Commit: 804980d1a2f6f18a0b01e710d393f2501bbcfb23
Parent: e98db29ddb5c4dc67104c0e4c5adfb3aff342110
Author: Randy Palamar
Date: Tue, 26 Mar 2024 11:17:54 -0600
add build.sh and fix build
Diffstat:
| M | Photon.cpp | | | 2 | +- |
| D | Utilities.cpp | | | 94 | ------------------------------------------------------------------------------- |
| D | Utilities.h | | | 140 | ------------------------------------------------------------------------------- |
| A | build.sh | | | 5 | +++++ |
| M | main.cpp | | | 4 | ++-- |
| A | utils.cpp | | | 93 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | utils.h | | | 141 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
7 files changed, 242 insertions(+), 237 deletions(-)
diff --git a/Photon.cpp b/Photon.cpp
@@ -3,7 +3,7 @@
//////////////////////////////////////////////////////////////////////
#include "Photon.h"
-#include "Utilities.h"
+#include "utils.h"
#include <math.h>
/////////////////////////////////////////
diff --git a/Utilities.cpp b/Utilities.cpp
@@ -1,94 +0,0 @@
-
-#include "Utilities.h"
-
-/***********************************************************
-* A random number generator from Numerical Recipes in C. ****/
-#define MBIG 1000000000
-#define MSEED 161803398
-#define MZ 0
-#define FAC 1.0E-9
-float ran3(int &idum)
-{
- static int inext,inextp;
- static long ma[56];
- static int iff=0;
- long mj,mk;
- int i,ii,k;
- if (idum < 0 || iff == 0)
- {
- iff=1;
- mj=MSEED-(idum < 0 ? -idum : idum);
- mj %= MBIG;
- ma[55]=mj;
- mk=1;
- for (i=1;i<=54;i++)
- {
- ii=(21*i) % 55;
- ma[ii]=mk;
- mk=mj-mk;
- if (mk < MZ) mk += MBIG;
- mj=ma[ii];
- }
- for (k=1;k<=4;k++)
- for (i=1;i<=55;i++)
- {
- ma[i] -= ma[1+(i+30) % 55];
- if (ma[i] < MZ) ma[i] += MBIG;
- }
- inext=0;
- inextp=31;
- idum=1;
- }
- if (++inext == 56)
- inext=1;
- if (++inextp == 56)
- inextp=1;
- mj=ma[inext]-ma[inextp];
- if (mj < MZ) mj += MBIG;
- ma[inext]=mj;
- return mj*FAC;
-}
-#undef MBIG
-#undef MSEED
-#undef MZ
-#undef FAC
-
-
-/***********************************************************
- * Generate a random number between 0 and 1. Take a
- * number as seed the first time entering the function.
- * The seed is limited to 1<<15.
- * Wang et al found that when idum is too large, ran3 may return
- * numbers beyond 0 and 1.
- ****/
-//#define STANDARDTEST 0 /* testing program using fixed rnd seed. */
-double RandomNum(void)
-{
- static bool first_time=1;
- static int idum; /* seed for ran3. */
- if(first_time)
- {
- #if STANDARDTEST /* Use fixed seed to test the program. */
- idum = - 1;
- #else
- idum = -(int)time(NULL)%(1<<15); /* use 16-bit integer as the seed. */
- #endif
- ran3(idum);
- first_time = 0;
- idum = 1;
- }
- return( (double)ran3(idum) );
-}
-
-/////////////////////////////////////////////
-int min(int d1,int d2)
-{
- if (d1<d2)
- {
- return d1;
- }
- else
- {
- return d2;
- }
-}
diff --git a/Utilities.h b/Utilities.h
@@ -1,140 +0,0 @@
-/* Providing global variables and functions*/
-#include <math.h>
-#include <new>
-#include <time.h>
-
-//global constants
-#ifndef PI
- #define PI 3.14159265
-#endif
-
-#ifndef ZERO
- #define ZERO 1.0e-6 //for small deflection angle
-#endif
-
-#ifndef n0
- #define n0 1.0 //refractive index of ambient medium
-#endif
-
-#ifndef BIGVAL
- #define BIGVAL 1e6//big value
-#endif
-
-//global variables
-#ifdef GLOBALORIGIN
- #define GLOBAL
-#else
- #define GLOBAL extern
-#endif
-GLOBAL double dx;
-GLOBAL double dy;
-GLOBAL int Nx;
-GLOBAL int Ny;
-GLOBAL double zc;
-GLOBAL double n;
-GLOBAL double mua;
-GLOBAL double mus;
-GLOBAL double mut;
-GLOBAL double g;
-GLOBAL double d;
-
-
-GLOBAL double th_in; // incident angle in degree
-
-GLOBAL double x_offset;
-GLOBAL double y_offset;
-
-//generate random data
-float ran3(int *idum);
-double RandomNum(void);
-
-
-//other auxilliary functions
-int min(int d1, int d2);
-#define SIGN(x) ((x)>=0?1:-1)
-
-
-////////allocte dynamic array/////////////////////////
-using namespace std;
-template <class T>
-T* alloc1D(int dim1, T t)
-{
- T* p;
- try
- {
- p=new T[dim1];
- }
- catch(bad_alloc)
- {
- cerr<<"Fail to allocate 1D array!"<<endl;
- exit(1);
- }
- for (int tmp1=0;tmp1<dim1;tmp1++)
- {
- p[tmp1]=t;
- }
- return p;
-}
-template <class T>
-void dealloc1D(T* p)
-{
- delete [] p;
-}
-///////////
-template <class T>
-T** alloc2D(int dim1,int dim2,T t)
-{
- T** p;
- try
- {
- p=new T*[dim1];
- for (int tmp1=0;tmp1<dim1;tmp1++)
- {
- p[tmp1]=alloc1D(dim2,t);
- }
- }
- catch (bad_alloc)
- {
- cerr<<"Fail to allocate 2D array!";
- }
- return p;
-}
-template <class T>
-void dealloc2D(int dim1,T** p)
-{
- for (int tmp1=0;tmp1<dim1;tmp1++)
- {
- dealloc1D(p[tmp1]);
- }
- delete [] p;
-}
-/////////
-template <class T>
-T*** alloc3D(int dim1,int dim2,int dim3,T t)
-{
- T*** p;
- try
- {
- p=new T**[dim1];
- for (int tmp1=0;tmp1<dim1;tmp1++)
- {
- p[tmp1]=alloc2D(dim2,dim3,t);
- }
- }
- catch (bad_alloc)
- {
- cerr<<"Fail to allocate 3D array!";
- }
- return p;
-}
-template <class T>
-void dealloc3D(int dim1,int dim2,T*** p)
-{
- for (int tmp1=0;tmp1<dim1;tmp1++)
- {
- dealloc2D(dim2,p[tmp1]);
- }
- delete [] p;
-}
-////////////////////////////////////////////////
-
diff --git a/build.sh b/build.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+srcs="main.cpp Photon.cpp utils.cpp"
+
+c++ -O3 -Wall -march=native $srcs -o mcml
diff --git a/main.cpp b/main.cpp
@@ -13,14 +13,14 @@ refrence: Wang, "Biomedical optics", chpater3&6 */
#include <string>
#define GLOBALORIGIN
-#include "Utilities.h"
+#include "utils.h"
#undef GLOABLORIGIN
#include "Photon.h"
////////////////////////////////////////////////
-void main()
+int main(void)
{
////////Input Interface////////////////////
cout<<"*****************************************"<<endl;
diff --git a/utils.cpp b/utils.cpp
@@ -0,0 +1,93 @@
+#include "utils.h"
+
+/***********************************************************
+* A random number generator from Numerical Recipes in C. ****/
+#define MBIG 1000000000
+#define MSEED 161803398
+#define MZ 0
+#define FAC 1.0E-9
+float ran3(int &idum)
+{
+ static int inext,inextp;
+ static long ma[56];
+ static int iff=0;
+ long mj,mk;
+ int i,ii,k;
+ if (idum < 0 || iff == 0)
+ {
+ iff=1;
+ mj=MSEED-(idum < 0 ? -idum : idum);
+ mj %= MBIG;
+ ma[55]=mj;
+ mk=1;
+ for (i=1;i<=54;i++)
+ {
+ ii=(21*i) % 55;
+ ma[ii]=mk;
+ mk=mj-mk;
+ if (mk < MZ) mk += MBIG;
+ mj=ma[ii];
+ }
+ for (k=1;k<=4;k++)
+ for (i=1;i<=55;i++)
+ {
+ ma[i] -= ma[1+(i+30) % 55];
+ if (ma[i] < MZ) ma[i] += MBIG;
+ }
+ inext=0;
+ inextp=31;
+ idum=1;
+ }
+ if (++inext == 56)
+ inext=1;
+ if (++inextp == 56)
+ inextp=1;
+ mj=ma[inext]-ma[inextp];
+ if (mj < MZ) mj += MBIG;
+ ma[inext]=mj;
+ return mj*FAC;
+}
+#undef MBIG
+#undef MSEED
+#undef MZ
+#undef FAC
+
+
+/***********************************************************
+ * Generate a random number between 0 and 1. Take a
+ * number as seed the first time entering the function.
+ * The seed is limited to 1<<15.
+ * Wang et al found that when idum is too large, ran3 may return
+ * numbers beyond 0 and 1.
+ ****/
+//#define STANDARDTEST 0 /* testing program using fixed rnd seed. */
+double RandomNum(void)
+{
+ static bool first_time=1;
+ static int idum; /* seed for ran3. */
+ if(first_time)
+ {
+ #if STANDARDTEST /* Use fixed seed to test the program. */
+ idum = - 1;
+ #else
+ idum = -(int)time(NULL)%(1<<15); /* use 16-bit integer as the seed. */
+ #endif
+ ran3(idum);
+ first_time = 0;
+ idum = 1;
+ }
+ return( (double)ran3(idum) );
+}
+
+/////////////////////////////////////////////
+int min(int d1,int d2)
+{
+ if (d1<d2)
+ {
+ return d1;
+ }
+ else
+ {
+ return d2;
+ }
+}
diff --git a/utils.h b/utils.h
@@ -0,0 +1,141 @@
+/* Providing global variables and functions*/
+#include <math.h>
+#include <new>
+#include <iostream>
+#include <time.h>
+
+//global constants
+#ifndef PI
+ #define PI 3.14159265
+#endif
+
+#ifndef ZERO
+ #define ZERO 1.0e-6 //for small deflection angle
+#endif
+
+#ifndef n0
+ #define n0 1.0 //refractive index of ambient medium
+#endif
+
+#ifndef BIGVAL
+ #define BIGVAL 1e6//big value
+#endif
+
+//global variables
+#ifdef GLOBALORIGIN
+ #define GLOBAL
+#else
+ #define GLOBAL extern
+#endif
+GLOBAL double dx;
+GLOBAL double dy;
+GLOBAL int Nx;
+GLOBAL int Ny;
+GLOBAL double zc;
+GLOBAL double n;
+GLOBAL double mua;
+GLOBAL double mus;
+GLOBAL double mut;
+GLOBAL double g;
+GLOBAL double d;
+
+
+GLOBAL double th_in; // incident angle in degree
+
+GLOBAL double x_offset;
+GLOBAL double y_offset;
+
+//generate random data
+float ran3(int *idum);
+double RandomNum(void);
+
+
+//other auxilliary functions
+int min(int d1, int d2);
+#define SIGN(x) ((x)>=0?1:-1)
+
+
+////////allocte dynamic array/////////////////////////
+using namespace std;
+template <class T>
+T* alloc1D(int dim1, T t)
+{
+ T* p;
+ try
+ {
+ p=new T[dim1];
+ }
+ catch(bad_alloc)
+ {
+ cerr<<"Fail to allocate 1D array!"<<endl;
+ exit(1);
+ }
+ for (int tmp1=0;tmp1<dim1;tmp1++)
+ {
+ p[tmp1]=t;
+ }
+ return p;
+}
+template <class T>
+void dealloc1D(T* p)
+{
+ delete [] p;
+}
+///////////
+template <class T>
+T** alloc2D(int dim1,int dim2,T t)
+{
+ T** p;
+ try
+ {
+ p=new T*[dim1];
+ for (int tmp1=0;tmp1<dim1;tmp1++)
+ {
+ p[tmp1]=alloc1D(dim2,t);
+ }
+ }
+ catch (bad_alloc)
+ {
+ cerr<<"Fail to allocate 2D array!";
+ }
+ return p;
+}
+template <class T>
+void dealloc2D(int dim1,T** p)
+{
+ for (int tmp1=0;tmp1<dim1;tmp1++)
+ {
+ dealloc1D(p[tmp1]);
+ }
+ delete [] p;
+}
+/////////
+template <class T>
+T*** alloc3D(int dim1,int dim2,int dim3,T t)
+{
+ T*** p;
+ try
+ {
+ p=new T**[dim1];
+ for (int tmp1=0;tmp1<dim1;tmp1++)
+ {
+ p[tmp1]=alloc2D(dim2,dim3,t);
+ }
+ }
+ catch (bad_alloc)
+ {
+ cerr<<"Fail to allocate 3D array!";
+ }
+ return p;
+}
+template <class T>
+void dealloc3D(int dim1,int dim2,T*** p)
+{
+ for (int tmp1=0;tmp1<dim1;tmp1++)
+ {
+ dealloc2D(dim2,p[tmp1]);
+ }
+ delete [] p;
+}
+////////////////////////////////////////////////
+