From aafd67f2d592799167864698ea07eb8aadcc86a7 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 25 May 2016 18:37:21 +0000
Subject: [PATCH] Merge branch 'master' of bitbucket.org:samop/trisurf-ng with work done on removing the memory leaks.

---
 src/sh.c |  113 +++++++++++++++++++++++++++++++++++++++++++++++++++-----
 1 files changed, 102 insertions(+), 11 deletions(-)

diff --git a/src/sh.c b/src/sh.c
index cc4d148..3f64939 100644
--- a/src/sh.c
+++ b/src/sh.c
@@ -1,15 +1,17 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
 #include<math.h>
 #include<stdlib.h>
 #include "general.h"
 #include "sh.h"
-
+#include "io.h"
+#include <string.h>
 
 
 ts_spharm *sph_init(ts_vertex_list *vlist, ts_uint l){
     ts_uint j,i;
     ts_spharm *sph=(ts_spharm *)malloc(sizeof(ts_spharm));
 
-    
+    sph->N=0;
     /* lets initialize Ylm for each vertex. */
     sph->Ylmi=(ts_double ***)calloc(l,sizeof(ts_double **));
     for(i=0;i<l;i++){
@@ -25,6 +27,11 @@
         sph->ulm[j]=(ts_double *)calloc(2*j+1,sizeof(ts_double));
     }
 
+    /* lets initialize sum of Ulm2 */
+    sph->sumUlm2=(ts_double **)calloc(l,sizeof(ts_double *));
+    for(j=0;j<l;j++){
+        sph->sumUlm2[j]=(ts_double *)calloc(2*j+1,sizeof(ts_double));
+    }
 
     /* lets initialize co */
 //NOTE: C is has zero based indexing. Code is imported from fortran and to comply with original indexes we actually generate one index more. Also second dimension is 2*j+2 instead of 2*j+2. elements starting with 0 are useles and should be ignored!
@@ -44,8 +51,10 @@
 
 ts_bool sph_free(ts_spharm *sph){
     int i,j;
+    if(sph==NULL) return TS_FAIL;
     for(i=0;i<sph->l;i++){
         if(sph->ulm[i]!=NULL) free(sph->ulm[i]);
+        if(sph->sumUlm2[i]!=NULL) free(sph->sumUlm2[i]);
         if(sph->co[i]!=NULL) free(sph->co[i]);
     }
         if(sph->co[sph->l]!=NULL) free(sph->co[sph->l]);
@@ -69,7 +78,7 @@
 }
 
 /* Gives you legendre polynomials. Taken from NR, p. 254 */
-ts_double plgndr(ts_int l, ts_int m, ts_float x){
+ts_double plgndr(ts_int l, ts_int m, ts_double x){
 	ts_double fact, pll, pmm, pmmp1, somx2;
 	ts_int i,ll;
 
@@ -183,7 +192,7 @@
 		K=-sqrt(1.0/(M_PI))*cos(m*fi);
 	}
 	
-	return K*sqrt((2.0*l+1.0)/2.0*fac1/fac2)*plgndr(l,abs(m),cos(theta));	
+	return K*sqrt((2.0*l+1.0)/2.0*(ts_double)(fac1/fac2))*plgndr(l,abs(m),cos(theta));	
 }
 
 
@@ -194,7 +203,7 @@
 #ifdef TS_DOUBLE_DOUBLE
     coord->e1=sqrt(x*x+y*y+z*z);
     if(z==0) coord->e3=M_PI/2.0;
-    else coord->e3=atan(sqrt(x*x+y*y)/z);
+    else coord->e3=atan2(sqrt(x*x+y*y),z);
     coord->e2=atan2(y,x);
 #endif
 #ifdef TS_DOUBLE_FLOAT
@@ -212,6 +221,23 @@
 
     return TS_SUCCESS;
 }
+
+
+ts_bool sph2cart(ts_coord *coord){
+    coord->coord_type=TS_COORD_CARTESIAN;
+    ts_double x,y,z;
+
+    x=coord->e1*cos(coord->e2)*sin(coord->e3);
+    y=coord->e1*sin(coord->e2)*sin(coord->e3);
+    z=coord->e1*cos(coord->e3);
+
+    coord->e1=x;
+    coord->e2=y;
+    coord->e3=z;
+
+    return TS_SUCCESS;
+}
+
 
 /* Function returns radius of the sphere with the same volume as vesicle (r0) */
 ts_double getR0(ts_vesicle *vesicle){
@@ -232,6 +258,7 @@
 ts_bool preparationSh(ts_vesicle *vesicle, ts_double r0){
 //TODO: before calling or during the call calculate area of each triangle! Can
 //be also done after vertexmove and bondflip //
+//DONE: in energy calculation! //
     ts_uint i,j;
     ts_vertex **vtx=vesicle->vlist->vtx;
     ts_vertex *cvtx;
@@ -274,7 +301,7 @@
     r=sqrtl(cvtx->x*cvtx->x+cvtx->y*cvtx->y+cvtx->z*cvtx->z);
 #endif
     cvtx->relR=(r-r0)/r0;
-    cvtx->solAngle=cvtx->projArea/cvtx->relR * cvtx->projArea/cvtx->relR;
+    cvtx->solAngle=cvtx->projArea/r/r;
     }
     return TS_SUCCESS;
 }
@@ -282,7 +309,7 @@
 
 
 ts_bool calculateYlmi(ts_vesicle *vesicle){
-    ts_uint i,j,k;
+    ts_int i,j,k;
     ts_spharm *sph=vesicle->sphHarmonics;
     ts_coord *coord=(ts_coord *)malloc(sizeof(ts_coord));
     ts_double fi, theta;
@@ -297,11 +324,30 @@
         for(i=1; i<sph->l; i++){
             for(j=0;j<i;j++){
 			m=j+1;
+//Nastudiraj!!!!!
                 sph->Ylmi[i][j][k]=sph->co[i][m]*cos((m-i-1)*fi)*pow(-1,m-i-1)*plgndr(i,abs(m-i-1),cos(theta));
+		if(i==2 && j==0){
+	/*	fprintf(stderr," **** vtx %d ****\n", k+1);
+		fprintf(stderr,"m-i-1 =%d\n",m-i-1);
+		fprintf(stderr,"fi =%e\n",fi);
+		fprintf(stderr,"(m-i-1)*fi =%e\n",((ts_double)(m-i-1))*fi);
+		fprintf(stderr,"-2*fi =%e\n",-2*fi);
+		fprintf(stderr,"m =%d\n",m);
+	
+		fprintf(stderr," cos(m-i-1)=%e\n",cos((m-i-1)*fi));
+		fprintf(stderr," cos(-2*fi)=%e\n",cos(-2*fi));
+		fprintf(stderr," sph->co[i][m]=%e\n",sph->co[i][m]);
+		fprintf(stderr," plgndr(i,abs(m-i-1),cos(theta))=%e\n",plgndr(i,abs(m-i-1),cos(theta)));
+*/
+		}
             }
-                sph->Ylmi[i][j+1][k]=sph->co[i][m+1]*plgndr(i,0,cos(theta));
-            for(j=i+1;j<2*i;j++){
+//Nastudiraj!!!!!
+		j=i;
+		m=j+1;
+                sph->Ylmi[i][j][k]=sph->co[i][m]*plgndr(i,0,cos(theta));
+            for(j=i+1;j<2*i+1;j++){
 			m=j+1;
+//Nastudiraj!!!!!
                 sph->Ylmi[i][j][k]=sph->co[i][m]*sin((m-i-1)*fi)*plgndr(i,m-i-1,cos(theta));
             }
         }
@@ -317,7 +363,7 @@
     ts_uint i,j,k;
     ts_vertex *cvtx;
     for(i=0;i<vesicle->sphHarmonics->l;i++){
-        for(j=0;j<2*i;j++) vesicle->sphHarmonics->ulm[i][j]=0.0;
+        for(j=0;j<2*i+1;j++) vesicle->sphHarmonics->ulm[i][j]=0.0;
     }
 
 //TODO: call calculateYlmi !!!
@@ -326,7 +372,7 @@
     for(k=0;k<vesicle->vlist->n; k++){
         cvtx=vesicle->vlist->vtx[k];
         for(i=0;i<vesicle->sphHarmonics->l;i++){
-            for(j=0;j<2*i;j++){
+            for(j=0;j<2*i+1;j++){
                 vesicle->sphHarmonics->ulm[i][j]+= cvtx->solAngle*cvtx->relR*vesicle->sphHarmonics->Ylmi[i][j][k];
             }
 
@@ -335,3 +381,48 @@
 
     return TS_SUCCESS;
 }
+
+
+
+
+
+ts_bool storeUlm2(ts_vesicle *vesicle){
+
+ts_spharm *sph=vesicle->sphHarmonics;
+ts_int i,j;
+for(i=0;i<sph->l;i++){
+    for(j=0;j<2*i+1;j++){
+	/* DEBUG fprintf(stderr,"sph->sumUlm2[%d][%d]=%e\n",i,j,sph->ulm[i][j]* sph->ulm[i][j]); */
+        sph->sumUlm2[i][j]+=sph->ulm[i][j]* sph->ulm[i][j];
+    }
+}
+	sph->N++;
+return TS_SUCCESS;
+}
+
+
+ts_bool saveAvgUlm2(ts_vesicle *vesicle){
+
+	FILE *fh;
+    char filename[10000];
+    strcpy(filename, command_line_args.path);
+    strcat(filename, "sph2out.dat");
+	fh=fopen(filename, "w");
+	if(fh==NULL){
+		err("Cannot open file %s for writing");
+		return TS_FAIL;
+	}
+
+	ts_spharm *sph=vesicle->sphHarmonics;
+	ts_int i,j;
+	fprintf(fh,"l,\tm,\tulm^2avg\n");
+	for(i=0;i<sph->l;i++){
+    		for(j=0;j<2*i+1;j++){
+		fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2[i][j]/(ts_double)sph->N);
+
+    		}
+    fprintf(fh,"\n");
+	}
+	fclose(fh);
+	return TS_SUCCESS;
+}

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