> currently is an alpha version there may be fairly drastic changes to the SDL specs in future releases until the first beta release.</td></tr>+</tbody>+</table>+<table class="docutils footnote" frame="void" id="id10" rules="none">+<colgroup><col class="label" /><col /></colgroup>+<tbody valign="top">+<tr><td class="label"><a class="fn-backref" href="#id4">[4]</a></td><td>An exception to this rule are line comments starting with <tt class="docutils literal"><span class="pre">--</span></tt> which ingnore everything until the next newline.</td></tr>+</tbody>+</table>+<table class="docutils footnote" frame="void" id="id11" rules="none">+<colgroup><col class="label" /><col /></colgroup>+<tbody valign="top">+<tr><td class="label"><a class="fn-backref" href="#id6">[5]</a></td><td>Rate expressions can contain any arithmetic expression involving the standard operators &quot;+&quot;, &quot;-&quot;, &quot;*&quot;, &quot;/&quot;, &quot;^&quot; (exponentiation), and the mathematical functions <tt class="docutils literal"><span class="pre">sqrt,</span> <span class="pre">exp,</span> <span class="pre">log,</span> <span class="pre">log2,</span> <span class="pre">log10,</span> <span class="pre">sin,</span> <span class="pre">cos,</span> <span class="pre">tan,</span> <span class="pre">asin,</span> <span class="pre">acos,</span> <span class="pre">atan,</span> <span class="pre">sinh,</span> <span class="pre">cosh,</span> <span class="pre">tanh,</span> <span class="pre">asinh,</span> <span class="pre">acosh,</span> <span class="pre">atanh,</span> <span class="pre">acosh,</span> <span class="pre">atanh,</span> <span class="pre">erf,</span> <span class="pre">erfc,</span> <span class="pre">abs</span></tt>.</td></tr>+</tbody>+</table>+</div>+</div>+</body>+</html>
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+ doc/simgi.rst view
@@ -0,0 +1,248 @@+================================================================+simgi - A Stochastic Gillespie Simulator for Molecular Systems+================================================================++:Author: Markus Dittrich++:email: haskelladdict at users dot sourceforge dot net++:Version: 0.1.1 (06/02/2009)+++Contents+---------++1) Introduction_+2) Status_+3) Download_+4) Compilation_ +5) `Simgi Model Generation Language (SGL)`_+6) `Example Input Files`_+7) Bugs_+8) References_++Introduction+------------++**simgi** is a fairly simple and straightforward stochastic simulator +based on Gillspie's [1]_ direct method. **simgi** is implemented in +pure Haskell, command line driven and comes with a flexible simulation+description language called `Simgi Model Generation Language (SGL)`_.+More information is available from the `project summary page <http://sourceforge.net/projects/simgi>`_.+++Status +------++The 0.1 release of **simgi** provides a fully functional simulator +but should still be treated as an alpha version since several parts +of the code are currently not fully optimal. This is particularly +true for the random number generator which presently leverages the +StdGen instance of RandomGen [2]_ and is probably not sufficient for +large simulations in terms of random number quality. Later revisions +of simgi will have a more sophisticated random number generator. +Nevertheless, for small systems (such as the examples in the +*Models/* directory) the current implementation should be sufficient. +++Download+--------++The current release of simgi can be downloaded `here <http://sourceforge.net/project/platformdownload.php?group_id=260550>`_.+++Compilation+-----------++Compilaton of **simgi** requires ++- `>=ghc-6.10 <http://haskell.org/ghc/>`_+- `>=gmp-4.3  <http://gmplib.org/>`_  ++To compile the documentation (not required), you will also need++- `>=docutils-0.5 <http://docutils.sourceforge.net/>`_+- latex, e.g., tetex or texlive+++Building of **simgi** can be done either via ++- the standard ``make, make check, make install``+- or via cabal++++Simgi Model Generation Language (SGL)+-------------------------------------++simgi simulations are described via `Simgi Model Generation Language +(SGL)`_. The corresponding simulation files typically have an *.sgl* +extension, but this is not enforced by the **simgi** simulation engine. ++A SGL file consists of zero or more descriptor blocks of the form++::++  def <block name>++    <block content>++  end++The (but see [3]_) formatting of the input files is very flexible. In+particular, neither newlines [4]_ nor extraneous whitespace matter. +Hence, the above SDL block could also be written on a single line. +However, it is strongly recommended to stick to a consistent and +"visually simple" layout to aid in "comprehending" the underlying+model.++**Comments** can be added to the SGL file and are parsed according to +the Haskell language specs++- simple line comments begin with a ``--`` token and treat everything +  until the next newline as a comment, including valid SDL commands. +  Hence, SDL blocks containing line comments need to be separated by +  newlines in order to be parsed correctly.+- block comments begin with a ``{-`` token and end with a ``-}`` +  token. Everything within a comment block is ignored by the parser +  and block comments can be nested.++Currently, the SDL specs define the following block types with their +respective block commands and block content:+++**parameter block:** *<block name> = parameters*++  The purpose of the parameter block is to describe the global +  simulation parameters. The following parameters are currently+  supported:++  *time = <double>*+    Maximum simulation time in seconds. Default is 0.0 s.++  *outputIter = <Integer>*+    Output will be kept in memory and written to the output file and +    stdout every *outputIter* iterations. Larger values should result +    in faster simulations but require more system memory. +    Default is to write output every 10000 iterations.++    Note: *outputIter* only affects how often output is written to +    the output file, not how much is being accumulated during a +    simulation (see outputFreq parameter).++  *outputFreq = <Integer>*+    Frequency with which output is generated. Default is 1000.++  *systemVol = <double>*+    Volume of the simulation system in liters. This is needed to +    properly compute the reaction rates in molar units. If rates +    should rather be interpreted as reaction propensities (like +    in [1]_) please set *systemVol = nil*. Default is a system+    volume of 1.0 liter.++  *outputFile = <quoted string>*:+    Name of the output file. This is the only required parameter +    in the parameter section. If not given, the simulation will +    terminate.++++**molecule block:** *<block name> = molecules*++  This block consist of a list of pairs of the form ::++     <String> <Integer>++  giving the name of each molecule and the number of molecules+  present initially. For example, the following molecule definition +  block defines molecules ``A`` and ``B`` with initial numbers of +  100 and 200, respectively ::++    def molecules+      A 100+      B 200+    end+++**reaction block**: *<block name> = reactions*++  This block describes the reactions between molecules defined in +  the molecule block. Reactions are specified via ::++     reactants -> product { rate expression }++  Here, ``reactants`` and ``products`` are of the form ::++     <Integer> <String> + <Integer> <String> + .....++  In this expression, ``<String>`` is the reactant or product name +  as defined in the molecule block and ``<Integer>`` an optional +  integer specifying the stoichiometry. If ``<Integer>`` is not +  explicitly given, it is assumed to be 1.++  The reaction rate can either be a fixed value of type ``<Double>`` +  or else an mathematical expression involving ``<Double>``, +  molecule names, and the current simulation time. Hence, **simgi** +  rate expressions can be arbitrary complex functions of the +  instantaneous simulation time and the instantaneous numbers of any+  molecule in the model. The parser will interpret any string in the +  rate expression as a molecule name in a case sensitive fashion, +  a mathematical operator or function (see [5]_ for supported +  functions), or the special variable TIME which refers to the +  current simulation time. Hence, do **not** use any of the +  mathematical keywords as a molecule name; this leads to undefined+  behavior.+  +  Here is an example reaction block for the two molecules ``A`` and +  ``B`` defined above::++    define reactions+      2A + B -> A  { 10.0e-5 }+      B      -> A  { 2.0e-5 * A * exp(-0.5*TIME) }+    end+   +  In the first reaction, 2 ``A`` molecules react with one ``B`` to +  yield another ``A`` at a rate of 10.0e-5 1/(Mol s). The second +  reaction describes a decay of ``B`` back to ``A`` at a rate +  that is computed based on the instantaneous number of ``A`` +  molecules present and which decays exponentially with simulation+  time.++  Internally, rate expressions are converted into a compute stack+  in RPN format which is evaluated at run-time. Even though this+  procedure is fairly efficient, there is some numerical overhead+  incurred at each iteration and the use of complicated rate +  expressions should therefore be avoided if possible.+++Example Input Files+-------------------++Below are several example input files detailing the use of SGL:++- `Lotka-Volterra Model <model_files/volterra.sgl>`_+- `Brusselator Model <model_files/brusselator.sgl>`_+- `Oregonator Model <model_files/oregonator.sgl>`_++These are also available in the *Models/* sub-directory in the source tree.+++Bugs+----++Please report all bugs and feature requests to +<haskelladdict at users dot sourceforge dot net>. +++References+----------++.. [1] Daniel T. Gillespie (1977). "Exact Stochastic Simulation of Coupled Chemical Reactions". The Journal of Physical Chemistry 81 (25): 2340-2361++.. [2] http://hackage.haskell.org/packages/archive/random/1.0.0.1/doc/html/System-Random#globalrng.html++.. [3] Since **simgi** currently is an alpha version there may be fairly drastic changes to the SDL specs in future releases until the first beta release.++.. [4] An exception to this rule are line comments starting with ``--`` which ingnore everything until the next newline.++.. [5] Rate expressions can contain any arithmetic expression involving the standard operators "+", "-", "*", "/", "^" (exponentiation), and the mathematical functions ``sqrt, exp, log, log2, log10, sin, cos, tan, asin, acos, atan, sinh, cosh, tanh, asinh, acosh, atanh, acosh, atanh, erf, erfc, abs``.
+ simgi.cabal view
@@ -0,0 +1,24 @@+Name:          simgi+Version:       0.1.1+License:       GPL+license-file:  COPYING+copyright:     (C) 2009 Markus Dittrich+category:      Scientific Simulation+Synopsis:      stochastic simulation engine+Description:   simgi is a stochastic simulation engine to model+               molecular systems using Gillespie's method.+Author:        <haskelladdict@users.sourceforge.net>+Maintainer:    <haskelladdict@users.sourceforge.net>+stability:     alpha+build-type:    Simple+Homepage:      http://simgi.sourceforge.net/+cabal-version: >= 1.6+extra-source-files: README++Executable simgi+  Build-Depends:  base, containers >= 0.1.0.0,+                  parsec == 2.1.*, mtl >= 1.1.0.2, haskell98,+                  random >= 1.0.0.1+  ghc-options:    -O2+  Main-Is:        simgi.hs+  hs-source-dirs: src
+ src/CommandLine.hs view
@@ -0,0 +1,85 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | main gsim driver+module CommandLine ( process_commandline +                   , Options(..)+                   ) where++-- imports+import Prelude+import System+import System.Console.GetOpt++-- local imports+import Messages+++-- | main driver for command line processing+process_commandline :: [String] -> IO ((CmdlRequest,String), [String])+process_commandline args = ++  let +    (actions, nonOpts, _) = getOpt RequireOrder options args+  in+    foldl (>>=) ( return defaultOptions ) actions >>= \opts ->++    let +      Options { cmdlRequest = request +              , cmdlString   = pattern+              } = opts+    in+      return ((request,pattern),nonOpts) ++++-- | possible options for commandline+data CmdlRequest = None | Help+++-- | data structure for keeping track of +-- selected command line options+data Options = Options {+  cmdlRequest :: CmdlRequest,+  cmdlString  :: String+}+++-- | default selections+defaultOptions :: Options+defaultOptions = Options {+  cmdlRequest = None,+  cmdlString  = ""+}+++-- | available command line flags+options :: [OptDescr (Options -> IO Options)]+options = [+  Option ['v'] ["version-info"] (NoArg version_info) +         "show version information"]+++-- | extractor function for version info+version_info :: Options -> IO Options+version_info _ =+  do+    show_version+    exitWith ExitSuccess
+ src/Engine.hs view
@@ -0,0 +1,210 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | the main compute Engine+module Engine ( create_initial_output+              , create_initial_state+              , gillespie_driver+              , module GenericModel+              ) where++-- imports+import Control.Monad.State+import qualified Data.Map as M+import Prelude+import Text.Printf+import System.IO++-- local imports+import ExtraFunctions+import GenericModel+import RpnCalc++-- import Debug.Trace++-- | main simulation driver+-- the simulator either stops when+-- 1) the number of iterations is exhausted+-- 2) the current time is > t_max, if t_max is set to+--    zero t_max is treated as being infinity +gillespie_driver :: Handle -> Double -> Integer -> ModelState -> IO ()+gillespie_driver handle simTime dmpIter state =  +  let (output, outState)  = runState run_gillespie $ state +      (curTime, newState) = update_state dmpIter outState+  in+    (write_output handle . reverse $ output)+    >> if curTime >= simTime+         then return ()+         else gillespie_driver handle simTime dmpIter newState++++-- | updates the state for the next iteration+update_state :: Integer -> ModelState -> (Double,ModelState)    +update_state dataDumpIter state@(ModelState { currentTime = t +                                            , maxIter     = it+                                            }) =+  (t, state { maxIter = it + dataDumpIter, outputList = [] })+++-- | actual compute loop+run_gillespie :: GillespieState [Output]+run_gillespie = get++  >>= \inState@(ModelState { molCount    = in_mols+                           , reactions   = in_reacts+                           , randNums    = (r1:r2:randRest)+                           , currentTime = t+                           , currentIter = it+                           , maxTime     = t_max+                           , maxIter     = it_max+                           , outputFreq  = freq+                           , outputList  = output+                           }) ->++    -- compute and update the next state+    let out_rates  = compute_rates in_reacts in_mols t []+        a_0        = sum out_rates+        tau        = (-1.0/a_0) * log(r1)+        t_new      = t+tau+        mu         = get_mu (a_0*r2) out_rates+        out_mols   = adjust_molcount in_mols in_reacts mu+        new_output = generate_output freq it t_new out_mols output+        newState   = inState { molCount    = out_mols+                             , rates       = out_rates+                             , randNums    = randRest+                             , currentTime = t_new+                             , currentIter = it+1+                             , outputList  = new_output+                             }+    in++    -- this prevents simulation from getting stuck+    -- FIXME: We need to come up with mechanism to propagate+    -- error message corresponding to cases such as this one to the user!+    if (is_equal tau 0.0)+      then let finalState = newState { currentTime = t_max } in+           put finalState >> return output+      else +        if ( it_max == it || t >= t_max )+          then return output+          else put newState >> run_gillespie+++-- | generate a new Output data structure based on the current+-- molecule counts+generate_output :: Integer -> Integer -> Double -> MoleculeMap +                -> [Output] -> [Output]+generate_output afreq it t amol outlist  +  | mod it afreq /= 0  = outlist+  | otherwise        = new_out:outlist++    where+      new_out = Output { iteration = it+                       , time      = t+                       , mols      = amol+                       }++++-- | depending on which reaction happened adjust the number of +-- molecules in the system+adjust_molcount :: MoleculeMap -> [Reaction] -> Int -> MoleculeMap+adjust_molcount theMap rs mID =++  let (Reaction { react = react_in }) = rs !! mID+  in+    adjustMap react_in theMap ++  where+    adjustMap :: [(String,Int)] -> MoleculeMap -> MoleculeMap+    adjustMap [] m = m+    adjustMap ((k,a):rands) m = let val   = (M.!) m k+                                    m_new = M.insert k (a+val) m+                                in+                                  adjustMap rands m_new+++-- | pick the \mu value for the randomly selected next reaction +-- reaction to happen+get_mu :: Double -> [Double] -> Int+get_mu val = length . takeWhile ( <val ) . scanl1 (+) ++                 +-- | compute the current value for the reaction probabilities based on +-- the number of molecules and reaction rates+compute_rates :: [Reaction] -> MoleculeMap -> Double +              -> RateList -> RateList+compute_rates [] _ _ rts = reverse rts+compute_rates ((Reaction {rate = c_in, aList = a_in }):rs) +  theMap theTime rts = +  +  case c_in of+    (Constant aRate)    -> compute_rates rs theMap theTime+       ((a_new aRate): rts)+    (Function rateFunc) -> compute_rates rs theMap theTime+       ((a_new . (rpn_compute theMap theTime) $ rateFunc):rts)+ +  where+    mult  = product $ map (\(a,f) -> f . fromIntegral $ +            (M.!) theMap a) a_in +    a_new = (*) mult +++-- | initialize the output data structure+create_initial_output :: ModelState -> Output+create_initial_output (ModelState { molCount = initialMols }) = +  +  Output { iteration = 1+         , time      = 0.0+         , mols      = initialMols+         }+++-- | set up the initial state+create_initial_state:: ModelState -> [Double] -> Output -> ModelState+create_initial_state state rand output = ++  state { rates       = defaultRateList+        , randNums    = rand+        , currentTime = 0.0+        , currentIter = 1+        , outputList  = [output]+        }+++-- | basic routine writing the simulation output to stdout+write_output :: Handle -> [Output] -> IO ()+write_output _ [] = return ()+write_output handle ((Output {iteration = it, time = t, mols = m}):xs) = +  let header = (printf "%-10d %18.15g" it t) :: String+      counts = create_count_string m+  in+    -- write molecule data to output file+    hPutStrLn handle (header ++ counts)++    -- write current iteration to stdout+    >> (putStrLn $ "iteration | time   --->   " ++ header)+    >> write_output handle xs++  where+    create_count_string :: MoleculeMap -> String+    create_count_string = foldr (\x a -> (printf "%10d " x) ++ a) +                          "" . M.elems
+ src/ExtraFunctions.hs view
@@ -0,0 +1,153 @@+{-# LANGUAGE ForeignFunctionInterface #-}+{-----------------------------------------------------------------+ +  (c) 2008-2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | definition of additional math and helper functions+module ExtraFunctions ( avogadroNum+                      , erf+                      , erfc+                      , fact +                      , is_equal+                      , is_equal_with+                      , real_exp +                      , to_int+                      , to_positive_int+                      ) where+++-- imports+import Foreign()+import Foreign.C.Types+import Prelude +++-- | a few constants+avogadroNum :: Double+avogadroNum = 6.0221415e23+++-- | use glibc DBL_EPSILON+dbl_epsilon :: Double+dbl_epsilon = 2.2204460492503131e-16++-- | comparison function for doubles via dbl_epsion+is_equal :: Double -> Double -> Bool+is_equal x y = abs(x-y) <= abs(x) * dbl_epsilon+++-- | comparison function for doubles via threshold+is_equal_with :: Double -> Double -> Double -> Bool+is_equal_with x y th = abs(x-y) <= abs(x) * th+++-- | function checking if a Double can be interpreted as a non+-- negative Integer. We need this since all parsing of numbers +-- is done with Doubles but some functions only work for +-- non-negative integers such as factorial.+-- To check if we are dealing with Double, we convert to an+-- Integer via floor and the compare if the numbers are identical.+-- If yes, the number seems to be an Integer and we return it,+-- otherwise Nothing+to_positive_int :: Double -> Maybe Integer+to_positive_int x = +  case (is_equal (fromInteger . floor $ x) x) && (x > 0.0) of+    True  -> Just $ floor x+    False -> Nothing+++-- | function checking if a Double can be interpreted as an+-- Integer. See is_positive_int for more detail+to_int :: Double -> Maybe Integer+to_int x = +  case is_equal (fromInteger . floor $ x) x of+    True  -> Just $ floor x+    False -> Nothing+++-- | helper function for defining real powers+-- NOTE: We use glibc's pow function since it is more+-- precise than implementing it ourselves via, e.g.,+-- pow a x = exp $ x * log a+foreign import ccall "math.h pow"+        c_pow :: CDouble -> CDouble -> CDouble++real_exp :: Double -> Double -> Double +real_exp a x = realToFrac $ c_pow (realToFrac a) (realToFrac x)+++-- | factorial function+fact :: Integer -> Integer+fact 0 = 1+fact n = n * fact (n-1)+++-- | error function erf(x)+-- we use a recursive solution of the Taylor series expansion+erf :: Double -> Double+erf x +  | x == 0.0     = 0.0            -- our recursive alg. loops forever+                                  -- in this case+  | abs(x) > 2.2 = 1.0 - erfc x   -- use erfc for numerical accuracy+  | otherwise    = 2.0 / sqrt(pi) * (erf_h x x 1.0)++  where+    erf_h old x_old n = let x_new = x_old * (x_next n)+                            tot   = old + x_new+                        in+                          if abs(x_new/tot) < dbl_epsilon+                          then tot+                          else erf_h tot x_new (n+1.0)++    -- Note: We need (2::Int) here to silence ghc+    x_next n = -(x^(2::Int)) * (2.0*n-1.0)/(n * (2.0*n+1.0))  ++++-- | complementary error function erfc(x) = 1 - erf(x)+-- we use a recursive solution of the continued fraction+-- expression of erfc(x) for it superior convergence +-- property. Here, we calculate the ith and (i+1)th convergent, (see+-- http://archives.math.utk.edu/articles/atuyl/confrac/intro.html)+-- and terminate when the relative difference is smaller than a+-- certain threshold. +erfc :: Double -> Double+erfc x +  | abs(x) < 2.2  = 1.0 - erf(x)   -- use erf(x) in [-2.2,2.2]+  | signum(x) < 0 = 2.0 - erfc(-x) -- continued fraction expansion+                                   -- only valid for x > 0+  | otherwise     = 1/sqrt(pi) * exp(-x^(2::Int))+                    * (erfc_h nc1 nc2 dc1 dc2 1.0)++  where+    nc1 = 1.0            :: Double -- numerator of 1st convergent+    nc2 = x              :: Double -- numerator of 2nd convergent+    dc1 = x              :: Double -- denominator of 1st convergent+    dc2 = x^(2::Int)+0.5 :: Double -- denominator of 2nd convergent++    erfc_h n1 n2 d1 d2 i = +      let num_new   = n1*i + n2*x+          denom_new = d1*i + d2*x+          d_old     = n2/d2+          d_new     = num_new/denom_new+      in+        if abs((d_old - d_new)/d_new) < dbl_epsilon+        then d_new+        else erfc_h n2 num_new d2 denom_new (i+0.5)+
+ src/GenericModel.hs view
@@ -0,0 +1,119 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | data structures needed for defining a stochastic model+module GenericModel ( defaultRateList+                    , GillespieState+                    , initialModelState+                    , ModelState(..)+                    , MoleculeMap+                    , Output(..)+                    , Rate(..)+                    , RateList+                    , Reaction(..)+                    ) where+++-- imports+import Control.Monad.State+import qualified Data.Map as M+import Prelude+++-- local imports+import RpnData+++-- | A MoleculeMap keeps track of the current number of molecules+type MoleculeMap = M.Map String Int+++-- | data type for reaction rates which can either be a Double+-- or an RpnStack describing a function to compute the rate+-- at run time+data Rate = Constant Double | Function RpnStack++-- | List of reactions and corresponding rates+type RateList    = [Double]++defaultRateList :: RateList+defaultRateList = [] +++-- | for each elementary reaction i we need to provide +--   1) the reaction rate c_i or rate function +--   2) the reaction order (first, second, ...)+--   2) aList describing which molecular species are participating+--      in a reaction (needed for computing h_mu in Gillespie's +--      notation) and a function mapping a molecule count to the+--      proper h_mu value (needed e.g. for cases where we have+--      2X terms where h_my would be 0.5*X*(X-1).+--   3) a list of tuple (i,j) describing that the count of molecule+--      i changes by j should this reaction take place+data Reaction = Reaction { rate       :: Rate+                         , aList      :: [(String,Double -> Double)]+                         , react      :: [(String,Int)]+                         }+++-- | Our model state+data ModelState = ModelState { molCount    :: MoleculeMap+                             , rates       :: RateList+                             , reactions   :: [Reaction]+                             , randNums    :: [Double]+                             , systemVol   :: Double+                             , currentTime :: Double+                             , currentIter :: Integer+                             , maxTime     :: Double+                             , maxIter     :: Integer+                             , outputFreq  :: Integer+                             , outputList  :: [Output]+                             , outfileName :: String+                             }++type GillespieState a = State ModelState a+++-- | data structure for keeping track of our output+data Output = Output { iteration :: Integer+                     , time      :: Double+                     , mols      :: MoleculeMap +                     }+  deriving(Show)+++-- | initial model state to be partially filled by the +-- parser from the input deck+initialModelState :: ModelState+initialModelState = ModelState { molCount    = M.empty+                               , rates       = []+                               , reactions   = []+                               , randNums    = []+                               , systemVol   = 1.0+                               , currentTime = 0.0+                               , currentIter = 0+                               , maxTime     = 0.0+                               , maxIter     = 10000+                               , outputFreq  = 1000+                               , outputList  = []+                               , outfileName = ""+                               }++
+ src/InputCheck.hs view
@@ -0,0 +1,128 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | module responsible for doing some basic input checking+module InputCheck ( check_input ) where++-- imports+import Control.Monad.Error()+import qualified Data.List as L+import qualified Data.Map as M+import Prelude++-- local imports+import GenericModel+import RpnData+++-- | small function checking for common errors in the input deck+-- since checking is currently fairly simple we'll do it by hand+-- should this ever become more extensive we should probably consider+-- using Control.Monad.Error+check_input :: ModelState -> Either String Bool +check_input (ModelState { molCount    = theMols+                        , reactions   = theReactions+                        , maxIter     = iterCount+                        , outputFreq  = outFreq+                        , outfileName = fileName+                        }) +  = check_molecules (defined_mols theMols) +      (react_mols theReactions)+    >> check_positive_outfreq outFreq+    >> check_positive_itercount iterCount+    >> check_filename fileName+    >> check_reaction_rate_functions (defined_mols theMols) +         (rate_mols theReactions)++ where+  -- | extract all reaction participants+  react_mols = L.nub . L.concat . map (map (fst) . react) +++  -- | extract all definied molecules+  defined_mols = M.keys +++  -- | extract all molecules appearing in reaction rate+  -- functions+  rate_mols theRates = +    let+      stacks    = foldr extract_rate_func [] . map rate $ theRates+    in+      L.nub . concat . map (foldr extract_rate_vars []) $ stacks++      where+        extract_rate_func (Function a) acc = a:acc+        extract_rate_func _            acc = acc++        extract_rate_vars (Variable a) acc = a:acc+        extract_rate_vars _            acc = acc+++-- | make sure the user specified an output file name+check_filename :: String -> Either String Bool+check_filename name +  | name == ""  = Left "Error: Please specify an output file name!"+  | otherwise   = Right True+++-- | make sure all molecules in reactions are defined+check_molecules :: [String] -> [String] -> Either String Bool+check_molecules defMols reactMols = +  let +    not_present = reactMols L.\\ defMols+  in+    case null not_present of+      True  -> Right True+      False -> Left $ +        "Error: The following molecules are not definied: " +        ++ (L.concat $ L.intersperse "," not_present)+++-- | make sure the user entered a positive integer for outputFreq+check_positive_outfreq :: Integer -> Either String Bool+check_positive_outfreq freq = +  if freq < 0 +    then Left "Error: outputFreq must be a positive integer!"+    else Right True+++-- | make sure the user entered a positive integer for outputFreq+check_positive_itercount :: Integer -> Either String Bool+check_positive_itercount iter = +  if iter < 0 +    then Left "Error: outputIter must be a positive integer!"+    else Right True+++-- | make sure the user defined reaction rate function reference+-- only existing molecule names+check_reaction_rate_functions :: [String] -> [String] +                              -> Either String Bool+check_reaction_rate_functions defMols rateMols =+  let +    no_mol = rateMols L.\\ defMols+  in+    case null no_mol of+      True  -> Right True+      False -> Left $+        "Error: The following molecules defined in reaction "+        ++ "rates do not exist: " +        ++ (L.concat $ L.intersperse "," no_mol)
+ src/InputParser.hs view
@@ -0,0 +1,317 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | input file parser +module InputParser ( input_parser ) where++-- imports+import Control.Monad+import qualified Data.Map as M+import Prelude+import TokenParser+++-- local imports+import ExtraFunctions+import GenericModel+import RpnData+import RpnParser++-- import Debug.Trace+++-- | main parser entry point+input_parser :: CharParser ModelState ModelState+input_parser = whiteSpace +               *> many ( choice [ try parse_parameter_def+                                , try parse_molecule_def+                                , try parse_reaction_def+                                ])+               *> eof+               >> getState+            <?> "main parser"+++-- | parser for simulation parameters+parse_parameter_def :: CharParser ModelState ()+parse_parameter_def = between (reserved "def" *> reserved "parameters")+                              (reserved "end")+                              (parse_parameters `sepBy` whiteSpace) +                      *> pure ()+                   <?> "parameter definitions"+++-- | parse the individual parameters+parse_parameters :: CharParser ModelState ()+parse_parameters = parse_time+                <|> parse_outputFile+                <|> parse_outputIter+                <|> parse_outputFreq+                <|> parse_systemVol+                <?> "time, outputIter, systemVol, outputFreq, outputFile"+++-- | parse the simulation time specs+parse_time :: CharParser ModelState ()+parse_time = join (updateState <$> insert_time +                   <$> (reserved "time" *> reservedOp "=" +                        *> parse_number))+  +  where+    insert_time t state = state { maxTime = t }+++-- | parse the value of the simulated system volume+parse_systemVol :: CharParser ModelState ()+parse_systemVol = join (updateState <$> insert_volume+                       <$> (reserved "systemVol" *> reservedOp "="+                           *> (parse_positive_number+                             <|> parse_systemVol_nil )))+               <?> "system volume"++  where+    -- needed to avoid monomorphism warning+    parse_systemVol_nil :: CharParser ModelState Double+    parse_systemVol_nil = reserved "nil" *> pure (-1.0)++    insert_volume vol state = state { systemVol = vol }+++-- | parse the name of the output file +-- accepts paths but will NOT create any of the parents+parse_outputFile :: CharParser ModelState ()+parse_outputFile = join (updateState <$> insert_filename+                     <$> (reserved "outputFile" *> reservedOp "="+                          *> parse_filename ))++  where+    insert_filename name state = state { outfileName = name }+++-- | parse a filename+parse_filename :: CharParser ModelState String+parse_filename = stringLiteral++++-- | parse the output iteration specification if present+parse_outputIter :: CharParser ModelState ()+parse_outputIter = join (updateState <$> insert_outputIter+                        <$> (reserved "outputIter" *> reservedOp "="+                             *> integer ))++  where+    insert_outputIter i state = state { maxIter = i }+++-- | parse the output iteration specification if present+parse_outputFreq :: CharParser ModelState ()+parse_outputFreq = join (updateState <$> insert_outputFreq+                        <$> (reserved "outputFreq" *> reservedOp "="+                             *> integer ))++  where+    insert_outputFreq i state = state { outputFreq = i }+++-- | parser for molecule definitions+parse_molecule_def :: CharParser ModelState ()+parse_molecule_def = join ( updateState <$> insert_molecules <$> +  between (reserved "def" *> reserved "molecules")+          (reserved "end")+          (parse_molecules `sepBy` whiteSpace) )+                  <?> "molecule definitions"++  where+    insert_molecules :: [(String, Int)] -> ModelState -> ModelState+    insert_molecules theMols state = +      state { molCount = M.fromList theMols }+++-- | parse a molecule name and the number of molecules of this type+parse_molecules :: CharParser ModelState (String,Int)+parse_molecules = make_molecule <$> (try molname) <*> integer+  where+    make_molecule mol aCount = (mol,fromInteger aCount)+++-- | parser for a molecule name +-- A molecule name can consist of letters and numbers but has to +-- start with a letter. The following keywords are reserved+molname :: CharParser ModelState String+molname = not_end ((:) <$> letter <*> many (alphaNum <?> ""))+        <?> "molecule name" +++-- | short checker making sure we don't scan beyond the "end" statement+-- of a block +not_end :: CharParser ModelState String -> CharParser ModelState String+not_end p = p >>= \name -> case name /= "end" of+                             True  -> pure name+                             False -> pzero+++-- | parser for reaction definitions+parse_reaction_def :: CharParser ModelState ()+parse_reaction_def = join ( updateState <$> insert_reactions <$>+                     between (reserved "def" *> reserved "reactions")+                             (reserved "end")+                             (parse_reaction `sepBy` whiteSpace) )+                  <?> "reaction definitions"+  +  where+    insert_reactions :: [Reaction] -> ModelState -> ModelState+    insert_reactions reacts state = state { reactions = reacts }+++-- | parser for a single reaction specification of the type+-- aA + bB + cC + .... -> n1P1 + n2P2 + ......   : rate :+-- NOTE: In order to convert the reaction rates (if requested+--       by the user) we also need to extract the system+--       volume)+parse_reaction :: CharParser ModelState Reaction+parse_reaction = setup_reaction +                 <$> (parse_react_prod <* reservedOp "->") +                 <*> parse_react_prod +                 <*> parse_rate+                 <*> (getState +                      >>= \(ModelState {systemVol = vol}) -> pure vol)  +  where+    -- | set up a Reaction data structure from the parsed reaction+    setup_reaction r p cin vol = +      let +        action  = create_react r p+        hFactor = create_hFact r +        theRate = if (vol < 0.0)    -- no rate conversion for systemVol = nil+                    then cin+                    else convert_rate cin (M.size r) vol+      in +        Reaction { rate       = theRate+                 , aList      = hFactor+                 , react      = action+                 }+++    -- | convert reaction propensities into rates if requested+    -- by the user. For constants we simply multiply, for+    -- rate functions we push the neccessary conversion onto+    -- the stack+    convert_rate theConst@(Constant c) order volume =+      case order of+        1 -> theConst+        _ -> Constant $ c/(avogadroNum * volume^(order-1))++    convert_rate theFunc@(Function stack) order volume =+      case order of+        1 -> theFunc+        _ -> let mult = 1.0/(avogadroNum * volume^(order-1)) in+               Function $ stack ++ [Number mult,BinFunc (*)]++++    -- | create the list holding the molecule number changes for +    -- this reaction+    create_react r p = let +                         reacts = M.map (*(-1)) r +                       in+                         M.assocs $ M.unionWith (+) reacts p+++    -- | create the list containing the h factors+    -- WARNING/FIXME: Currently, things are ill defined if the number of+    -- molecules for species A is below the stoichiometric reactant+    -- coefficient; i.e. if #A = 2 then 3A -> ... does not make sense+    create_hFact :: (M.Map String Int) -> [(String, Double -> Double)]+    create_hFact     = create_hFact_h [] . M.assocs  +    +      where+        create_hFact_h acc [] = acc+        create_hFact_h acc ((k,v):xs) = +          let +            v_int = fromIntegral v :: Double+          in+            create_hFact_h ((k,\x -> (1.0/v_int) +              * generate_lambda v_int x):acc) xs++            where+              generate_lambda :: Double -> Double -> Double+              generate_lambda 1 x   = x+              generate_lambda n x   = (x-n+1) * generate_lambda (n-1) x   +++-- | parse rate parses a reaction rate. This can either be a simple+-- constant of a full blown infix math expression.+-- Reaction rates must be enclosed by colons ":"+parse_rate :: CharParser ModelState Rate+parse_rate = (try parse_constant_rate) <|> parse_rate_function+          <?> "rate constant or rate function"+++-- | parser for a simple rate constant expression+parse_constant_rate :: CharParser ModelState Rate+parse_constant_rate = Constant <$> braces parse_number+                   <?> "rate constant" +++-- | parser for a rate function+parse_rate_function :: CharParser ModelState Rate+parse_rate_function = Function <$> braces parse_infix_to_rpn+                   <?> "rate function" +++-- | parse list of reactants/products of reaction+-- we expect to parse a stream that looks like+-- n_1 R1 + n_2 R2 + n_3 R3 + .....+-- If n_i is missing we assume it is 1.0+parse_react_prod :: CharParser ModelState (M.Map String Int)+parse_react_prod = (reserved "nil" *> pure (M.empty))+                <|> (M.fromList <$> ((make_tuple <$> option 1 integer +                    <*> (try molname <* whiteSpace)) +                         `sepBy` reservedOp "+") )+                <?> "reactant or product list"+  +  where+    make_tuple x y = (y, fromInteger x)+++-- | parse a number, can be used with 'many' and other parser+-- combinators; integers are automatically promoted to double+parse_number :: CharParser ModelState Double+parse_number = converter <$> naturalOrFloat+            <?> "signed integer or double"+  where+    converter val = case val of+                      Left i  -> (fromInteger i)+                      Right x -> x+++-- | parse a positive number, can be used with 'many' and other +-- parser combinators; integers are automatically promoted to double+parse_positive_number :: CharParser ModelState Double+parse_positive_number = naturalOrFloat +  >>= \num -> case num of+                Left ival  -> if (ival > 0)+                                then return (fromInteger ival)+                                else pzero+                Right dval -> if (dval > 0)+                                then return dval+                                else pzero++  <?> "unsigned integer or double"
+ src/Messages.hs view
@@ -0,0 +1,45 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | main gsim driver+module Messages ( show_version +                , startup_message+                , usage+                ) where++-- imports+import Prelude+++-- | show version info+show_version :: IO ()+show_version = putStrLn "This is simgi v0.1.1 (C) 2009 Markus Dittrich"+++-- | show a brief startup message+startup_message :: IO ()+startup_message = show_version +  >> putStrLn "\nstarting simulation ..... here we go\n"++++-- | provide brief usage info+usage :: IO ()+usage = putStrLn "Usage: simgi <input file>"
+ src/PrettyPrint.hs view
@@ -0,0 +1,72 @@+{-----------------------------------------------------------------+ +  (c) 2008-2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | PrettyPrint provides tools for colored output to the terminal+module PrettyPrint ( Color(..)+                   , Intensity(..)+                   , color_string+                   , color_string_int+                   ) where+++-- imports+import Prelude+++-- define colors+data Color = Black | Red | Green | Yellow | Blue | Magenta +           | Cyan | White | Reset +           deriving(Enum)+++-- define intensity +data Intensity = Normal | Bold+               deriving(Eq)+++-- convert a color into the corresponding color code string+get_color_code :: Color -> String+get_color_code = show . fromEnum +++-- convert an intensity to the corresponding color code string+get_intensity_code :: Intensity -> String+get_intensity_code x+  | x == Normal  = "22"+  | x == Bold    = "1"+  | otherwise    = "1"+++-- convenience wrapper around color string for bold colors+color_string :: Color -> String -> String+color_string = color_string_int Bold+                ++-- convert a standard string into one graphically rendered+-- allows customization of color and intensity+color_string_int :: Intensity -> Color -> String -> String+color_string_int intensity col str = +    "\ESC[" +    ++ (get_intensity_code intensity) +    ++ ";3" +    ++ (get_color_code col) +    ++ "m"+    ++ str +    ++ "\ESC[0;m"
+ src/RpnCalc.hs view
@@ -0,0 +1,64 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | RpnCalc defines the data structures and a calculator engine+-- for computing mathematical expressions that have been parsed+-- into reverse polish notations+module RpnCalc ( rpn_compute ) where+++-- imports +import qualified Data.Map as M+import Prelude++-- local imports+import GenericModel+import RpnData+++-- | computes an expressions based on an rpn stack+-- NOTE: This function expects the RPNstack to be sanitized+-- with respect to the variables, i.e., all variables in+-- the stack are assumed to exist in the MoleculeMap+rpn_compute :: MoleculeMap -> Double -> RpnStack -> Double+rpn_compute _      _    [(Number x)] = x+rpn_compute molMap theTime xs           = num ++  where+    (Number num) = head . foldl evaluate [] $ xs++    -- evaluate unary function (sin, cos, ..)+    evaluate ((Number x):ys) (UnaFunc f) = +      (Number $ f x):ys++    -- evaluate binary function (*,+,..)+    evaluate ((Number x):(Number y):ys) (BinFunc f) =+      (Number $ f y x):ys++    -- extrace current time+    evaluate ys (Time) = (Number theTime):ys++    -- extract molecule variable+    evaluate ys (Variable x) = (Number $ replace_var x):ys+      where+        replace_var :: String -> Double+        replace_var = fromIntegral . (M.!) molMap++    evaluate ys item = item:ys
+ src/RpnData.hs view
@@ -0,0 +1,52 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | RpnCalc defines the data structures and a calculator engine+-- for computing mathematical expressions that have been parsed+-- into reverse polish notations+module RpnData ( RpnItem(..)+               , RpnStack+               ) where+++-- imports +import Prelude+++-- | RpnItem describes all items that can be present in our+-- rpn stack+data RpnItem = Time+               | Number Double +               | Variable String+               | UnaFunc (Double -> Double) +               | BinFunc (Double -> Double -> Double)++type RpnStack = [RpnItem]+++instance Show RpnItem where+  show (Time)       = "TIME"+  show (Number x)   = show x+  show (BinFunc x)  = show (x 1 2) +  show (UnaFunc x)  = show (x 1)+  show (Variable x) = x+++
+ src/RpnParser.hs view
@@ -0,0 +1,185 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | module parsing an infix math equation into an compute stack+-- in reverse polish notation (rpn)+module RpnParser ( parse_infix_to_rpn ) where++-- imports+import Control.Monad+import Prelude++-- local imports+import ExtraFunctions+import GenericModel+import RpnData+import TokenParser++-- import Debug.Trace++-- | parses a mathematical infix expression and converts+-- into a stack in rpn+parse_infix_to_rpn :: CharParser ModelState RpnStack +parse_infix_to_rpn = add_term -- >>= \inp -> trace (show inp) (return inp)+                  <?> "infix math expression"+++-- | parser for expressions chained via "+" +add_term :: CharParser ModelState RpnStack+add_term = concat . insert_adds <$> +             sub_term `sepBy` (reservedOp "+")+        <?> "addition term"+  +  where+    insert_adds [] = []+    insert_adds (x:xs) = x:foldr (\y a -> y:[BinFunc (+)]:a) [] xs+++-- | parser for expressions chained via "-"+sub_term :: CharParser ModelState RpnStack+sub_term = concat . insert_subs <$> +             div_term `sepBy` (reservedOp "-")+        <?> "subtraction term"+  +  where+    insert_subs [] = []+    insert_subs (x:xs) = x:foldr (\y a -> y:[BinFunc (-)]:a) [] xs+++-- | parser for expressions chained via "*" +div_term :: CharParser ModelState RpnStack+div_term = concat . insert_divs <$> +             mul_term `sepBy` (reservedOp "/")+        <?> "division term"++  where+    insert_divs [] = []+    insert_divs (x:xs) = x:foldr (\y a -> y:[BinFunc (/)]:a) [] xs+++-- | parser for expressions chained via "/"+mul_term :: CharParser ModelState RpnStack+mul_term = concat . insert_muls <$> +             exp_term `sepBy` (reservedOp "*")+        <?> "product term"++  where+    insert_muls [] = []+    insert_muls (x:xs) = x:foldr (\y a -> y:[BinFunc (*)]:a) [] xs+++-- | parser for potentiation operations "^"+exp_term :: CharParser ModelState RpnStack+exp_term = concat . insert_exps <$> (whiteSpace *> factor) `sepBy` (reservedOp "^")+        <?> "exponent"++  where+    insert_exps [] = []+    insert_exps (x:xs) = x:foldr (\y a -> y:[BinFunc real_exp]:a) [] xs+++-- | parser for individual factors, i.e, numbers,+-- variables or operations+factor :: CharParser ModelState RpnStack+factor = try parse_single_number  -- need try due to the unary "-"+      <|> try signed_parenthesis  -- (otherwise we get stuck)+      <|> parse_functions+      <|> parse_variable+      <?> "token or variable"         +++-- | parse all operations of type (Double -> Double)+-- we currently know about+parse_functions :: CharParser ModelState RpnStack+parse_functions = (msum $ extract_ops builtinFunctions)+               <?> "builtin unary function"+  where+    extract_ops = foldr (\(x,y) acc -> +                         ((reserved x *> execute y):acc)) [] +    execute op  =  ( (insert_func op) <$>+                    (  parens add_term +                    <|> parse_single_number+                    <|> parse_variable+                    ))+               <?> "function parsing"++    insert_func _ [] = []+    insert_func f xs = xs ++ [UnaFunc f]+++-- | parse a potentially signed expression enclosed in parenthesis.+-- In the case of parenthesised expressions we +-- parse -(...) as (-1.0)*(...)+signed_parenthesis :: CharParser ModelState RpnStack+signed_parenthesis = push_parens <$> parse_sign <*> parens add_term+                  <?> "signed parenthesis"++  where+    push_parens sign xs = xs ++ [Number sign,BinFunc (*)]+++-- | parse a single number; integers are automatically promoted +-- to double+-- NOTE: Due to the notFollowedBy this parser can not be used+-- with 'many' and other parser combinators.+parse_single_number :: CharParser ModelState RpnStack+parse_single_number = push <$> (parse_number <* notFollowedBy alphaNum)+                   <?> "signed integer or double"+  where+    push x = [Number x]+++-- | parse a number, can be used with 'many' and other parser+-- combinators; integers are automatically promoted to double+parse_number :: CharParser ModelState Double+parse_number = converter <$> parse_sign <*> naturalOrFloat +            <?> "signed integer or double"+  where +    converter sign val = case val of+                           Left i  -> sign * (fromInteger i)+                           Right x -> sign * x+++-- | parse the sign of a numerical expression+parse_sign :: CharParser ModelState Double+parse_sign = option 1.0 ( whiteSpace *> char '-' *> pure (-1.0) )+          <?> "sign"+++-- | this is how valid variable names have to look like+parse_variable :: CharParser ModelState RpnStack+parse_variable = +  push <$> parse_sign +  <*> ((:) <$> letter <*> many (alphaNum <?> "") <* whiteSpace)+              <?> "variable"+  where+    -- in case of a unary minus we also push the necessary+    -- multiplication by (-1) onto the stack+    push sign x =+      if sign >= 0 +        then+          if x == "TIME" +            then [Time]+            else [Variable x]+        else+          if x == "TIME"+            then [Time,Number (-1.0),BinFunc (*)]+            else [Variable x, Number (-1.0), BinFunc(*)]+
+ src/TokenParser.hs view
@@ -0,0 +1,184 @@+{-----------------------------------------------------------------+ +  (c) 2008-2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | functionality related to parsing tokens+module TokenParser ( module Control.Applicative+                   , module Text.ParserCombinators.Parsec+                   , braces+                   , builtinFunctions+                   , comma+                   , charLiteral+                   , float+                   , integer+                   , parens+                   , keywords+                   , lexer+                   , naturalOrFloat+                   , operators+                   , reservedOp+                   , reserved+                   , semi+                   , stringLiteral+                   , symbol+                   , whiteSpace+                   ) where+++-- imports+import Control.Applicative+import Control.Monad (ap, MonadPlus (..))+import Prelude+import Text.ParserCombinators.Parsec hiding (many,optional, (<|>)) +import qualified Text.ParserCombinators.Parsec.Token as PT+import Text.ParserCombinators.Parsec.Language (haskellDef+                                              , opLetter+                                              , reservedOpNames+                                              , reservedNames )++-- local imports+import ExtraFunctions+++{- Definitions for Applicative Parsec instance -}++-- | Applicative instance for Monad+instance Applicative (GenParser s a) where+  pure  = return+  (<*>) = ap+++-- |Alternative instance for MonadPlus+instance Alternative (GenParser s a) where+  empty = mzero+  (<|>) = mplus++++{- set up the Token Parser -}++-- | builtin functions of the form (Double -> Double)+builtinFunctions :: [(String, Double -> Double)]+builtinFunctions = [ ("sqrt",sqrt)+                   , ("exp",exp)+                   , ("log",log)+                   , ("log2", logBase 2)+                   , ("log10", logBase 10)+                   , ("sin",sin)+                   , ("cos",cos)+                   , ("tan",tan)+                   , ("asin", asin)+                   , ("acos", acos)+                   , ("atan", atan)+                   , ("sinh", sinh)+                   , ("cosh", cosh)+                   , ("tanh", tanh)+                   , ("asinh", sinh)+                   , ("acosh", cosh)+                   , ("atanh", atanh)+                   , ("erf", erf)+                   , ("erfc", erfc)+                   , ("abs", abs)+                   ]+++-- | all other keywords that are not regular functions+keywords :: [String]+keywords = [ "def", "molecules", "reactions", "time", "outputIter"+           , "nil", "outputFreq", "outputFile", "systemVol"+           ]++operators :: [String]+operators = ["+","->","::","=","{","}"]+++-- | function generating a token parser based on a +-- lexical parser combined with a language record definition+lexer :: PT.TokenParser st+lexer  = PT.makeTokenParser +         ( haskellDef { reservedOpNames = operators+                      , opLetter      = oneOf "*+/^"+                      , reservedNames = keywords +                            ++ map fst builtinFunctions+                      } )+++-- | token parser for parenthesis+parens :: CharParser st a -> CharParser st a+parens = PT.parens lexer++-- | token parser for parenthesis+braces :: CharParser st a -> CharParser st a+braces = PT.braces lexer+++-- | token parser for Integer+integer :: CharParser st Integer+integer = PT.integer lexer+++-- | token parser for Char+stringLiteral :: CharParser st String+stringLiteral = PT.stringLiteral lexer+++-- | token parser for Char+charLiteral :: CharParser st Char+charLiteral = PT.charLiteral lexer+++-- | token parser for Double+float :: CharParser st Double+float = PT.float lexer+++-- | token parser for Either Integer Double+naturalOrFloat :: CharParser st (Either Integer Double)+naturalOrFloat = PT.naturalOrFloat lexer+++-- | token parser for keywords+reservedOp :: String -> CharParser st ()+reservedOp = PT.reservedOp lexer+++-- | token parser for keywords+reserved :: String -> CharParser st ()+reserved = PT.reserved lexer+++-- | token parser for whitespace+whiteSpace :: CharParser st ()+whiteSpace = PT.whiteSpace lexer+++-- | token parser for semicolon+semi :: CharParser st String+semi = PT.semi lexer+++-- | token parser for comma+comma :: CharParser st String+comma = PT.comma lexer+++-- | token parser for symbol+symbol :: String -> CharParser st String+symbol = PT.symbol lexer+
+ src/simgi.hs view
@@ -0,0 +1,88 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | main gsim driver+module Main where++-- imports+import Prelude+import System.IO+import System.Random+import System.Environment++-- local imports+import CommandLine+import Engine+import InputCheck+import InputParser+import Messages+import TokenParser++-- import Debug.Trace+++-- | main+main :: IO ()+main = ++  -- process command line arguments+  getArgs >>= process_commandline +  >>= \((_,_),files) -> ++  -- reject anything but a single input file+  if length files /= 1 +    then usage+    else++      -- read input file and extract content+      readFile (head files)+      >>= \content -> ++        -- parse input file+        case runParser input_parser initialModelState "" content of+          Left er           -> putStrLn (show er)+          Right parsedState -> +            case check_input parsedState of+              Left err -> putStrLn err+              Right _  -> newStdGen+                >>= \gen -> ++                -- set up simuation+                let +                  rands         = randomRs (0,1) gen :: [Double] +                  initialOutput = create_initial_output parsedState+                  initialState  = create_initial_state parsedState +                                  rands initialOutput+                  totalTime     = maxTime parsedState +                  dataDumpIter  = maxIter parsedState+                  outFile       = outfileName parsedState+                in++                  -- open output file+                  openFile outFile WriteMode +                  >>= \handle -> startup_message++                  -- ready to run the simulation+                  >> gillespie_driver handle totalTime dataDumpIter +                                  initialState ++                  -- close output file+                  >> hClose handle+
+ test/Makefile view
@@ -0,0 +1,15 @@+++default: check+++.PHONY: check clean+check:+	make -C rpnstack_test+	make -C reversible_test+++clean:+	make -C rpnstack_test clean+	make -C reversible_test clean+
+ test/reversible_test/Makefile view
@@ -0,0 +1,19 @@++SRC_LOCATION=../../src+SIMGI_PATH=${SRC_LOCATION}/simgi++default: check++.PHONY: check clean+check:+	ghc -i$(SRC_LOCATION) --make check_deviation.hs+	ghc -i$(SRC_LOCATION) --make average.hs+	@echo+	@echo "Running reversible reaction test."+	@echo "This may take a while ...."+	@./run_test.sh ${SIMGI_PATH}+	@echo+	++clean:+	rm -f *.hi *.o check_deviation average
+ test/reversible_test/average.hs view
@@ -0,0 +1,34 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | short helper script for averaging a file containing a single+-- column of doubles+module Main where+++main :: IO ()+main = getContents+       >>= \content -> +         let+            items     = map (read) . lines $ content :: [Double]+            theSum    = foldr (+) 0 items+            average   = theSum/(fromIntegral . length $ items)+         in+           putStrLn (show average)
+ test/reversible_test/check_deviation.hs view
@@ -0,0 +1,45 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | short helper script for averaging a file containing a single+-- column of doubles+module Main where++-- imports+import System+import System.Environment+++main :: IO Int+main = getArgs +       >>= \(name:value:tol:_) -> readFile name+       >>= \content -> +         let+            items     = map (read) . lines $ content :: [Double]+            theSum    = foldr (+) 0 items+            average   = theSum/(fromIntegral . length $ items)+            expected  = read value :: Double+            tolerance = read tol :: Double+            deviation = abs((average - expected)/expected)+         in+           if ( deviation < tolerance )+             then exitWith ExitSuccess+             else exitWith $ ExitFailure 1+
+ test/reversible_test/reversible.sgl view
@@ -0,0 +1,25 @@+{-----------------------------------------------------++  this is the input deck for the oregonator model +  (C) 2009 Markus Dittrich++------------------------------------------------------}++def parameters+  time       = 1.0e-4+  systemVol  = 1.25e-19+  outputIter = 50000+  outputFreq = 10+  outputFile = "reversible.dat"+end++def molecules+  a 1000+  b 1000+  c 0+end++def reactions+  a + b -> c  { 1e6*10 }+  c -> a + b  { 1e5 }+end
+ test/reversible_test/run_test.sh view
@@ -0,0 +1,53 @@+#!/bin/bash+#+# short wrapper for runing a number of reversible+# simulations and then checking if we can reproduce+# the correct average product concentration+#++# +simgi_exe="${1}"++# create a global tempfile to collect the data+globalFile=$(mktemp simgi.XXXXXXXXXXXXX)++for ((counter=0; counter <= 100; counter++)); do++  # provide a little "progressbar"+  printf "."++  # run and process+  ${simgi_exe} reversible.sgl >& /dev/null +  tail -n 400 reversible.dat | gawk ' { print $5}' | ./average >> ${globalFile} || return 1++  # unlink+  rm -f reversible.dat || return 1+  +done++# check if we're within the specs+# the expected number of products is 430.643462709951+# and we allow 0.5% tolerance+./check_deviation ${globalFile} 430.643462709951 5e-3+status=$?++# brief output+if [[ ${status} == 0 ]]; then+  echo+  echo+  echo "Congratulations - the reversible reaction test passed!"+  echo+  echo+else+  echo+  echo+  echo "Error - the reversible reaction test failed. Please check!"+  echo+  echo+fi++# remove files+rm -f ${globalFile}++# return status of deviation check+exit ${status}
+ test/rpnstack_test/Makefile view
@@ -0,0 +1,15 @@++SRC_LOCATION=../../src+++default: check+++.PHONY: check clean+check:+	ghc -i$(SRC_LOCATION) --make RpnStackTest.hs+	@./RpnStackTest+++clean:+	rm -f *.hi *.o RpnStackTest
+ test/rpnstack_test/RpnStackTest.hs view
@@ -0,0 +1,227 @@+{-----------------------------------------------------------------+ +  (c) 2009 Markus Dittrich + +  This program is free software; you can redistribute it +  and/or modify it under the terms of the GNU General Public +  License Version 3 as published by the Free Software Foundation. + +  This program is distributed in the hope that it will be useful,+  but WITHOUT ANY WARRANTY; without even the implied warranty of+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the+  GNU General Public License Version 3 for more details.+ +  You should have received a copy of the GNU General Public +  License along with this program; if not, write to the Free +  Software Foundation, Inc., 59 Temple Place - Suite 330, +  Boston, MA 02111-1307, USA.++--------------------------------------------------------------------}++-- | this routine tests the functionality in our RPNStack, i.e.,+-- the infix to RPN parser as well as the compute engine+module Main where+++-- imports +import Control.Monad.Writer+import qualified Data.Map as M+import Prelude+import System.Exit++-- local imports+import ExtraFunctions+import GenericModel+import PrettyPrint+import RpnParser+import RpnCalc+import TokenParser+++-----------------------------------------------------------------+-- +-- test data specifications+--+-----------------------------------------------------------------++-- | set up the test data+-- Format : (parse expression, expected result)+type TestCase = (String, Double)++++-- | simple tests without access to local variables+simpleTests :: [TestCase]+simpleTests = +  [ ("3+4", 7.0) +  , ("3 +4", 7.0)+  , ("  3+  4", 7.0)+  , (" 3 +  4   ", 7.0)+  , ("-3 + 3   ", 0.0)+  , ("3*4+4", 16.0)+  , ("3 * 4+4 ", 16.0)+  , ("3+4*5", 23.0)+  , ("(3+4)*5", 35.0)+  , (" ( 3 + 4    )*  5", 35.0)+  , ("sqrt(2)^2", 2.0)+  , ("(-2)^2", 4.0)+  , ("exp(-1)", 0.36787944117144233)+  , ("log(exp(3)) * 3^2", 27.0)+  , ("log (  exp ( 3)   ) *3   ^2", 27.0)+  , ("((((((((3*(3+(3*3) + 4) + 2) +3)-34) -4)+1))))", 16.0)+  , ("(1*(1 * (1 *(((((3*(3+(3*3) + 4) + 2) +3)-34) -4)+1))))", 16.0)+  , ("log(exp(2) - sqrt(2))", 1.7875577437560926)+  , ("2 * 3.14 * sqrt(2)", 8.88126117170303786)+  ]+++-- | variable tests+variableTests :: [TestCase]+variableTests =+  [ ("3*x", 3000)+  , ("sqrt(x)^2", 1000)+  , ("x+y*z", 1000)+  , ("x + y *   z", 1000)+  , ("(x+y)*z", 0)+  , ("(x  + y)* z", 0)+  , ("exp(z)*TIME", 12.345)+  , ("exp(z ) *  TIME  ", 12.345)+  , ("-x * -y", 2.0e6)+  , ("x*exp(-TIME)", 4.351456244655325e-3)+  , ("x-x +x -x -y + y", 0.0)+  , ("-TIME/TIME + TIME - TIME + 1.0", 0.0)+  ]+++----------------------------------------------------------------+-- tests with access to local variables and time+----------------------------------------------------------------++++----------------------------------------------------------------+-- Molecule maps and definitions for specific simulation times+----------------------------------------------------------------++-- | testmap containing a set of molecules and their +-- concentrations+testMap_1 :: MoleculeMap+testMap_1 = M.fromList [("x",1000),("y",2000),("z",0)]++-- | a simulation time+time_1 :: Double+time_1 = 12.345+++++----------------------------------------------------------------+--+--  main driver routines+--+----------------------------------------------------------------+++-- | main test driver+main :: IO ()+main = putStrLn "\n\n\nTesting RPN stack (parser/compute engine)"++  -- run simple tests+  >> (putStr $ color_string Cyan "\nSimple tests:\n")+  >> let simpleOut = execWriter $ test_driver +           testMap_1 time_1 simpleTests+     in+  examine_output simpleOut >>= \simpleStatus ->+++  -- run variable tests+  (putStr $ color_string Cyan "\n\nVariable tests:\n")+  >> let varOut = execWriter $ test_driver testMap_1 time_1+                               variableTests+     in+  examine_output varOut >>= \varStatus ->+++  -- evaluate status and return+  let status = simpleStatus && varStatus in+    if status == True then+      exitWith ExitSuccess+    else+      exitWith $ ExitFailure 1 +++-- | examine the output of a test routine+-- | helper function for examining the output of a good test run+-- (i.e. one that should succeed), prints out the result for each +-- test, collects the number of successes/failures and returns +-- True in case all tests succeeded and False otherwise+examine_output :: [TestResult] -> IO Bool+examine_output = foldM examine_output_h True+                 +  where+    examine_output_h :: Bool -> TestResult -> IO Bool+    examine_output_h acc (TestResult status token target actual) = do+      if status == True then do+          putStr   $ color_string Blue "["+          putStr   $ color_string White "OK"+          putStr   $ color_string Blue  "] "+          putStr   $ color_string Green " Successfully evaluated "+          putStrLn $ color_string Yellow token+          return $ acc && True+        else do+          putStr   $ color_string Blue "["+          putStr   $ color_string Red "TROUBLE"+          putStr   $ color_string Blue "] "+          putStr   $ color_string Green " Failed to evaluate "+          putStrLn $ color_string Yellow token+          putStrLn $ color_string Green "\t\texpected : " +                       ++ (show target)+          putStrLn $ color_string Green "\t\tgot      : " +                       ++ (show actual)+          return False+++-- | driver for running a test routine that results in a+-- successful evaluation of a test expression+test_driver :: MoleculeMap -> Double -> [TestCase] +            -> Writer [TestResult] ()+test_driver _ _ []          = return ()+test_driver mol time (x:xs) =++  let expr     = fst x+      expected = snd x+  in++    -- parse expression+    case runParser parse_infix_to_rpn initialModelState "" expr of+      Left er -> tell [TestResult False expr (show expected) (show er)]+      Right stack ->++        -- evalute RPN stack+        let result = rpn_compute mol time stack in+          examine_result expected result expr +          >> test_driver mol time xs++          where+            examine_result target out expr = +              if is_equal target out+                then +                  tell [TestResult True expr (show target) (show out)]+                else +                  tell [TestResult False expr (show target) (show out)]+          ++-- | data structure for keeping track of our test results+-- which consist of a bool indicating success+-- or failure, the test token as well as the expected and+-- received result+data TestResult = TestResult { status :: Bool+                             , token  :: String+                             , target :: String+                             , actual :: String+                             }+++defaultResult :: TestResult+defaultResult = TestResult False "" "" ""+