Removed TODO in favor of BugsEverywhere bugtracking.

See http://bugseverywhere.org for details on BE.

I also removed the following entry from TODO:
  maybe histogram without dice rolling for identical domains?
since I decided it was a bad idea.  Better to focus the simulation on
what it's good at.  Of course, I may change my mind later and
reinstate the issue ;).

diff --git a/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body
new file mode 100644 (file)
index 0000000..c4f68e0
--- /dev/null
+++ b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body
@@ -0,0 +1,8 @@
+Exponential rising tension (ERT)
+  f = E0 / alpha ( e^(alpha x) - 1 )
+Enhanced WLC (with stretching)
+  f = kB T/p { 1/4 [1/(1-x/L-f/K)² - 1] + x/L - f/K }
+Enhanced FJC (with stretching)
+  x/L = [coth(Lk f/ kB T)- kB T/Lk f](1+f/K)
+from Leuba & Zlatanova.  Biology at the Single-Molecule Level.  p13
+

diff --git a/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values
new file mode 100644 (file)
index 0000000..ddd71e8
--- /dev/null
+++ b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values
@@ -0,0 +1,8 @@
+Author: W. Trevor King <wking@drexel.edu>
+
+
+Content-type: text/plain
+
+
+Date: Thu, 13 Aug 2009 00:13:11 +0000
+

diff --git a/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values
new file mode 100644 (file)
index 0000000..5da6eb0
--- /dev/null
+++ b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values
@@ -0,0 +1,17 @@
+creator: W. Trevor King <wking@drexel.edu>
+
+
+reporter: W. Trevor King <wking@drexel.edu>
+
+
+severity: minor
+
+
+status: open
+
+
+summary: Further tension models
+
+
+time: Thu, 13 Aug 2009 00:12:51 +0000
+

diff --git a/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body
new file mode 100644 (file)
index 0000000..f020f92
--- /dev/null
+++ b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body
@@ -0,0 +1,4 @@
+$ bin/sawsim -v1 -s A,null -N -s B,null -k A,B,const,1
+sawsim: build/list.c:221: list_element: Assertion `0==1' failed.
+Aborted
+

diff --git a/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values
new file mode 100644 (file)
index 0000000..731f294
--- /dev/null
+++ b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values
@@ -0,0 +1,8 @@
+Author: W. Trevor King <wking@drexel.edu>
+
+
+Content-type: text/plain
+
+
+Date: Wed, 12 Aug 2009 20:46:22 +0000
+

diff --git a/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values
new file mode 100644 (file)
index 0000000..ced2a81
--- /dev/null
+++ b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values
@@ -0,0 +1,17 @@
+creator: W. Trevor King <wking@drexel.edu>
+
+
+reporter: W. Trevor King <wking@drexel.edu>
+
+
+severity: minor
+
+
+status: open
+
+
+summary: list_element fails when -N eats s argument...
+
+
+time: Wed, 12 Aug 2009 20:46:10 +0000
+

diff --git a/.be/settings b/.be/settings
new file mode 100644 (file)
index 0000000..739d28c
--- /dev/null
+++ b/.be/settings
@@ -0,0 +1,2 @@
+rcs_name: git
+

diff --git a/.be/version b/.be/version
new file mode 100644 (file)
index 0000000..990837e
--- /dev/null
+++ b/.be/version
@@ -0,0 +1 @@
+Bugs Everywhere Tree 1 0

diff --git a/TODO b/TODO
deleted file mode 100644 (file)
index eb0d3be..0000000
--- a/TODO
+++ /dev/null
@@ -1,11 +0,0 @@
-maybe histogram without dice rolling for identical domains?
-
-Further tension models:
-  Exponential rising tension (ERT)
-    f = E0 / alpha ( e^(alpha x) - 1 )
-  Enhanced WLC (with stretching)
-    f = kB T/p { 1/4 [1/(1-x/L-f/K)² - 1] + x/L - f/K }
-  Enhanced FJC (with stretching)
-    x/L = [coth(Lk f/ kB T)- kB T/Lk f](1+f/K)
-from Leuba & Zlatanova.  Biology at the Single-Molecule Level.  p13
-