Fix to theoretical end-to-end distance calculation for 3D chains.

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

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 = ./.;
 

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))
 

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.

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': '[email protected]',
         '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',

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 = ./.;