From 423577e3580a1a0f833e397051d258636a237760 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Mon, 18 May 2015 22:55:11 +0800
Subject: [PATCH 01/13] develop branch upload test

---
 .../GraduateProject_DNASelfAssembling.cpp        |  8 ++++++--
 .../GraduateProject_PatchesAndPresets.cpp        | 16 +++++++++++-----
 .../GraduateProject_PatchesAndPresets.h          |  1 +
 GraduateProject_DNASelfAssembling/stdafx.h       |  6 +++++-
 4 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index 8f4aabc..71e023c 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -3,6 +3,8 @@
 
 #include "stdafx.h"
 
+mt19937 gen(123456);
+
 int programInitiation(){
 	ornt2bpornt_init();
 	unitcell_init();
@@ -13,8 +15,10 @@ int _tmain(int argc, _TCHAR* argv[])
 	programInitiation();
 	patchPreset();
 
-
-
+	for (int i = 0; i < N; i++){
+		cout << i << '\t';
+		mol[i].displayPatch();
+	}
 
 	return 0;
 }
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
index f7f1b5d..ccbc140 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
@@ -5,10 +5,7 @@ atom_in_unitcell atom_in_unitcell::set(int nx, int ny, int nz, int nsd, int norn
 	sd = nsd;
 	int mainOrnt = nornt0;
 	int subOrnt = 0, subOrnt_as_pow = 7 - nornt0^nornt1;
-	while (subOrnt_as_pow > 1){
-		subOrnt_as_pow >>= 1;
-		subOrnt++;
-	}
+	for (; subOrnt_as_pow > 1; subOrnt_as_pow >>= 1)subOrnt++;
 	ornt = mainOrnt + 8 * subOrnt;
 	return *this;
 }
@@ -28,8 +25,10 @@ int unitcell_init(){
 DNAmol::DNAmol(){
 	px.x = px.y = px.z = 0;
 	ornt = 0;
-	for (int i = 0; i < 4; i++){
+	int i, j;
+	for (i = 0; i < 4; i++){
 		correctbond[i] = -1;
+		for (j = 0; j < 8; j++)patch[i][j] = 'T';
 	}
 }
 DNAmol DNAmol::put(int nx, int ny, int nz, int nornt){
@@ -42,6 +41,13 @@ DNAmol DNAmol::put(const atom_in_unitcell &a, int x_init, int y_init, int z_init
 	ornt = a.ornt;
 	return *this;
 }
+int DNAmol::displayPatch()const{
+	for (int i = 0; i < 4; i++){
+		cout.write(patch[i], 8);
+	}
+	cout << endl;
+	return 0;
+}
 int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
 DNAmol *mol;
 int N; // Total molecules.
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
index 06bd024..826128c 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
@@ -17,6 +17,7 @@ struct DNAmol{
 	DNAmol();
 	DNAmol put(int nx, int ny, int nz, int nornt);
 	DNAmol put(const atom_in_unitcell &a, int x_init, int y_init, int z_init);
+	int displayPatch()const;
 };
 extern DNAmol *mol;
 extern int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
diff --git a/GraduateProject_DNASelfAssembling/stdafx.h b/GraduateProject_DNASelfAssembling/stdafx.h
index 6b55041..06a10fc 100644
--- a/GraduateProject_DNASelfAssembling/stdafx.h
+++ b/GraduateProject_DNASelfAssembling/stdafx.h
@@ -13,10 +13,14 @@
 // TODO:  在此处引用程序需要的其他头文件
 #include<iostream>
 #include<fstream>
+#include<random>
 
 using namespace std;
 
 #include<math.h>
 
 #include"GraduateProject_PositionAndOrientation.h"
-#include"GraduateProject_PatchesAndPresets.h"
\ No newline at end of file
+#include"GraduateProject_PatchesAndPresets.h"
+
+
+extern mt19937 gen;
\ No newline at end of file

From 14f70531df5100c243d73edd977e7434fec3b9c9 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Tue, 19 May 2015 01:39:00 +0800
Subject: [PATCH 02/13] patches assigned

---
 .../GraduateProject_PatchesAndPresets.cpp      | 18 +++++++++++++++++-
 .../GraduateProject_PatchesAndPresets.h        |  3 +++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
index ccbc140..7f79eea 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
@@ -52,6 +52,16 @@ int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using p
 DNAmol *mol;
 int N; // Total molecules.
 
+char nt[4] = { 'A', 'C', 'G', 'T' };
+int ntSerial(char which_nt){
+	switch (which_nt){
+	case'A':return 0;
+	case'C':return 1;
+	case'G':return 2;
+	case'T':return 3;
+	}
+}
+
 int stageClear(){
 	int i, j, k;
 	for (i = 0; i < _Nx; i++){
@@ -96,6 +106,7 @@ int correctbonding(int n0serial, int n01x, int n01y, int n01z){
 	int ornt1 = 7 - ornt0;
 	int n0ps = -1, n1ps = -1; // patch serial for the right bonding. -1 if not exist.
 	int m;
+	int temp_ntSerial;
 	for (m = 0; m < 4; m++){
 		if (ornt2bpornt[mol[n0serial].ornt][m] == ornt0){
 			n0ps = m; break;
@@ -110,7 +121,12 @@ int correctbonding(int n0serial, int n01x, int n01y, int n01z){
 		mol[n0serial].correctbond[n0ps] = n1serial;
 		mol[n1serial].correctbond[n1ps] = n0serial;
 		// patch assign
-
+		static uniform_int_distribution<> patchDis(0, 3);
+		for (int i = 0; i < 8; i++){
+			temp_ntSerial = patchDis(gen);
+			mol[n0serial].patch[n0ps][i] = nt[temp_ntSerial];
+			mol[n1serial].patch[n1ps][7 - i] = nt[3 - temp_ntSerial];
+		}
 		return 0;
 	}
 	return 1;
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
index 826128c..2729b65 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
@@ -23,4 +23,7 @@ extern DNAmol *mol;
 extern int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
 extern int N; // Total molecules.
 
+extern char nt[4];
+int ntSerial(char which_nt);
+
 int patchPreset();
\ No newline at end of file

From e8139bd6f95f01b8949d9c5a16ee4c1e1d9eedd5 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Wed, 20 May 2015 00:30:20 +0800
Subject: [PATCH 03/13] initial distribution

---
 .../GraduateProject_DNASelfAssembling.cpp           |  5 +++--
 .../GraduateProject_DNASelfAssembling.vcxproj       |  2 ++
 ...raduateProject_DNASelfAssembling.vcxproj.filters |  6 ++++++
 .../GraduateProject_PatchesAndPresets.cpp           | 13 +++++++++++++
 .../GraduateProject_PatchesAndPresets.h             |  1 +
 GraduateProject_DNASelfAssembling/stdafx.h          |  1 +
 6 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index 71e023c..83364c8 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -14,12 +14,13 @@ int _tmain(int argc, _TCHAR* argv[])
 {
 	programInitiation();
 	patchPreset();
+	simulationPrepare();
 
 	for (int i = 0; i < N; i++){
-		cout << i << '\t';
-		mol[i].displayPatch();
+		cout << i << '\t' << mol[i].px << endl;
 	}
 
+
 	return 0;
 }
 
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
index 2683d53..2b6389e 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
@@ -81,6 +81,7 @@
   <ItemGroup>
     <ClInclude Include="GraduateProject_PatchesAndPresets.h" />
     <ClInclude Include="GraduateProject_PositionAndOrientation.h" />
+    <ClInclude Include="GraduateProject_Simulation.h" />
     <ClInclude Include="stdafx.h" />
     <ClInclude Include="targetver.h" />
   </ItemGroup>
@@ -88,6 +89,7 @@
     <ClCompile Include="GraduateProject_DNASelfAssembling.cpp" />
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp" />
     <ClCompile Include="GraduateProject_PositionAndOrientation.cpp" />
+    <ClCompile Include="GraduateProject_Simulation.cpp" />
     <ClCompile Include="stdafx.cpp">
       <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">Create</PrecompiledHeader>
       <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">Create</PrecompiledHeader>
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
index ee49a70..25f3fd9 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
@@ -30,6 +30,9 @@
     <ClInclude Include="GraduateProject_PatchesAndPresets.h">
       <Filter>澶存枃浠�</Filter>
     </ClInclude>
+    <ClInclude Include="GraduateProject_Simulation.h">
+      <Filter>澶存枃浠�</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="stdafx.cpp">
@@ -44,5 +47,8 @@
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp">
       <Filter>婧愭枃浠�</Filter>
     </ClCompile>
+    <ClCompile Include="GraduateProject_Simulation.cpp">
+      <Filter>婧愭枃浠�</Filter>
+    </ClCompile>
   </ItemGroup>
 </Project>
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
index 7f79eea..65d8faa 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
@@ -48,6 +48,13 @@ int DNAmol::displayPatch()const{
 	cout << endl;
 	return 0;
 }
+int DNAmol::displayPatch(ofstream &out)const{
+	for (int i = 0; i < 4; i++){
+		out.write(patch[i], 8);
+	}
+	out << endl;
+	return 0;
+}
 int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
 DNAmol *mol;
 int N; // Total molecules.
@@ -146,11 +153,17 @@ int nucleotidePreset(){
 			}
 		}
 	}
+	ofstream out("F:\\DNAPatches.txt");
+	for (m = 0; m < N; m++){
+		mol[m].displayPatch(out);
+	}
+	out.close();
 	return 0;
 }
 int patchPreset(){
 	stageClear();
 	molPreset();
 	nucleotidePreset();
+	stageClear();
 	return 0;
 }
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
index 2729b65..dcb5320 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
@@ -18,6 +18,7 @@ struct DNAmol{
 	DNAmol put(int nx, int ny, int nz, int nornt);
 	DNAmol put(const atom_in_unitcell &a, int x_init, int y_init, int z_init);
 	int displayPatch()const;
+	int displayPatch(ofstream &out)const;
 };
 extern DNAmol *mol;
 extern int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
diff --git a/GraduateProject_DNASelfAssembling/stdafx.h b/GraduateProject_DNASelfAssembling/stdafx.h
index 06a10fc..4c791d9 100644
--- a/GraduateProject_DNASelfAssembling/stdafx.h
+++ b/GraduateProject_DNASelfAssembling/stdafx.h
@@ -21,6 +21,7 @@ using namespace std;
 
 #include"GraduateProject_PositionAndOrientation.h"
 #include"GraduateProject_PatchesAndPresets.h"
+#include"GraduateProject_Simulation.h"
 
 
 extern mt19937 gen;
\ No newline at end of file

From a6402721438ebcdf656c9f143042274a469e2194 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Wed, 20 May 2015 00:35:50 +0800
Subject: [PATCH 04/13] Revert "initial distribution"

This reverts commit e8139bd6f95f01b8949d9c5a16ee4c1e1d9eedd5.
---
 .../GraduateProject_DNASelfAssembling.cpp           |  5 ++---
 .../GraduateProject_DNASelfAssembling.vcxproj       |  2 --
 ...raduateProject_DNASelfAssembling.vcxproj.filters |  6 ------
 .../GraduateProject_PatchesAndPresets.cpp           | 13 -------------
 .../GraduateProject_PatchesAndPresets.h             |  1 -
 GraduateProject_DNASelfAssembling/stdafx.h          |  1 -
 6 files changed, 2 insertions(+), 26 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index 83364c8..71e023c 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -14,13 +14,12 @@ int _tmain(int argc, _TCHAR* argv[])
 {
 	programInitiation();
 	patchPreset();
-	simulationPrepare();
 
 	for (int i = 0; i < N; i++){
-		cout << i << '\t' << mol[i].px << endl;
+		cout << i << '\t';
+		mol[i].displayPatch();
 	}
 
-
 	return 0;
 }
 
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
index 2b6389e..2683d53 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
@@ -81,7 +81,6 @@
   <ItemGroup>
     <ClInclude Include="GraduateProject_PatchesAndPresets.h" />
     <ClInclude Include="GraduateProject_PositionAndOrientation.h" />
-    <ClInclude Include="GraduateProject_Simulation.h" />
     <ClInclude Include="stdafx.h" />
     <ClInclude Include="targetver.h" />
   </ItemGroup>
@@ -89,7 +88,6 @@
     <ClCompile Include="GraduateProject_DNASelfAssembling.cpp" />
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp" />
     <ClCompile Include="GraduateProject_PositionAndOrientation.cpp" />
-    <ClCompile Include="GraduateProject_Simulation.cpp" />
     <ClCompile Include="stdafx.cpp">
       <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">Create</PrecompiledHeader>
       <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">Create</PrecompiledHeader>
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
index 25f3fd9..ee49a70 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
@@ -30,9 +30,6 @@
     <ClInclude Include="GraduateProject_PatchesAndPresets.h">
       <Filter>澶存枃浠�</Filter>
     </ClInclude>
-    <ClInclude Include="GraduateProject_Simulation.h">
-      <Filter>澶存枃浠�</Filter>
-    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="stdafx.cpp">
@@ -47,8 +44,5 @@
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp">
       <Filter>婧愭枃浠�</Filter>
     </ClCompile>
-    <ClCompile Include="GraduateProject_Simulation.cpp">
-      <Filter>婧愭枃浠�</Filter>
-    </ClCompile>
   </ItemGroup>
 </Project>
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
index 65d8faa..7f79eea 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
@@ -48,13 +48,6 @@ int DNAmol::displayPatch()const{
 	cout << endl;
 	return 0;
 }
-int DNAmol::displayPatch(ofstream &out)const{
-	for (int i = 0; i < 4; i++){
-		out.write(patch[i], 8);
-	}
-	out << endl;
-	return 0;
-}
 int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
 DNAmol *mol;
 int N; // Total molecules.
@@ -153,17 +146,11 @@ int nucleotidePreset(){
 			}
 		}
 	}
-	ofstream out("F:\\DNAPatches.txt");
-	for (m = 0; m < N; m++){
-		mol[m].displayPatch(out);
-	}
-	out.close();
 	return 0;
 }
 int patchPreset(){
 	stageClear();
 	molPreset();
 	nucleotidePreset();
-	stageClear();
 	return 0;
 }
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
index dcb5320..2729b65 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
@@ -18,7 +18,6 @@ struct DNAmol{
 	DNAmol put(int nx, int ny, int nz, int nornt);
 	DNAmol put(const atom_in_unitcell &a, int x_init, int y_init, int z_init);
 	int displayPatch()const;
-	int displayPatch(ofstream &out)const;
 };
 extern DNAmol *mol;
 extern int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
diff --git a/GraduateProject_DNASelfAssembling/stdafx.h b/GraduateProject_DNASelfAssembling/stdafx.h
index 4c791d9..06a10fc 100644
--- a/GraduateProject_DNASelfAssembling/stdafx.h
+++ b/GraduateProject_DNASelfAssembling/stdafx.h
@@ -21,7 +21,6 @@ using namespace std;
 
 #include"GraduateProject_PositionAndOrientation.h"
 #include"GraduateProject_PatchesAndPresets.h"
-#include"GraduateProject_Simulation.h"
 
 
 extern mt19937 gen;
\ No newline at end of file

From 8e79e0c9c13e47fe07f7329f8c41cbde5dce49a5 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Wed, 20 May 2015 00:36:23 +0800
Subject: [PATCH 05/13] initial distribution

---
 .../GraduateProject_Simulation.cpp            | 36 +++++++++++++++++++
 .../GraduateProject_Simulation.h              |  3 ++
 2 files changed, 39 insertions(+)
 create mode 100644 GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
 create mode 100644 GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
new file mode 100644
index 0000000..f59d18e
--- /dev/null
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
@@ -0,0 +1,36 @@
+#include"stdafx.h"
+
+/*
+	The algorithm used in this function has LOW efficiency, and needs to be improved.
+	
+	We put the DNA molecules in the lattice randomly in the following manner:
+	1: generate a random number as the position in the lattice;
+	2: if the position is not taken, put the molecule in it, otherwise repeat 1;
+	3: repeat 1 - 2 for all molecules.
+
+	The ratio of useful to useless repetitions could be extremely LOW when the lattice becomes crowded.
+	Assume the lattice with n different positions in which m is already taken,
+	then the expectation value for the repetitions required to put a new molecule is n/(n-m).
+	The overall time complexity to put k molecules is O(n ln(n/(n-k)))
+	where the best case is O(k), and the worst case is O(\infty).
+
+	This information should be removed after revising.
+*/
+int simulationPrepare(){
+	static uniform_int_distribution<long> transDis_x(0, _Nx - 1);
+	static uniform_int_distribution<long> transDis_y(0, _Ny - 1);
+	static uniform_int_distribution<long> transDis_z(0, _Nz - 1);
+	static uniform_int_distribution<> orntDis(0, 23);
+	int x, y, z;
+	for (int m = 0; m < N; m++){
+		do{
+			x = transDis_x(gen);
+			y = transDis_y(gen);
+			z = transDis_z(gen);
+		} while (stage[x][y][z] >= 0);
+		stage[x][y][z] = m;
+		mol[m].put(x, y, z, orntDis(gen));
+	}
+
+	return 0;
+}
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
new file mode 100644
index 0000000..a7cbfb7
--- /dev/null
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
@@ -0,0 +1,3 @@
+#pragma once
+
+int simulationPrepare();
\ No newline at end of file

From 1ea2cf868a2fd2a54faa492d5185d78938dde562 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Wed, 20 May 2015 00:41:21 +0800
Subject: [PATCH 06/13] change 2

---
 .../GraduateProject_DNASelfAssembling.cpp           |  5 +++--
 .../GraduateProject_PatchesAndPresets.cpp           | 13 +++++++++++++
 .../GraduateProject_PatchesAndPresets.h             |  1 +
 GraduateProject_DNASelfAssembling/stdafx.h          |  1 +
 4 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index 71e023c..83364c8 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -14,12 +14,13 @@ int _tmain(int argc, _TCHAR* argv[])
 {
 	programInitiation();
 	patchPreset();
+	simulationPrepare();
 
 	for (int i = 0; i < N; i++){
-		cout << i << '\t';
-		mol[i].displayPatch();
+		cout << i << '\t' << mol[i].px << endl;
 	}
 
+
 	return 0;
 }
 
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
index 7f79eea..65d8faa 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
@@ -48,6 +48,13 @@ int DNAmol::displayPatch()const{
 	cout << endl;
 	return 0;
 }
+int DNAmol::displayPatch(ofstream &out)const{
+	for (int i = 0; i < 4; i++){
+		out.write(patch[i], 8);
+	}
+	out << endl;
+	return 0;
+}
 int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
 DNAmol *mol;
 int N; // Total molecules.
@@ -146,11 +153,17 @@ int nucleotidePreset(){
 			}
 		}
 	}
+	ofstream out("F:\\DNAPatches.txt");
+	for (m = 0; m < N; m++){
+		mol[m].displayPatch(out);
+	}
+	out.close();
 	return 0;
 }
 int patchPreset(){
 	stageClear();
 	molPreset();
 	nucleotidePreset();
+	stageClear();
 	return 0;
 }
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
index 2729b65..dcb5320 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
@@ -18,6 +18,7 @@ struct DNAmol{
 	DNAmol put(int nx, int ny, int nz, int nornt);
 	DNAmol put(const atom_in_unitcell &a, int x_init, int y_init, int z_init);
 	int displayPatch()const;
+	int displayPatch(ofstream &out)const;
 };
 extern DNAmol *mol;
 extern int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
diff --git a/GraduateProject_DNASelfAssembling/stdafx.h b/GraduateProject_DNASelfAssembling/stdafx.h
index 06a10fc..4c791d9 100644
--- a/GraduateProject_DNASelfAssembling/stdafx.h
+++ b/GraduateProject_DNASelfAssembling/stdafx.h
@@ -21,6 +21,7 @@ using namespace std;
 
 #include"GraduateProject_PositionAndOrientation.h"
 #include"GraduateProject_PatchesAndPresets.h"
+#include"GraduateProject_Simulation.h"
 
 
 extern mt19937 gen;
\ No newline at end of file

From 4ab8ac00b10861ca11c435fd3254a7246a840fdc Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Wed, 20 May 2015 00:45:23 +0800
Subject: [PATCH 07/13] change 3

---
 .../GraduateProject_DNASelfAssembling.vcxproj               | 2 ++
 .../GraduateProject_DNASelfAssembling.vcxproj.filters       | 6 ++++++
 2 files changed, 8 insertions(+)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
index 2683d53..2b6389e 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
@@ -81,6 +81,7 @@
   <ItemGroup>
     <ClInclude Include="GraduateProject_PatchesAndPresets.h" />
     <ClInclude Include="GraduateProject_PositionAndOrientation.h" />
+    <ClInclude Include="GraduateProject_Simulation.h" />
     <ClInclude Include="stdafx.h" />
     <ClInclude Include="targetver.h" />
   </ItemGroup>
@@ -88,6 +89,7 @@
     <ClCompile Include="GraduateProject_DNASelfAssembling.cpp" />
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp" />
     <ClCompile Include="GraduateProject_PositionAndOrientation.cpp" />
+    <ClCompile Include="GraduateProject_Simulation.cpp" />
     <ClCompile Include="stdafx.cpp">
       <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">Create</PrecompiledHeader>
       <PrecompiledHeader Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">Create</PrecompiledHeader>
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
index ee49a70..25f3fd9 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
@@ -30,6 +30,9 @@
     <ClInclude Include="GraduateProject_PatchesAndPresets.h">
       <Filter>澶存枃浠�</Filter>
     </ClInclude>
+    <ClInclude Include="GraduateProject_Simulation.h">
+      <Filter>澶存枃浠�</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="stdafx.cpp">
@@ -44,5 +47,8 @@
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp">
       <Filter>婧愭枃浠�</Filter>
     </ClCompile>
+    <ClCompile Include="GraduateProject_Simulation.cpp">
+      <Filter>婧愭枃浠�</Filter>
+    </ClCompile>
   </ItemGroup>
 </Project>
\ No newline at end of file

From e1939e508623bd5c762f05a0a7bed98bc391ed05 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Thu, 21 May 2015 01:12:54 +0800
Subject: [PATCH 08/13] 20150521 daily

---
 .../GraduateProject_DNASelfAssembling.cpp     |  1 +
 .../GraduateProject_Simulation.cpp            | 45 ++++++++++++++++---
 .../GraduateProject_Simulation.h              |  3 +-
 3 files changed, 42 insertions(+), 7 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index 83364c8..26ef0d4 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -15,6 +15,7 @@ int _tmain(int argc, _TCHAR* argv[])
 	programInitiation();
 	patchPreset();
 	simulationPrepare();
+	simulationProcess();
 
 	for (int i = 0; i < N; i++){
 		cout << i << '\t' << mol[i].px << endl;
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
index f59d18e..478abe4 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
@@ -1,5 +1,20 @@
 #include"stdafx.h"
 
+bool couldPlaceMolecule(int x, int y, int z){
+	int i, j, k;
+	ppos npx;
+	for (i = -1; i <= 1; i++){
+		for (j = -1; j <= 1; j++){
+			for (k = -1; k <= 1; k++){
+				npx = ppos(x + i, y + j, z + k);
+				if (i*i + j*j + k*k != 3 && stage[npx.x][npx.y][npx.z] >= 0){
+					return false;
+				}
+			}
+		}
+	}
+	return true;
+}
 /*
 	The algorithm used in this function has LOW efficiency, and needs to be improved.
 	
@@ -14,23 +29,41 @@
 	The overall time complexity to put k molecules is O(n ln(n/(n-k)))
 	where the best case is O(k), and the worst case is O(\infty).
 
-	This information should be removed after revising.
+	As for this case, every DNA molecule would in average consume 4 of the lattice positions,
+	thus making the stage easily get crowded.
+
+	====== This information should be removed after revising. ======
 */
 int simulationPrepare(){
-	static uniform_int_distribution<long> transDis_x(0, _Nx - 1);
-	static uniform_int_distribution<long> transDis_y(0, _Ny - 1);
-	static uniform_int_distribution<long> transDis_z(0, _Nz - 1);
-	static uniform_int_distribution<> orntDis(0, 23);
+	uniform_int_distribution<long> transDis_x(0, _Nx - 1);
+	uniform_int_distribution<long> transDis_y(0, _Ny - 1);
+	uniform_int_distribution<long> transDis_z(0, _Nz - 1);
+	uniform_int_distribution<> orntDis(0, 23);
 	int x, y, z;
 	for (int m = 0; m < N; m++){
 		do{
 			x = transDis_x(gen);
 			y = transDis_y(gen);
 			z = transDis_z(gen);
-		} while (stage[x][y][z] >= 0);
+		} while (!couldPlaceMolecule(x, y, z));
 		stage[x][y][z] = m;
 		mol[m].put(x, y, z, orntDis(gen));
 	}
 
+	return 0;
+}
+
+#define k_B 1.381E-23
+#define N_A 6.023E23
+
+
+int moveStep(int s){
+
+	return 0;
+}
+int simulationProcess(){
+	int totalSteps = 10000;
+	int step = 0;
+
 	return 0;
 }
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
index a7cbfb7..d8d4485 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
@@ -1,3 +1,4 @@
 #pragma once
 
-int simulationPrepare();
\ No newline at end of file
+int simulationPrepare();
+int simulationProcess();
\ No newline at end of file

From a2ca5d1b7905ccf18dd980a1296901aacdc7b805 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Fri, 22 May 2015 01:03:53 +0800
Subject: [PATCH 09/13] 20150521 daily

---
 .../GraduateProject_DNASelfAssembling.cpp     |   5 -
 .../GraduateProject_PatchesAndPresets.cpp     |  34 +++--
 .../GraduateProject_PatchesAndPresets.h       |   5 +
 .../GraduateProject_Simulation.cpp            | 129 +++++++++++++++---
 .../GraduateProject_Simulation.h              |   6 +
 5 files changed, 140 insertions(+), 39 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index 26ef0d4..ce0a2bc 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -17,11 +17,6 @@ int _tmain(int argc, _TCHAR* argv[])
 	simulationPrepare();
 	simulationProcess();
 
-	for (int i = 0; i < N; i++){
-		cout << i << '\t' << mol[i].px << endl;
-	}
-
-
 	return 0;
 }
 
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
index 65d8faa..42281ac 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.cpp
@@ -55,6 +55,14 @@ int DNAmol::displayPatch(ofstream &out)const{
 	out << endl;
 	return 0;
 }
+int DNAmol::findPatchSerial(int whichOrnt)const{ // Find the patch serial in the designated orientation. -1 if not found.
+	for (int m = 0; m < 4; m++){
+		if (ornt2bpornt[ornt][m] == whichOrnt){
+			return m;
+		}
+	}
+	return -1;
+}
 int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
 DNAmol *mol;
 int N; // Total molecules.
@@ -68,6 +76,17 @@ int ntSerial(char which_nt){
 	case'T':return 3;
 	}
 }
+int ntSerialPair[4] = { 3, 2, 1, 0 };
+char ntPair(char which_nt){
+	return nt[ntSerialPair[ntSerial(which_nt)]];
+}
+int couldPatchInteract[4][4] = {
+	{ 0, 1, 1, 0 },
+	{ 1, 0, 0, 1 },
+	{ 1, 0, 0, 1 },
+	{ 0, 1, 1, 0 }
+};
+int isPatchConsequent[4] = { 1, 0, 0, 1 };
 
 int stageClear(){
 	int i, j, k;
@@ -112,19 +131,10 @@ int correctbonding(int n0serial, int n01x, int n01y, int n01z){
 	int ornt0 = 4 * (n01x + 1) / 2 + 2 * (n01y + 1) / 2 + (n01z + 1) / 2;
 	int ornt1 = 7 - ornt0;
 	int n0ps = -1, n1ps = -1; // patch serial for the right bonding. -1 if not exist.
-	int m;
 	int temp_ntSerial;
-	for (m = 0; m < 4; m++){
-		if (ornt2bpornt[mol[n0serial].ornt][m] == ornt0){
-			n0ps = m; break;
-		}
-	}
-	for (m = 0; m < 4; m++){
-		if (ornt2bpornt[mol[n1serial].ornt][m] == ornt1){
-			n1ps = m; break;
-		}
-	}
-	if (n0ps >= 0 && n1ps >= 0 && abs(n0ps - n1ps) == 2){
+	n0ps = mol[n0serial].findPatchSerial(ornt0);
+	n1ps = mol[n1serial].findPatchSerial(ornt1);
+	if (n0ps >= 0 && n1ps >= 0 && couldPatchInteract[n0ps][n1ps]){
 		mol[n0serial].correctbond[n0ps] = n1serial;
 		mol[n1serial].correctbond[n1ps] = n0serial;
 		// patch assign
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
index dcb5320..b6a47eb 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_PatchesAndPresets.h
@@ -19,6 +19,7 @@ struct DNAmol{
 	DNAmol put(const atom_in_unitcell &a, int x_init, int y_init, int z_init);
 	int displayPatch()const;
 	int displayPatch(ofstream &out)const;
+	int findPatchSerial(int whichOrnt)const; // Find the patch serial in the designated orientation. -1 if not found.
 };
 extern DNAmol *mol;
 extern int stage[_Nx][_Ny][_Nz]; // To store DNAmol serial. -1 if not occupied. Using periodic boundary conditions.
@@ -26,5 +27,9 @@ extern int N; // Total molecules.
 
 extern char nt[4];
 int ntSerial(char which_nt);
+extern int ntSerialPair[4];
+char ntPair(char which_nt);
+extern int couldPatchInteract[4][4];
+extern int isPatchConsequent[4]; // If the nucleotide sequence in a patch is 5'-3', it is consequent.
 
 int patchPreset();
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
index 478abe4..a1bdf06 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
@@ -15,26 +15,26 @@ bool couldPlaceMolecule(int x, int y, int z){
 	}
 	return true;
 }
-/*
-	The algorithm used in this function has LOW efficiency, and needs to be improved.
-	
-	We put the DNA molecules in the lattice randomly in the following manner:
-	1: generate a random number as the position in the lattice;
-	2: if the position is not taken, put the molecule in it, otherwise repeat 1;
-	3: repeat 1 - 2 for all molecules.
-
-	The ratio of useful to useless repetitions could be extremely LOW when the lattice becomes crowded.
-	Assume the lattice with n different positions in which m is already taken,
-	then the expectation value for the repetitions required to put a new molecule is n/(n-m).
-	The overall time complexity to put k molecules is O(n ln(n/(n-k)))
-	where the best case is O(k), and the worst case is O(\infty).
-
-	As for this case, every DNA molecule would in average consume 4 of the lattice positions,
-	thus making the stage easily get crowded.
-
-	====== This information should be removed after revising. ======
-*/
 int simulationPrepare(){
+	/*
+		The following algorithm used has LOW efficiency, and needs to be improved.
+
+		We put the DNA molecules in the lattice randomly in the following manner:
+		1: generate a random number as the position in the lattice;
+		2: if the position is not taken, put the molecule in it, otherwise repeat 1;
+		3: repeat 1 - 2 for all molecules.
+
+		The ratio of useful to useless repetitions could be extremely LOW when the lattice becomes crowded.
+		Assume the lattice with n different positions in which m is already taken,
+		then the expectation value for the repetitions required to put a new molecule is n/(n-m).
+		The overall time complexity to put k molecules is O(n ln(n/(n-k)))
+		where the best case is O(k), and the worst case is O(\infty).
+
+		As for this case, every DNA molecule would in average consume 4 of the lattice positions,
+		thus making the stage easily get crowded.
+
+		====== This information should be removed after revising. ======
+	*/
 	uniform_int_distribution<long> transDis_x(0, _Nx - 1);
 	uniform_int_distribution<long> transDis_y(0, _Ny - 1);
 	uniform_int_distribution<long> transDis_z(0, _Nz - 1);
@@ -53,17 +53,102 @@ int simulationPrepare(){
 	return 0;
 }
 
-#define k_B 1.381E-23
-#define N_A 6.023E23
+const double delta_H_NN_init = 0.2E3;
+const double delta_S_NN_init = -5.7;
+double T; // Kelvin
 
+double energy_local(int s){
+	/*
+	This energy includes the repulsive energy (100K) and the hybridization free energy for the matched patches,
+	allowing for single internal mismatches.
 
-int moveStep(int s){
+	The free energy is determined using the nearest-neighbor parametrization (pH 7),
+	taking into account terminal A-T penalties,
+	                    internal mismatches,
+						dangling ends, and
+						temperature and salt concentration dependence,
+	but do not consider loops or bulges.
+
+	References:
+	1. A. Reinhardt and D. Frenkel, Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures, Phys. Rev. Lett. 112, 238103 (2014)
+	2. J. SantaLucia, Jr. and D. Hicks, The Thermodynamics of DNA Structural Motifs, Annu. Rev. Biophys. Biomol. Struct. 33, 415 (2004)
+	*/
+	int i, j, k, nearests;
+	ppos npx;
+
+	double E_repulsive; // Joules
+	nearests = 0;
+	for (i = -1; i <= 1; i += 2){
+		for (j = -1; j <= 1; j += 2){
+			for (k = -1; k <= 1; k += 2){
+				npx = mol[s].px + ppos(i, j, k);
+				if (stage[npx.x][npx.y][npx.z] >= 0)nearests++;
+			}
+		}
+	}
+	E_repulsive = nearests*k_B*100;
+
+	/*
+	For a given number of basepairs in a certain duplex, and a given salt concentration,
+	the free energy corrections by sodium dependence is constant, thus ignored when calculating energy differences.
+	*/
+	double E_patches_cal = 0;
+	for (i = -1; i <= 1; i += 2){
+		for (j = -1; j <= 1; j += 2){
+			for (k = -1; k <= 1; k += 2){
+				npx = mol[s].px + ppos(i, j, k);
+				int s1 = stage[npx.x][npx.y][npx.z];
+				if (s1 >= 0){
+					int ornt0 = 4 * (i + 1) / 2 + 2 * (j + 1) / 2 + (k + 1) / 2;
+					int ornt1 = 7 - ornt0;
+					int n0ps = -1, n1ps = -1; // patch serial for the relative bonding. -1 if not exist.
+					n0ps = mol[s].findPatchSerial(ornt0);
+					n1ps = mol[s].findPatchSerial(ornt1);
+					if (n0ps >= 0 && n1ps >= 0 && couldPatchInteract[n0ps][n1ps]){
+						int mismatches = 0, internalMismatches = 0;
+						int m;
+						for (m = 0; m < 8; m++){
+							if (ntPair(mol[s].patch[n0ps][m]) != mol[s1].patch[n1ps][7 - m]){
+								mismatches++;
+								if (m > 0 && m < 7)internalMismatches++;
+							}
+						}
+						switch (mismatches){
+						case 0:
+							E_patches_cal += delta_H_NN_init - T*delta_S_NN_init;
+							for (m = 0; m < 7; m++){
 
+							}
+							break;
+						case 1:
+							if (internalMismatches == 1){
+
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+
+	cout << E_repulsive << endl;
+	
+
+	return 0;
+}
+int moveStep(int s){
+	double E0 = energy_local(s);
 	return 0;
 }
 int simulationProcess(){
 	int totalSteps = 10000;
 	int step = 0;
+	T = 300;
+
+	for (int i = 0; i < N; i++){
+		cout << i << '\t';
+		moveStep(i);
+	}
 
 	return 0;
 }
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
index d8d4485..4b35cea 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
@@ -1,4 +1,10 @@
 #pragma once
 
+#define k_B 1.381E-23 // SI units
+#define N_A 6.023E23 // SI units
+
+#define cal2J 4.184 // thermochemical calorie
+
+extern double T;
 int simulationPrepare();
 int simulationProcess();
\ No newline at end of file

From 429d49ed4a13de68b865fd69d468fc59c3202fe2 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Fri, 22 May 2015 14:23:14 +0800
Subject: [PATCH 10/13] NN_dH_kcal 20150522

---
 .../GraduateProject_DNASelfAssembling.vcxproj |  2 +
 ...eProject_DNASelfAssembling.vcxproj.filters |  6 +++
 .../GraduateProject_Data.cpp                  | 31 ++++++++++++
 .../GraduateProject_Data.h                    | 16 +++++++
 .../GraduateProject_Simulation.cpp            | 48 ++++++++++---------
 GraduateProject_DNASelfAssembling/stdafx.h    |  1 +
 6 files changed, 82 insertions(+), 22 deletions(-)
 create mode 100644 GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
 create mode 100644 GraduateProject_DNASelfAssembling/GraduateProject_Data.h

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
index 2b6389e..3d077c7 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj
@@ -79,6 +79,7 @@
     <Text Include="ReadMe.txt" />
   </ItemGroup>
   <ItemGroup>
+    <ClInclude Include="GraduateProject_Data.h" />
     <ClInclude Include="GraduateProject_PatchesAndPresets.h" />
     <ClInclude Include="GraduateProject_PositionAndOrientation.h" />
     <ClInclude Include="GraduateProject_Simulation.h" />
@@ -86,6 +87,7 @@
     <ClInclude Include="targetver.h" />
   </ItemGroup>
   <ItemGroup>
+    <ClCompile Include="GraduateProject_Data.cpp" />
     <ClCompile Include="GraduateProject_DNASelfAssembling.cpp" />
     <ClCompile Include="GraduateProject_PatchesAndPresets.cpp" />
     <ClCompile Include="GraduateProject_PositionAndOrientation.cpp" />
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
index 25f3fd9..15a4163 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.vcxproj.filters
@@ -33,6 +33,9 @@
     <ClInclude Include="GraduateProject_Simulation.h">
       <Filter>澶存枃浠�</Filter>
     </ClInclude>
+    <ClInclude Include="GraduateProject_Data.h">
+      <Filter>澶存枃浠�</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="stdafx.cpp">
@@ -50,5 +53,8 @@
     <ClCompile Include="GraduateProject_Simulation.cpp">
       <Filter>婧愭枃浠�</Filter>
     </ClCompile>
+    <ClCompile Include="GraduateProject_Data.cpp">
+      <Filter>婧愭枃浠�</Filter>
+    </ClCompile>
   </ItemGroup>
 </Project>
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
new file mode 100644
index 0000000..062f984
--- /dev/null
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
@@ -0,0 +1,31 @@
+#include"stdafx.h"
+
+const double NN_dH_kcal[4][4][4] = {
+	{ // AX/TY
+		{ 1.2, 2.3, -0.6, -7.6 },
+		{ 5.3, 0.0, -8.4, 0.7 },
+		{ -0.7, -7.8, -3.1, 1.0 },
+		{ -7.2, -1.2, -2.5, -2.7 }
+	},
+	{ // CX/GY
+		{ -0.9, 1.9, -0.7, -8.5 },
+		{ 0.6, -1.5, -8.0, -0.8 },
+		{ -4.0, -10.6, -4.9, -4.1 },
+		{ -7.8, -1.5, -2.8, -5.0 }
+	},
+	{ // GX/CY
+		{ -2.9, 5.2, -0.6, -8.2 },
+		{ -0.7, 3.6, -9.8, 2.3 },
+		{ 0.5, -8.0, -6.0, 3.3 },
+		{ -8.4, 5.2, -4.4, -2.2 }
+	},
+	{ // TX/AY
+		{ 4.7, 3.4, 0.7, -7.2 },
+		{ 7.6, 6.1, -8.2, 1.2 },
+		{ 3.0, -8.5, 1.6, -0.1 },
+		{ -7.6, 1.0, -1.3, 0.2 }
+	}
+};
+const double NN_dS_cal[4][4][4];
+const double NN_dH_init_kcal = 0.2;
+const double NN_dS_init_cal = -5.7;
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Data.h b/GraduateProject_DNASelfAssembling/GraduateProject_Data.h
new file mode 100644
index 0000000..a10fe82
--- /dev/null
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Data.h
@@ -0,0 +1,16 @@
+#pragma once
+
+extern const double NN_dH_kcal[4][4][4];
+extern const double NN_dS_cal[4][4][4];
+/*
+	NN_dH_kcal[a][b][c], NN_dS_cal[a][b][c]
+
+	5'  ---  a  ---  b  ---  3'
+	         |       |
+	3'  ---  a' ---  c  ---  5'
+
+	where a' is the paired nucleotide of a.
+	If c = b' then the index [a][b][b'] and [b'][a'][a] must refer to the same value.
+*/
+extern const double NN_dH_init_kcal;
+extern const double NN_dS_init_cal;
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
index a1bdf06..19dcee6 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
@@ -57,13 +57,37 @@ const double delta_H_NN_init = 0.2E3;
 const double delta_S_NN_init = -5.7;
 double T; // Kelvin
 
+double energy_local_patch(int s, int n0ps, int s1, int n1ps){
+	double E_patch_cal = 0;
+	int mismatches = 0, internalMismatches = 0;
+	int m;
+	for (m = 0; m < 8; m++){
+		if (ntPair(mol[s].patch[n0ps][m]) != mol[s1].patch[n1ps][7 - m]){
+			mismatches++;
+			if (m > 0 && m < 7)internalMismatches++;
+		}
+	}
+	switch (mismatches){
+	case 0:
+		E_patch_cal += delta_H_NN_init - T*delta_S_NN_init;
+		for (m = 0; m < 7; m++){
+
+		}
+		break;
+	case 1:
+		if (internalMismatches == 1){
+
+		}
+	}
+	return E_patch_cal;
+}
 double energy_local(int s){
 	/*
 	This energy includes the repulsive energy (100K) and the hybridization free energy for the matched patches,
 	allowing for single internal mismatches.
 
 	The free energy is determined using the nearest-neighbor parametrization (pH 7),
-	taking into account terminal A-T penalties,
+	taking into account terminal A-T penalties (not applicable because the DNA brick would not allow for a duplex to end together),
 	                    internal mismatches,
 						dangling ends, and
 						temperature and salt concentration dependence,
@@ -105,26 +129,7 @@ double energy_local(int s){
 					n0ps = mol[s].findPatchSerial(ornt0);
 					n1ps = mol[s].findPatchSerial(ornt1);
 					if (n0ps >= 0 && n1ps >= 0 && couldPatchInteract[n0ps][n1ps]){
-						int mismatches = 0, internalMismatches = 0;
-						int m;
-						for (m = 0; m < 8; m++){
-							if (ntPair(mol[s].patch[n0ps][m]) != mol[s1].patch[n1ps][7 - m]){
-								mismatches++;
-								if (m > 0 && m < 7)internalMismatches++;
-							}
-						}
-						switch (mismatches){
-						case 0:
-							E_patches_cal += delta_H_NN_init - T*delta_S_NN_init;
-							for (m = 0; m < 7; m++){
-
-							}
-							break;
-						case 1:
-							if (internalMismatches == 1){
-
-							}
-						}
+						E_patches_cal += energy_local_patch(s, n0ps, s1, n1ps);
 					}
 				}
 			}
@@ -132,7 +137,6 @@ double energy_local(int s){
 	}
 
 	cout << E_repulsive << endl;
-	
 
 	return 0;
 }
diff --git a/GraduateProject_DNASelfAssembling/stdafx.h b/GraduateProject_DNASelfAssembling/stdafx.h
index 4c791d9..2016a7b 100644
--- a/GraduateProject_DNASelfAssembling/stdafx.h
+++ b/GraduateProject_DNASelfAssembling/stdafx.h
@@ -22,6 +22,7 @@ using namespace std;
 #include"GraduateProject_PositionAndOrientation.h"
 #include"GraduateProject_PatchesAndPresets.h"
 #include"GraduateProject_Simulation.h"
+#include"GraduateProject_Data.h"
 
 
 extern mt19937 gen;
\ No newline at end of file

From 551863e8624ceb26608d530e8337f39675ff25e7 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Fri, 22 May 2015 15:41:19 +0800
Subject: [PATCH 11/13] NN_dS_cal 20150522

---
 .../GraduateProject_DNASelfAssembling.cpp     | 13 +++++++
 .../GraduateProject_Data.cpp                  | 39 ++++++++++++++++++-
 2 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index ce0a2bc..ad452d7 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -17,6 +17,19 @@ int _tmain(int argc, _TCHAR* argv[])
 	simulationPrepare();
 	simulationProcess();
 
+	double check[4][4][4];
+	int i, j, k;
+	double T37 = 273.15 + 37;
+	for (i = 0; i < 4; i++){
+		for (j = 0; j < 4; j++){
+			for (k = 0; k < 4; k++){
+				check[i][j][k] = NN_dH_kcal[i][j][k] - T37*NN_dS_cal[i][j][k] / 1000;
+				cout << "  \t" << check[i][j][k];
+			}
+			cout << endl;
+		}
+	}
+
 	return 0;
 }
 
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
index 062f984..3235e3a 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
@@ -26,6 +26,41 @@ const double NN_dH_kcal[4][4][4] = {
 		{ -7.6, 1.0, -1.3, 0.2 }
 	}
 };
-const double NN_dS_cal[4][4][4];
+const double NN_dS_cal[4][4][4] = {
+	{ // AX/TY
+		{ 1.7, 4.6, -2.3, -21.3 },
+		{ 14.6, -4.4, -22.4, 0.2 },
+		{ -2.3, -21.0, -9.5, 0.9 },
+		{ -20.4, -6.2, -8.3, -10.8 }
+	},
+	{ // CX/GY
+		{ -4.2, 3.7, -2.3, -22.7 },
+		{ -0.6, -7.2, -19.9, -4.5 },
+		{ -13.2, -27.2, -15.3, -11.7 },
+		{ -21.0, -6.1, -8.0, -15.8 }
+	},
+	{ // GX/CY
+		{ -9.8, 14.2, -1.0, -22.2 },
+		{ -3.8, 8.9, -24.4, 5.4 },
+		{ 3.2, -19.9, -15.8, 10.4 },
+		{ -22.4, 13.5, -12.3, -8.4 }
+	},
+	{ // TX/AY
+		{ 12.9, 8.0, 0.7, -21.3 },
+		{ 20.2, 16.4, -22.2, 0.7 },
+		{ 7.4, -22.7, 3.6, -1.7 },
+		{ -21.3, 0.7, -5.3, -1.5 }
+	}
+};
 const double NN_dH_init_kcal = 0.2;
-const double NN_dS_init_cal = -5.7;
\ No newline at end of file
+const double NN_dS_init_cal = -5.7;
+/*
+	References:
+
+	1. J. SantaLucia, Jr. and D. Hicks, The Thermodynamics of DNA Structural Motifs, Annu. Rev. Biophys. Biomol. Struct. 33, 415 (2004)
+	2. Allawi HT, SantaLucia J Jr. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 36:10581-94 (1997)
+	3. Allawi HT, SantaLucia J Jr. Nearestneighbor thermodynamics of internal A-C mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435-44 (1998)
+	4. Allawi HT, SantaLucia J Jr. Nearestneighbor thermodynamics parameters for internal G-A mismatches in DNA. Biochemistry 37:2170-79 (1998)
+	5. Allawi HT, SantaLucia J Jr. Thermodynamics of internal C-T mismatches in DNA. Nucleic Acids Res. 26:2694-701 (1998)
+	6. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry 38:3468-77 (1999)
+*/

From 96909c923b748e2700f5aa2d9f346506eb0e2fc7 Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Fri, 22 May 2015 21:02:17 +0800
Subject: [PATCH 12/13] DanglingEnds Data

---
 .../GraduateProject_DNASelfAssembling.cpp     | 14 ----
 .../GraduateProject_Data.cpp                  | 69 +++++++++++++++++++
 .../GraduateProject_Data.h                    | 24 ++++++-
 .../GraduateProject_Simulation.cpp            |  8 ++-
 4 files changed, 97 insertions(+), 18 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
index ad452d7..9b7f935 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_DNASelfAssembling.cpp
@@ -17,19 +17,5 @@ int _tmain(int argc, _TCHAR* argv[])
 	simulationPrepare();
 	simulationProcess();
 
-	double check[4][4][4];
-	int i, j, k;
-	double T37 = 273.15 + 37;
-	for (i = 0; i < 4; i++){
-		for (j = 0; j < 4; j++){
-			for (k = 0; k < 4; k++){
-				check[i][j][k] = NN_dH_kcal[i][j][k] - T37*NN_dS_cal[i][j][k] / 1000;
-				cout << "  \t" << check[i][j][k];
-			}
-			cout << endl;
-		}
-	}
-
 	return 0;
 }
-
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
index 3235e3a..0f367cf 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Data.cpp
@@ -52,8 +52,26 @@ const double NN_dS_cal[4][4][4] = {
 		{ -21.3, 0.7, -5.3, -1.5 }
 	}
 };
+int NN_dG_check(){
+	double check[4][4][4];
+	int i, j, k;
+	double T37 = 273.15 + 37;
+	for (i = 0; i < 4; i++){
+		for (j = 0; j < 4; j++){
+			for (k = 0; k < 4; k++){
+				check[i][j][k] = NN_dH_kcal[i][j][k] - T37*NN_dS_cal[i][j][k] / 1000;
+				cout << "  \t" << check[i][j][k];
+			}
+			cout << endl;
+		}
+		cout << endl;
+	}
+	return 0;
+}
 const double NN_dH_init_kcal = 0.2;
 const double NN_dS_init_cal = -5.7;
+const double NN_dH_ATPenalty_kcal = 2.2;
+const double NN_dS_ATPenalty_cal = 6.9;
 /*
 	References:
 
@@ -64,3 +82,54 @@ const double NN_dS_init_cal = -5.7;
 	5. Allawi HT, SantaLucia J Jr. Thermodynamics of internal C-T mismatches in DNA. Nucleic Acids Res. 26:2694-701 (1998)
 	6. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry 38:3468-77 (1999)
 */
+
+extern const double NN_dH_DE_kcal[2][4][4] = {
+	{
+		{ 0.2, 0.6, -1.1, -6.9 },
+		{ -6.3, -4.4, -5.1, -4.0 },
+		{ -3.7, -4.0, -3.9, -4.9 },
+		{ -2.9, -4.1, -4.2, -0.2 }
+	},
+	{
+		{ -0.5, 4.7, -4.1, -3.8 },
+		{ -5.9, -2.6, -3.2, -5.2 },
+		{ -2.1, -0.2, -3.9, -4.4 },
+		{ -0.7, 4.4, -1.6, 2.9 }
+	}
+};
+extern const double NN_dS_DE_cal[2][4][4] = {
+	{
+		{ 2.3, 3.3, -1.6, -20.0 },
+		{ -17.1, -12.6, -14.0, -10.9 },
+		{ -10.0, -11.9, -10.9, -13.8 },
+		{ -7.6, -13.0, -15.0, -0.5 }
+	},
+	{
+		{ -1.1, 14.2, -13.1, -12.6 },
+		{ -16.5, -7.4, -10.4, -15.0 },
+		{ -3.9, -0.1, -11.2, -13.1 },
+		{ -0.8, 14.9, -3.6, 10.4 }
+	}
+};
+int NN_dG_DE_check(){
+	double check[2][4][4];
+	int i, j, k;
+	double T37 = 273.15 + 37;
+	for (i = 0; i < 2; i++){
+		for (j = 0; j < 4; j++){
+			for (k = 0; k < 4; k++){
+				check[i][j][k] = NN_dH_DE_kcal[i][j][k] - T37*NN_dS_DE_cal[i][j][k] / 1000;
+				cout << "  \t" << check[i][j][k];
+			}
+			cout << endl;
+		}
+		cout << endl;
+	}
+	return 0;
+}
+/*
+	References:
+
+	1. J. SantaLucia, Jr. and D. Hicks, The Thermodynamics of DNA Structural Motifs, Annu. Rev. Biophys. Biomol. Struct. 33, 415 (2004)
+	2. Bommarito S, Peyret N, SantaLucia J Jr. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28:1929-34 (2000)
+*/
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Data.h b/GraduateProject_DNASelfAssembling/GraduateProject_Data.h
index a10fe82..27fc1b8 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Data.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Data.h
@@ -12,5 +12,27 @@ extern const double NN_dS_cal[4][4][4];
 	where a' is the paired nucleotide of a.
 	If c = b' then the index [a][b][b'] and [b'][a'][a] must refer to the same value.
 */
+//int NN_dG_check();
 extern const double NN_dH_init_kcal;
-extern const double NN_dS_init_cal;
\ No newline at end of file
+extern const double NN_dS_init_cal;
+extern const double NN_dH_ATPenalty_kcal;
+extern const double NN_dS_ATPenalty_cal;
+
+extern const double NN_dH_DE_kcal[2][4][4];
+extern const double NN_dS_DE_cal[2][4][4];
+/*
+	NN_dH_DE_kcal[0,1][a][b], NN_dS_DE_cal[0,1][a][b]
+
+	0 mode: 5' dangling ends
+
+		5'  ---  b  ---  a  ---  3'
+		                 |
+						 a' ---  5'
+
+	1 mode: 3' dangling ends
+
+		                 a' ---  3'
+						 |
+		3'  ---  b  ---  a  ---  5'
+*/
+//int NN_dG_DE_check();
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
index 19dcee6..c704e0d 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
@@ -87,7 +87,7 @@ double energy_local(int s){
 	allowing for single internal mismatches.
 
 	The free energy is determined using the nearest-neighbor parametrization (pH 7),
-	taking into account terminal A-T penalties (not applicable because the DNA brick would not allow for a duplex to end together),
+	taking into account terminal A-T penalties,
 	                    internal mismatches,
 						dangling ends, and
 						temperature and salt concentration dependence,
@@ -113,8 +113,10 @@ double energy_local(int s){
 	E_repulsive = nearests*k_B*100;
 
 	/*
-	For a given number of basepairs in a certain duplex, and a given salt concentration,
-	the free energy corrections by sodium dependence is constant, thus ignored when calculating energy differences.
+	1. For a given number of basepairs in a certain duplex, and a given salt concentration,
+	   the free energy corrections by sodium dependence is constant, thus ignored when calculating energy differences.
+	2. The initiation energy is not applicable because the DNA brick would not allow for a duplex to start together.
+	3. The terminal A-T penalty is not applicable because the DNA brick would not allow for a duplex to end together.
 	*/
 	double E_patches_cal = 0;
 	for (i = -1; i <= 1; i += 2){

From 3332e095a86aa8ca232c22ee10a68fc97100a04c Mon Sep 17 00:00:00 2001
From: drelatgithub <drel@sohu.com>
Date: Sat, 23 May 2015 01:41:55 +0800
Subject: [PATCH 13/13] 20150522 daily

---
 .../GraduateProject_Simulation.cpp            | 120 +++++++++++++++---
 .../GraduateProject_Simulation.h              |   4 +-
 2 files changed, 105 insertions(+), 19 deletions(-)

diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
index c704e0d..99ce34d 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.cpp
@@ -15,6 +15,9 @@ bool couldPlaceMolecule(int x, int y, int z){
 	}
 	return true;
 }
+bool couldPlaceMolecule(ppos px){
+	return couldPlaceMolecule(px.x, px.y, px.z);
+}
 int simulationPrepare(){
 	/*
 		The following algorithm used has LOW efficiency, and needs to be improved.
@@ -53,33 +56,48 @@ int simulationPrepare(){
 	return 0;
 }
 
-const double delta_H_NN_init = 0.2E3;
-const double delta_S_NN_init = -5.7;
 double T; // Kelvin
 
 double energy_local_patch(int s, int n0ps, int s1, int n1ps){
-	double E_patch_cal = 0;
+	double E_patch_kcal = 0;
 	int mismatches = 0, internalMismatches = 0;
 	int m;
+	int a, b, c;
 	for (m = 0; m < 8; m++){
 		if (ntPair(mol[s].patch[n0ps][m]) != mol[s1].patch[n1ps][7 - m]){
 			mismatches++;
 			if (m > 0 && m < 7)internalMismatches++;
 		}
 	}
+	int s53 = isPatchConsequent[n0ps] ? s : s1, ps53 = isPatchConsequent[n0ps] ? n0ps : n1ps;
+	int s35 = isPatchConsequent[n0ps] ? s1 : s, ps35 = isPatchConsequent[n0ps] ? n1ps : n0ps;
 	switch (mismatches){
 	case 0:
-		E_patch_cal += delta_H_NN_init - T*delta_S_NN_init;
 		for (m = 0; m < 7; m++){
-
+			a = ntSerial(mol[s53].patch[ps53][m]);
+			b = ntSerial(mol[s53].patch[ps53][m + 1]);
+			c = ntSerial(mol[s35].patch[ps35][6 - m]);
+			E_patch_kcal += NN_dH_kcal[a][b][c] - T*NN_dS_cal[a][b][c] / 1000;
 		}
 		break;
 	case 1:
 		if (internalMismatches == 1){
-
+			for (m = 0; m < 7; m++){
+				a = ntSerial(mol[s53].patch[ps53][m]);
+				b = ntSerial(mol[s53].patch[ps53][m + 1]);
+				c = ntSerial(mol[s35].patch[ps35][6 - m]);
+				E_patch_kcal += NN_dH_kcal[a][b][c] - T*NN_dS_cal[a][b][c] / 1000;
+				if (ntPair(b) != c){
+					a = ntSerial(mol[s35].patch[ps35][5 - m]);
+					b = ntSerial(mol[s35].patch[ps35][6 - m]);
+					c = ntSerial(mol[s53].patch[ps53][m + 1]);
+					E_patch_kcal += NN_dH_kcal[a][b][c] - T*NN_dS_cal[a][b][c] / 1000;
+					m++;
+				}
+			}
 		}
 	}
-	return E_patch_cal;
+	return E_patch_kcal;
 }
 double energy_local(int s){
 	/*
@@ -118,7 +136,7 @@ double energy_local(int s){
 	2. The initiation energy is not applicable because the DNA brick would not allow for a duplex to start together.
 	3. The terminal A-T penalty is not applicable because the DNA brick would not allow for a duplex to end together.
 	*/
-	double E_patches_cal = 0;
+	double E_patches_kcal = 0; // 1000 calories per mol
 	for (i = -1; i <= 1; i += 2){
 		for (j = -1; j <= 1; j += 2){
 			for (k = -1; k <= 1; k += 2){
@@ -129,32 +147,98 @@ double energy_local(int s){
 					int ornt1 = 7 - ornt0;
 					int n0ps = -1, n1ps = -1; // patch serial for the relative bonding. -1 if not exist.
 					n0ps = mol[s].findPatchSerial(ornt0);
-					n1ps = mol[s].findPatchSerial(ornt1);
+					n1ps = mol[s1].findPatchSerial(ornt1);
 					if (n0ps >= 0 && n1ps >= 0 && couldPatchInteract[n0ps][n1ps]){
-						E_patches_cal += energy_local_patch(s, n0ps, s1, n1ps);
+						E_patches_kcal += energy_local_patch(s, n0ps, s1, n1ps);
 					}
 				}
 			}
 		}
 	}
 
-	cout << E_repulsive << endl;
-
-	return 0;
+	double E_total = E_repulsive + E_patches_kcal * 1000 * cal2J / N_A;
+	return E_total;
 }
 int moveStep(int s){
 	double E0 = energy_local(s);
+	static uniform_int_distribution<> translateOrRotate(0, 1);
+	static uniform_int_distribution<> anotherOrnt(0, 22); // only 23 possible orientations in order to exclude the original orientation
+	static uniform_int_distribution<> anotherCoor(-1, 1);
+	static uniform_real_distribution<> judge(0, 1); // Metropolis Criterion
+	if (translateOrRotate(gen)){
+		int oOrnt = mol[s].ornt;
+		int nOrnt = anotherOrnt(gen);
+		nOrnt = (nOrnt >= oOrnt) ? (nOrnt + 1) : nOrnt;
+		mol[s].ornt = nOrnt;
+		double E1 = energy_local(s);
+		if (E1 > E0 && judge(gen) > exp(-(E1 - E0) / k_B / T)){
+			mol[s].ornt = oOrnt;
+		}
+	}
+	else{
+		ppos opx = mol[s].px;
+		ppos npx = opx + ppos(anotherCoor(gen), anotherCoor(gen), anotherCoor(gen));
+		if (stage[npx.x][npx.y][npx.z] == -1){
+			mol[s].px = npx;
+			stage[opx.x][opx.y][opx.z] = -1;
+			stage[npx.x][npx.y][npx.z] = s;
+			double E1 = energy_local(s);
+			if (E1 > E0 && judge(gen) > exp(-(E1 - E0) / k_B / T)){
+				mol[s].px = opx;
+				stage[opx.x][opx.y][opx.z] = s;
+				stage[npx.x][npx.y][npx.z] = -1;
+			}
+		}
+	}
 	return 0;
 }
 int simulationProcess(){
 	int totalSteps = 10000;
-	int step = 0;
-	T = 300;
+	int step;
+	T = 315;
 
-	for (int i = 0; i < N; i++){
-		cout << i << '\t';
-		moveStep(i);
+	for (step = 0; step < 200000; step++){
+		if (step % 1000 == 999)cout << step + 1 << '\t' << maxCorrectSize() << endl;
+		for (int i = 0; i < N; i++){
+			moveStep(i);
+		}
 	}
 
 	return 0;
+}
+
+int anotherMoleculeCombined(int *mark, int previousSerial){
+	int ok = 1;
+	mark[previousSerial] = 1;
+	for (int i = 0; i < 4; i++){
+		if (mol[previousSerial].correctbond[i] >= 0 && !mark[mol[previousSerial].correctbond[i]]){
+			// do not derive the difference of ppos because it would render no negative offsets
+			int dx = mol[mol[previousSerial].correctbond[i]].px.x - mol[previousSerial].px.x;
+			int dy = mol[mol[previousSerial].correctbond[i]].px.y - mol[previousSerial].px.y;
+			int dz = mol[mol[previousSerial].correctbond[i]].px.z - mol[previousSerial].px.z;
+			if (abs(dx) == 1 && abs(dy) == 1 && abs(dz) == 1){
+				ok += anotherMoleculeCombined(mark, mol[previousSerial].correctbond[i]);
+			}
+		}
+	}
+	return ok;
+}
+int maxCorrectSize(){
+	int *mark = new int[N];
+	int max = 0, temp;
+	int p;
+	for (p = 0; p < N; p++){
+		mark[p] = 0;
+	}
+	p = 0;
+	while (p < N){
+		if (!mark[p]){
+			temp = anotherMoleculeCombined(mark, p);
+			if (max < temp)max = temp;
+		}
+		p++;
+	}
+
+	delete[]mark;
+	return max;
 }
\ No newline at end of file
diff --git a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
index 4b35cea..076386f 100644
--- a/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
+++ b/GraduateProject_DNASelfAssembling/GraduateProject_Simulation.h
@@ -7,4 +7,6 @@
 
 extern double T;
 int simulationPrepare();
-int simulationProcess();
\ No newline at end of file
+int simulationProcess();
+
+int maxCorrectSize();