Squashed 'moose-core/' changes from 6a6bcc1..bd86fb5

bd86fb5 Update INSTALL.md
3602353 Update README.md
f96dbda Merge pull request #155 from dilawar/master
50d720b Merge branch 'master' into master
b408e36 Instead of simple sin/cos use fmod and divide method. Sin/cosine functions gets value of 1 or many points near the maxima when simulation time is large (T for sin/cos). This changes fixes that.

git-subtree-dir: moose-core
git-subtree-split: bd86fb53a865dce7d482e21f959513e5621b1062

INSTALL.md

@@ -2,14 +2,13 @@
 
 Use our repositories hosted at [Open Build Service](http://build.opensuse.org).
 We have packages for Debian, Ubuntu, CentOS, Fedora, OpenSUSE/SUSE, RHEL,
-Scientific Linux.  Visit the following page and follow the instructions there. 
+Scientific Linux.  Visit the following page for instructions.
 
 https://software.opensuse.org/download.html?project=home:moose&package=moose
 
 # Building MOOSE from source
 
-If you really want to build `MOOSE` from source, you can either use `cmake` (recommended) 
-or GNU `make` based flow.
+To build `MOOSE` from source, you can either use `cmake` (recommended) or GNU `make` based flow.
 
 Download the latest source code of moose from github or sourceforge.
 
@@ -21,21 +20,9 @@ For moose-core:
 
 - gsl-1.16 or higher.
 - libhdf5-dev (optional) 
-- libsbml-dev (5.9.0, optional)
 - python-dev 
 - python-numpy 
 
-__Note on libsbml__
-Make sure that `libsml` is installed with `zlib` and `lxml` support. Following instructions 
-are known to work.
-
-    - wget http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/libSBML-5.9.0-core-src.tar.gz
-    - tar -xzvf libSBML-5.9.0-core-src.tar.gz 
-    - cd libsbml-5.9.0 
-    - ./configure --prefix=/usr --with-zlib --with-bzip2 --with-libxml 
-    - make 
-    - sudo make install 
-
 On Ubuntu-12.04 or higher, these can be installed with:
     
     sudo apt-get install python-dev python-numpy libhdf5-dev cmake libgsl0-dev g++ 
@@ -81,17 +68,17 @@ calling make:
     export LDFLAGS= -L/opt/libsbml/lib
 
   
-## Release build:
+### Release build:
 
     cd moose
     make BUILD=release
 
-## Debug build:
+### Debug build:
     
     cd moose
     make BUILD=debug
 
-## Python 3K
+### Python 3K
 
 By default, MOOSE is built for Python 2. In case you want to build MOOSE for
 Python 3K, you need to pass the additional flag:

README.md

 [![Build Status - master](https://travis-ci.org/BhallaLab/moose-core.svg?branch=master)](https://travis-ci.org/BhallaLab/moose-core) 
 
 This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains 
-C++ codebase and its python interface. For more details about MOOSE simulation, see https://github.com/BhallaLab/moose/blob/master/README.md 
+C++ codebase and python interface. For more details about MOOSE simulator, see https://github.com/BhallaLab/moose/blob/master/README.md 
 
-This repository is sufficient for using MOOSE as python module. If you want to build `moose-python` using this repository, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md .
+This repository is sufficient for using MOOSE as a python module. If you just want to build moose python module, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md .

scheduling/Clock.cpp

@@ -733,23 +733,17 @@ void Clock::handleStep( const Eref& e, unsigned long numSteps )
             ++k;
         }
 
-        // Don't write too much. When 10% of simulation is over, write to
-        // the file. We need 10 points. We just use a sine function
-        // which cross 0 ten time in this time interval.
-        // NOTE: Dont use == 0.0 since we may never get a sample for
-        // which sine is 0.0. Hoever, getting 1.0 or -1.0 is very likely
-        // since sin function is relatively flat when its value is near
-        // 1.0/-1.0.
-        // NOTE: Use cosine instead of sin to sample 0%, 10% etc.
+        // When 10% of simulation is over, notify user when notify_ is set to
+        // true.
         if( notify_ )
         {
-            if( cos(20 * M_PI * currentTime_ / runTime_) == 1.0)
+            if( fmod(100 * currentTime_ / runTime_ , 10.0) == 0.0 )
             {
                 time( &rawtime );
                 timeinfo = localtime( &rawtime );
                 strftime(now, 80, "%c", timeinfo);
                 cout << "@ " << now << ": " << 100 * currentTime_ / runTime_ 
-                    << "% of total " << runTime_ << " is over." << endl;
+                    << "% of total " << runTime_ << " seconds is over." << endl;
             }
         }
     }