From 486497eb8e483b582c16e433327160eacf96c5bc Mon Sep 17 00:00:00 2001
From: Simon Rochester <simon.rochester@gmail.com>
Date: Thu, 27 Sep 2012 23:37:48 -0700
Subject: Added list of DM variables to output, and comments at the beginning
 and end of each text file.

---
 mathemathica_fwm/RbXMDSSetup.nb | 237 +++++++++++++++++++++++++++-------------
 1 file changed, 160 insertions(+), 77 deletions(-)

diff --git a/mathemathica_fwm/RbXMDSSetup.nb b/mathemathica_fwm/RbXMDSSetup.nb
index 74e4394..7b10959 100755
--- a/mathemathica_fwm/RbXMDSSetup.nb
+++ b/mathemathica_fwm/RbXMDSSetup.nb
@@ -727,7 +727,6 @@ Cell[BoxData[
           "\"\<\!\(\*SuperscriptBox[\(\[VeryThinSpace]\), \
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            RowBox[{"SingleLetterItalics", "\[Rule]", "False"}]}], "]"}], ",", 
-         
          RowBox[{"{", 
           RowBox[{
            RowBox[{"-", "2.9"}], ",", "0"}], "}"}]}], "]"}], ",", 
@@ -738,7 +737,6 @@ Cell[BoxData[
           "\"\<\!\(\*SuperscriptBox[\(\[VeryThinSpace]\), \
 \(2\)]\)\!\(\*SubscriptBox[\(P\), \(1/2\)]\)\>\"", ",", 
            RowBox[{"SingleLetterItalics", "\[Rule]", "False"}]}], "]"}], ",", 
-         
          RowBox[{"{", 
           RowBox[{
            RowBox[{"-", "2.9"}], ",", "1.6"}], "}"}]}], "]"}], ",", 
@@ -749,7 +747,6 @@ Cell[BoxData[
           "\"\<\!\(\*SuperscriptBox[\(\[VeryThinSpace]\), \
 \(2\)]\)\!\(\*SubscriptBox[\(P\), \(3/2\)]\)\>\"", ",", 
            RowBox[{"SingleLetterItalics", "\[Rule]", "False"}]}], "]"}], ",", 
-         
          RowBox[{"{", 
           RowBox[{
            RowBox[{"-", "2.9"}], ",", "2.7"}], "}"}]}], "]"}]}], "}"}]}], ",", 
@@ -1377,7 +1374,6 @@ Cell[BoxData[{
         RowBox[{"{", 
          RowBox[{
           RowBox[{"-", "2.9"}], ",", "2.7"}], "}"}]}], "]"}]}], "}"}]}], ",", 
-   
    RowBox[{"ImageSize", "\[Rule]", 
     RowBox[{"3.5", " ", "72"}]}], ",", 
    RowBox[{"ImagePadding", "\[Rule]", 
@@ -1418,8 +1414,8 @@ Cell[BoxData[{
     RowBox[{
      RowBox[{
       RowBox[{"Position", "[", 
-       RowBox[{"vars", ",", "#"}], "]"}], "&"}], "/@", "%"}], ",", "1"}], 
-   "]"}]}], "\[IndentingNewLine]", 
+       RowBox[{"vars", ",", "#"}], "]"}], "&"}], "/@", "delvars1"}], ",", 
+    "1"}], "]"}]}], "\[IndentingNewLine]", 
  RowBox[{"vars1", "=", 
   RowBox[{"Delete", "[", 
    RowBox[{"vars", ",", "delpos1"}], "]"}]}]}], "Input"],
@@ -1509,13 +1505,17 @@ Cell[BoxData[{
    "}"}]}], "\[IndentingNewLine]", 
  RowBox[{"StringReplace", "[", 
   RowBox[{
-   RowBox[{"StringJoin", "[", 
-    RowBox[{
+   RowBox[{
+   "\"\<//---------------- Constants.txt starts ------------------\n\>\"", "<>", 
+    RowBox[{"StringJoin", "[", 
      RowBox[{
-      RowBox[{"\"\<const double \>\"", "<>", 
-       RowBox[{"ToString", "@", 
-        RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\<;\\n\>\""}], "&"}], "/@",
-      "%"}], "]"}], ",", 
+      RowBox[{
+       RowBox[{"\"\<const double \>\"", "<>", 
+        RowBox[{"ToString", "@", 
+         RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\<;\\n\>\""}], "&"}], "/@",
+       "%"}], "]"}], "<>", 
+    "\"\<//---------------- Constants.txt ends   ------------------\n\>\""}], 
+   ",", 
    RowBox[{"{", 
     RowBox[{
      RowBox[{"\"\<==\>\"", "\[Rule]", "\"\<=\>\""}], ",", 
@@ -1690,15 +1690,19 @@ Cell[BoxData[{
      RowBox[{"1", "/", 
       SqrtBox["2"]}], "\[Rule]", 
      RowBox[{"1", "/", "rt2"}]}]}], "}"}]}], "\[IndentingNewLine]", 
- RowBox[{"StringReplace", "[", 
+ RowBox[{"StringReplace", "[", "\[IndentingNewLine]", 
   RowBox[{
-   RowBox[{"StringJoin", "[", 
-    RowBox[{
+   RowBox[{
+   "\"\<//---------------- RbEquations.txt starts ------------------\n\>\"", "<>", 
+    RowBox[{"StringJoin", "[", 
      RowBox[{
       RowBox[{
-       RowBox[{"ToString", "@", 
-        RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\<;\\n\>\""}], "&"}], "/@",
-      "%"}], "]"}], ",", 
+       RowBox[{
+        RowBox[{"ToString", "@", 
+         RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\<;\\n\>\""}], "&"}], "/@",
+       "%"}], "]"}], "<>", "\[IndentingNewLine]", 
+    "\"\<//---------------- RbEquations.txt ends  ------------------\n\>\""}],
+    ",", 
    RowBox[{"{", 
     RowBox[{
      RowBox[{"\"\<==\>\"", "\[Rule]", "\"\<=\>\""}], ",", 
@@ -1738,8 +1742,7 @@ Cell[BoxData[{
       RowBox[{"\"\<delta\>\"", "<>", "a"}]}], ",", 
      RowBox[{
       RowBox[{"\"\<k(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], "\[RuleDelayed]", 
-      RowBox[{"\"\<Kvec\>\"", "<>", "a"}]}]}], "}"}]}], "]"}]}], "Input",
- CellChangeTimes->{{3.557696286875835*^9, 3.557696298394461*^9}}],
+      RowBox[{"\"\<Kvec\>\"", "<>", "a"}]}]}], "}"}]}], "]"}]}], "Input"],
 
 Cell[BoxData[
  RowBox[{"Export", "[", 
@@ -1749,6 +1752,80 @@ Cell[BoxData[
      RowBox[{"NotebookDirectory", "[", "]"}], ",", 
      "\"\<RbEquations.txt\>\""}], "]"}], ",", "%"}], "]"}]], "Input"],
 
+Cell["List of variables", "Text"],
+
+Cell[BoxData[
+ RowBox[{"StringReplace", "[", "\[IndentingNewLine]", 
+  RowBox[{
+   RowBox[{
+   "\"\<//---------------- RbChosenRho.txt starts ------------------\n\>\"", "<>", 
+    RowBox[{"StringJoin", "[", 
+     RowBox[{
+      RowBox[{
+       RowBox[{
+        RowBox[{"ToString", "@", 
+         RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\< \>\""}], "&"}], "/@", 
+      RowBox[{"(", 
+       RowBox[{
+        RowBox[{"vars1", "/.", "labelrep"}], "/.", 
+        RowBox[{
+         RowBox[{
+          SubscriptBox["\[Rho]", 
+           RowBox[{"s1_", ",", "s2_"}]], "[", "t_", "]"}], "\[RuleDelayed]", 
+         RowBox[{"r", "[", 
+          RowBox[{"s1", ",", "s2"}], "]"}]}]}], ")"}]}], "]"}], "<>", 
+    "\[IndentingNewLine]", 
+    "\"\<\n//---------------- RbChosenRho.txt ends  ------------------\n\
+\>\""}], ",", 
+   RowBox[{"{", 
+    RowBox[{
+     RowBox[{"\"\<==\>\"", "\[Rule]", "\"\<=\>\""}], ",", 
+     RowBox[{
+      RowBox[{"Shortest", "[", 
+       RowBox[{
+       "\"\<dr(\\\"\>\"", "~~", "a__", "~~", "\"\<\\\",\\\"\>\"", "~~", "b__",
+         "~~", "\"\<\\\")\>\""}], "]"}], ":>", 
+      RowBox[{"\"\<dr\>\"", "<>", "a", "<>", "b", "<>", "\"\<_dt\>\""}]}], 
+     ",", 
+     RowBox[{
+      RowBox[{"Shortest", "[", 
+       RowBox[{
+       "\"\<r(\\\"\>\"", "~~", "a__", "~~", "\"\<\\\",\\\"\>\"", "~~", "b__", 
+        "~~", "\"\<\\\")\>\""}], "]"}], ":>", 
+      RowBox[{"\"\<r\>\"", "<>", "a", "<>", "b"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<ha(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+      "\[RuleDelayed]", 
+      RowBox[{"\"\<ha\>\"", "<>", "a"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<hb(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+      "\[RuleDelayed]", 
+      RowBox[{"\"\<hb\>\"", "<>", "a"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<g(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], "\[RuleDelayed]", 
+      RowBox[{"\"\<g\>\"", "<>", "a"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<W(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], "\[RuleDelayed]", 
+      RowBox[{"\"\<E\>\"", "<>", "a"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<Wc(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+      "\[RuleDelayed]", 
+      RowBox[{"\"\<Ec\>\"", "<>", "a"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<d(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], "\[RuleDelayed]", 
+      RowBox[{"\"\<d\>\"", "<>", "a"}]}], ",", 
+     RowBox[{
+      RowBox[{"\"\<k(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], "\[RuleDelayed]", 
+      RowBox[{"\"\<k\>\"", "<>", "a"}]}]}], "}"}]}], "]"}]], "Input"],
+
+Cell[BoxData[
+ RowBox[{"Export", "[", 
+  RowBox[{
+   RowBox[{"ToFileName", "[", 
+    RowBox[{
+     RowBox[{"NotebookDirectory", "[", "]"}], ",", 
+     "\"\<RbChosenRho.txt\>\""}], "]"}], ",", "%"}], "]"}]], "Input"],
+
 Cell["Convert initial conditions to c form.", "Text"],
 
 Cell[BoxData[{
@@ -1838,15 +1915,19 @@ Cell[BoxData[{
      RowBox[{"1", "/", 
       SqrtBox["2"]}], "\[Rule]", 
      RowBox[{"1", "/", "rt2"}]}]}], "}"}]}], "\[IndentingNewLine]", 
- RowBox[{"StringReplace", "[", 
+ RowBox[{"StringReplace", "[", "\[IndentingNewLine]", 
   RowBox[{
-   RowBox[{"StringJoin", "[", 
-    RowBox[{
+   RowBox[{
+   "\"\<//---------------- RbInits.txt starts ------------------\n\>\"", "<>", 
+    RowBox[{"StringJoin", "[", 
      RowBox[{
       RowBox[{
-       RowBox[{"ToString", "@", 
-        RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\<;\\n\>\""}], "&"}], "/@",
-      "%"}], "]"}], ",", 
+       RowBox[{
+        RowBox[{"ToString", "@", 
+         RowBox[{"CForm", "[", "#", "]"}]}], "<>", "\"\<;\\n\>\""}], "&"}], "/@",
+       "%"}], "]"}], "<>", "\[IndentingNewLine]", 
+    "\"\<//---------------- RbInits.txt ends  ------------------\n\>\""}], 
+   ",", 
    RowBox[{"{", 
     RowBox[{
      RowBox[{"\"\<==\>\"", "\[Rule]", "\"\<=\>\""}], ",", 
@@ -1886,8 +1967,7 @@ Cell[BoxData[{
       RowBox[{"\"\<d\>\"", "<>", "a"}]}], ",", 
      RowBox[{
       RowBox[{"\"\<k(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], "\[RuleDelayed]", 
-      RowBox[{"\"\<k\>\"", "<>", "a"}]}]}], "}"}]}], "]"}]}], "Input",
- CellChangeTimes->{{3.557577072451949*^9, 3.557577074196031*^9}}],
+      RowBox[{"\"\<k\>\"", "<>", "a"}]}]}], "}"}]}], "]"}]}], "Input"],
 
 Cell[BoxData[
  RowBox[{"Export", "[", 
@@ -2100,7 +2180,6 @@ Cell[BoxData[
       RowBox[{
        RowBox[{
        "subsys", "\[LeftDoubleBracket]", "k", "\[RightDoubleBracket]"}], ",", 
-       
        RowBox[{
         RowBox[{"4", "\[Pi]", " ", "\[ImaginaryI]", " ", 
          RowBox[{"Energy", "[", 
@@ -2110,7 +2189,6 @@ Cell[BoxData[
            "]"}], "]"}], " ", "n0", " ", 
          RowBox[{
          "rmes", "\[LeftDoubleBracket]", "k", "\[RightDoubleBracket]"}], " ", 
-         
          RowBox[{
          "polarizationcomponents1", "\[LeftDoubleBracket]", "k", 
           "\[RightDoubleBracket]"}]}], "/.", "delreps1"}]}], "]"}], "]"}], 
@@ -2257,7 +2335,6 @@ Cell[BoxData[{
      RowBox[{"Power", "[", 
       RowBox[{
        RowBox[{"_", "?", "NumericQ"}], ",", "_"}], "]"}]}], "\[RuleDelayed]", 
-    
     RowBox[{"N", "[", "a", "]"}]}]}], "//", 
   "Simplify"}], "\[IndentingNewLine]", 
  RowBox[{"StringJoin", "[", 
@@ -2271,51 +2348,57 @@ Cell[BoxData[{
      RowBox[{"ToString", "@", "j"}], "<>", "\"\<];\\n\>\""}], ",", 
     RowBox[{"{", 
      RowBox[{"j", ",", "4"}], "}"}]}], "]"}], "]"}], "\[IndentingNewLine]", 
- RowBox[{"StringReplace", "[", 
-  RowBox[{"%", ",", 
-   RowBox[{"{", 
-    RowBox[{
-     RowBox[{"\"\<==\>\"", "\[Rule]", "\"\<=\>\""}], ",", 
-     RowBox[{
-      RowBox[{"\"\<eta(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
-      "\[RuleDelayed]", 
-      RowBox[{"\"\<eta\>\"", "<>", "a"}]}], ",", 
-     RowBox[{
-      RowBox[{"Shortest", "[", 
-       RowBox[{
-       "\"\<dr(\\\"\>\"", "~~", "a__", "~~", "\"\<\\\",\\\"\>\"", "~~", "b__",
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-      RowBox[{"\"\<dr\>\"", "<>", "a", "<>", "b", "<>", "\"\<_dt\>\""}]}], 
-     ",", 
-     RowBox[{
-      RowBox[{"Shortest", "[", 
-       RowBox[{
-       "\"\<r(\\\"\>\"", "~~", "a__", "~~", "\"\<\\\",\\\"\>\"", "~~", "b__", 
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-      RowBox[{"\"\<r\>\"", "<>", "a", "<>", "b"}]}], ",", 
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-     RowBox[{
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-     RowBox[{
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-      "\[RuleDelayed]", 
-      RowBox[{"\"\<Ec\>\"", "<>", "a"}]}], ",", 
+ RowBox[{"\"\<//---------------- RbPropEquations.txt starts \
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+  RowBox[{"StringReplace", "[", 
+   RowBox[{"%", ",", 
+    RowBox[{"{", 
      RowBox[{
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-      RowBox[{"\"\<d\>\"", "<>", "a"}]}]}], "}"}]}], 
-  "]"}], "\[IndentingNewLine]", 
+      RowBox[{"\"\<==\>\"", "\[Rule]", "\"\<=\>\""}], ",", 
+      RowBox[{
+       RowBox[{"\"\<eta(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
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+       RowBox[{"\"\<eta\>\"", "<>", "a"}]}], ",", 
+      RowBox[{
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+        RowBox[{
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+        RowBox[{
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+      RowBox[{
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+       "\[RuleDelayed]", 
+       RowBox[{"\"\<ha\>\"", "<>", "a"}]}], ",", 
+      RowBox[{
+       RowBox[{"\"\<hb(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+       "\[RuleDelayed]", 
+       RowBox[{"\"\<hb\>\"", "<>", "a"}]}], ",", 
+      RowBox[{
+       RowBox[{"\"\<g(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+       "\[RuleDelayed]", 
+       RowBox[{"\"\<g\>\"", "<>", "a"}]}], ",", 
+      RowBox[{
+       RowBox[{"\"\<dW(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+       "\[RuleDelayed]", 
+       RowBox[{"\"\<dE\>\"", "<>", "a", "<>", "\"\<_dz\>\""}]}], ",", 
+      RowBox[{
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+       "\[RuleDelayed]", 
+       RowBox[{"\"\<Ec\>\"", "<>", "a"}]}], ",", 
+      RowBox[{
+       RowBox[{"\"\<d(\>\"", "~~", "a_", "~~", "\"\<)\>\""}], 
+       "\[RuleDelayed]", 
+       RowBox[{"\"\<d\>\"", "<>", "a"}]}]}], "}"}]}], "]"}], "<>", 
+  "\[IndentingNewLine]", 
+  "\"\<//---------------- RbPropEquations.txt ends  ------------------\n\
+\>\""}], "\[IndentingNewLine]", 
  RowBox[{"Export", "[", 
   RowBox[{
    RowBox[{"ToFileName", "[", 
@@ -2325,10 +2408,10 @@ Cell[BoxData[{
 }, Open  ]]
 },
 WindowSize->{956, 1004},
-WindowMargins->{{0, Automatic}, {26, Automatic}},
+WindowMargins->{{0, Automatic}, {Automatic, 0}},
 PrivateNotebookOptions->{"FileOutlineCache"->False},
 ShowSelection->True,
-FrontEndVersion->"8.0 for Linux x86 (32-bit) (February 23, 2011)",
+FrontEndVersion->"8.0 for Microsoft Windows (64-bit) (October 6, 2011)",
 StyleDefinitions->"Default.nb"
 ]
 
-- 
cgit v1.2.3