From 080610a5bab920c3245a6091be3db3a16a63ade4 Mon Sep 17 00:00:00 2001
From: kmdouglass <kyle.m.douglass@gmail.com>
Date: Wed, 28 Jun 2017 21:15:17 +0200
Subject: [PATCH] Fix to theoretical end-to-end distance calculation for 3D
 chains.

---
 CHANGELOG.md          | 6 ++++++
 PolymerCpp.nix        | 2 +-
 PolymerCpp/helpers.py | 4 ++--
 docs/conf.py          | 4 ++--
 setup.py              | 4 ++--
 shell.nix             | 2 +-
 6 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d0ad8a..5ccc6bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [v0.1.3]
+### Fixed
+- Fixed a bug in calculating the theoretical end-to-end distance of 3D
+  wormlike chains.
+	
 ## [v0.1.2]
 ### Fixed
 - Fixed a typo in the MANIFEST.in file that caused the header files
@@ -37,6 +42,7 @@ All notable changes to this project will be documented in this file.
 - Fixed off-by-one error in the wormlike chain generation code.
 - Errors in computation of chain statistics
 
+[v0.1.3]: https://github.com/kmdouglass/PolymerCpp/compare/v0.1.2...v0.1.3
 [v0.1.2]: https://github.com/kmdouglass/PolymerCpp/compare/v0.1.1...v0.1.2
 [v0.1.1]: https://github.com/kmdouglass/PolymerCpp/compare/v0.1.0...v0.1.1
 [v0.1.0]: https://github.com/kmdouglass/PolymerCpp/compare/v0.0.1...v0.1.0
diff --git a/PolymerCpp.nix b/PolymerCpp.nix
index 82efaf5..080461c 100644
--- a/PolymerCpp.nix
+++ b/PolymerCpp.nix
@@ -2,7 +2,7 @@ with import <nixpkgs> {};
 
 pkgs.python35Packages.buildPythonPackage rec {
   name = "PolymerCpp-${version}";
-  version = "0.1.2";
+  version = "0.1.3";
 
   src = ./.;
 
diff --git a/PolymerCpp/helpers.py b/PolymerCpp/helpers.py
index 70d8734..7e03625 100644
--- a/PolymerCpp/helpers.py
+++ b/PolymerCpp/helpers.py
@@ -242,13 +242,13 @@ def theory_R_WLC(contour_length, persistence_length, dim=3):
     if dim == 2:
         term1 = 4 * persistence_length * contour_length
         term2 = 2 * persistence_length / contour_length
+        term3 = 1 - np.exp(-contour_length / 2 / persistence_length)
     elif dim == 3:
         term1 = 2 * persistence_length * contour_length
         term2 = persistence_length / contour_length
+        term3 = 1 - np.exp(-contour_length / persistence_length)
     else:
         raise ValueError('dim must be either 2 or 3. {} was supplied'.format(dim))
-
-    term3 = 1 - np.exp(-contour_length / 2 / persistence_length)
             
     R = np.sqrt(term1 * (1 - term2 * term3))
 
diff --git a/docs/conf.py b/docs/conf.py
index 2e43405..316c795 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -74,9 +74,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.2'
+version = '0.1.3'
 # The full version, including alpha/beta/rc tags.
-release = '0.1.2'
+release = '0.1.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/setup.py b/setup.py
index ad1cd70..bbb5b82 100644
--- a/setup.py
+++ b/setup.py
@@ -21,12 +21,12 @@
                     extra_compile_args = ['-std=c++11','-O2', '-fPIC'])
 
 config={'name': 'PolymerCpp',
-        'version': '0.1.2',
+        'version': '0.1.3',
         'description': '2D and 3D wormlike chain generator for Python and written in C++',
         'author': 'Kyle M. Douglass, Marcel Stefko',
         'author_email': 'kyle.m.douglass@gmail.com',
         'url': 'https://github.com/kmdouglass/PolymerCpp',
-        'download_url': 'https://github.com/kmdouglass/PolymerCpp/archive/v0.1.2.tar.gz',
+        'download_url': 'https://github.com/kmdouglass/PolymerCpp/archive/v0.1.3.tar.gz',
         'keywords': ['polymer', 'wormlike chain', 'random walk'],
         'classifiers': ['Topic :: Scientific/Engineering :: Physics',
                         'Programming Language :: Python :: 3',
diff --git a/shell.nix b/shell.nix
index 431a2df..f7f4950 100644
--- a/shell.nix
+++ b/shell.nix
@@ -4,7 +4,7 @@ with import <nixpkgs> {};
 
     PolymerCpp = pkgs.python35Packages.buildPythonPackage rec {
       name = "PolymerCpp-${version}";
-      version = "0.1.2";
+      version = "0.1.3";
 
       src = ./.;