Removed unnecessary ODE.h file and made iteration a Class function. Not

viable for grid approaches though. Signed-off-by: Schellenberger <schellenberger@inb.uni-luebeck.de>
miscco · 1ea3c063f4a7891b53198e9e78919a3380d11afd · miscco committed Aug 27, 2014 · Aug 27, 2014 · 1ea3c06
1 parent 4f9ea29
commit 1ea3c063f4a7891b53198e9e78919a3380d11afd
Unified Split

Showing with 54 additions and 68 deletions.

+17 −2 Main.cpp

+0 −59 ODE.h

+15 −0 Thalamic_Column.cpp

+5 −4 Thalamic_Column.h

+17 −3 Thalamus.cpp
diff --git a/Main.cpp b/Main.cpp
@@ -28,7 +28,6 @@
 #include <iostream>
 #include <ctime>
 #include "Thalamic_Column.h"
-#include "ODE.h"
 
 /****************************************************************************************************/
 /*										Fixed simulation settings									*/
@@ -44,6 +43,22 @@ extern const double h	= sqrt(dt);							/* squareroot of dt for SRK iteration	*/
 
 
 /****************************************************************************************************/
+/*									Constants for SRK4 iteration									*/
+/****************************************************************************************************/
+extern const vector<double> B1 = {0,
+								  0.626708569400000081728308032325,
+								  1.7296310295000001389098542858846,
+		 	 	 	 	 	 	  1.2703689705000000831347506391467};
+extern const vector<double> B2 = {0,
+								  0.78000033203198970710445792065002,
+								  1.28727807507536762265942797967,
+								  0.44477273249350995909523476257164};
+/****************************************************************************************************/
+/*										 		end													*/
+/****************************************************************************************************/
+
+
+/****************************************************************************************************/
 /*										Main simulation routine										*/
 /****************************************************************************************************/
 int main(void) {
@@ -56,7 +71,7 @@ int main(void) {
 
 	/* Simulation */
 	for (int t=0; t< T*res; ++t) {
-		ODE (Thalamus);
+		Thalamus.iterate_ODE();
 	}
 	time (&end);
 
diff --git a/ODE.h b/ODE.h
@@ -1,59 +0,0 @@
-/*
-*	Copyright (c) 2014 Michael Schellenberger Costa
-*
-*	Permission is hereby granted, free of charge, to any person obtaining a copy
-*	of this software and associated documentation files (the "Software"), to deal
-*	in the Software without restriction, including without limitation the rights
-*	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-*	copies of the Software, and to permit persons to whom the Software is
-*	furnished to do so, subject to the following conditions:
-*
-*	The above copyright notice and this permission notice shall be included in
-*	all copies or substantial portions of the Software.
-*
-*	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-*	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-*	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-*	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-*	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-*	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-*	THE SOFTWARE.
-*/
-
-/****************************************************************************************************/
-/*									Implementation of the ODE solver								*/
-/****************************************************************************************************/
-#pragma once
-#include "Thalamic_Column.h"
-
-/****************************************************************************************************/
-/*										Evaluation of SRK4											*/
-/****************************************************************************************************/
-inline void ODE(Thalamic_Column& Thalamus) {
-	/* First calculating every ith RK moment. Has to be in order, 1th moment first */
-	for (int i=1; i<=4; ++i) {
-		Thalamus.set_RK(i);
-	}
-
-	/* Add moments */
-	Thalamus.add_RK();
-}
-/****************************************************************************************************/
-/*										 		end													*/
-/****************************************************************************************************/
-
-
-/****************************************************************************************************/
-/*									Parameters for SRK4	integration									*/
-/****************************************************************************************************/
-extern const vector<double> B1 = {0,
-								  0.626708569400000081728308032325,
-								  1.7296310295000001389098542858846,
-		 	 	 	 	 	 	  1.2703689705000000831347506391467};
-extern const vector<double> B2 = {0,
-								  0.78000033203198970710445792065002,
-								  1.28727807507536762265942797967,
-								  0.44477273249350995909523476257164};
-/****************************************************************************************************/
-/*										 		end													*/
-/****************************************************************************************************/
diff --git a/Thalamic_Column.cpp b/Thalamic_Column.cpp
@@ -303,3 +303,18 @@ void Thalamic_Column::add_RK(void) {
 /****************************************************************************************************/
 /*										 		end			 										*/
 /****************************************************************************************************/
+
+
+/****************************************************************************************************/
+/*										Evaluation of SRK4											*/
+/****************************************************************************************************/
+void Thalamic_Column::iterate_ODE(void) {
+	/* First calculating every ith RK moment. Has to be in order, 1th moment first */
+	for (int i=1; i<=4; ++i) {
+		set_RK(i);
+	}
+	add_RK();
+}
+/****************************************************************************************************/
+/*										 		end													*/
+/****************************************************************************************************/
diff --git a/Thalamic_Column.h b/Thalamic_Column.h
@@ -101,6 +101,7 @@ class Thalamic_Column {
 	/* ODE functions */
 	void 	set_RK		(int);
 	void 	add_RK	 	(void);
+	void	iterate_ODE (void);
 
 	/* Data storage  access */
 	friend void get_data (int, Thalamic_Column&, _REPEAT(double*, 2));
@@ -144,8 +145,8 @@ class Thalamic_Column {
 	const double 	theta_r		= -58.6;
 
 	/* Sigmoid gain in mV */
-	const double 	sigma_t		= 3;
-	const double 	sigma_r		= 3;
+	const double 	sigma_t		= 4;
+	const double 	sigma_r		= 4;
 
 	/* Scaling parameter for sigmoidal mapping (dimensionless) */
 	const double 	C1          = (3.14159265/sqrt(3));
@@ -207,9 +208,9 @@ class Thalamic_Column {
 	double			input		= 0.0;
 
 	/* Connectivities (dimensionless) */
-	const double 	N_tr		= 5;
+	const double 	N_tr		= 6;
 	const double 	N_rt		= 5;
-	const double 	N_rr		= 50;
+	const double 	N_rr		= 100;
 
 	friend class 	Stim;
 };
diff --git a/Thalamus.cpp b/Thalamus.cpp
@@ -27,13 +27,11 @@
 /*		The Simulation requires the following boost libraries:	Preprocessor						*/
 /*																Random								*/
 /****************************************************************************************************/
-#include <ctime>
 #include "mex.h"
 #include "matrix.h"
 #include "Thalamic_Column.h"
 #include "Stimulation.h"
 #include "saves.h"
-#include "ODE.h"
 
 /****************************************************************************************************/
 /*										Fixed simulation settings									*/
@@ -49,6 +47,22 @@ extern const double h	= sqrt(dt);							/* squareroot of dt for SRK iteration	*/
 
 
 /****************************************************************************************************/
+/*									Constants for SRK4 iteration									*/
+/****************************************************************************************************/
+extern const vector<double> B1 = {0,
+								  0.626708569400000081728308032325,
+								  1.7296310295000001389098542858846,
+		 	 	 	 	 	 	  1.2703689705000000831347506391467};
+extern const vector<double> B2 = {0,
+								  0.78000033203198970710445792065002,
+								  1.28727807507536762265942797967,
+								  0.44477273249350995909523476257164};
+/****************************************************************************************************/
+/*										 		end													*/
+/****************************************************************************************************/
+
+
+/****************************************************************************************************/
 /*										Simulation routine	 										*/
 /*										lhs defines outputs											*/
 /*										rhs defines inputs											*/
@@ -80,7 +94,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
 	/* Simulation */
 	int count = 0;
 	for (int t=0; t<Time; ++t) {
-		ODE (Thalamus);
+		Thalamus.iterate_ODE();
 		Stimulation.check_stim(t);
 		if(t>=onset*res && t%red==0){
 			get_data(count, Thalamus, Pr_Vt, Pr_Vr);