trisurf-ng.git - Gitblit

It works, png is output. The only problem is that some triangles are missing

Samo Penic

2014-06-13 a61c001cd35ff70a314ef417c4beda9c7e68d3ad

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88f451	1	#include<math.h>
SP	2	#include<stdlib.h>
	3	#include "general.h"
	4	#include "sh.h"
	5
074a17	6
SP	7
	8	ts_spharm sph_init(ts_vertex_list vlist, ts_uint l){
eb8605	9	ts_uint j,i;
074a17	10	ts_spharm sph=(ts_spharm )malloc(sizeof(ts_spharm));
SP	11
262607	12	sph->N=0;
eb8605	13	/* lets initialize Ylm for each vertex. */
SP	14	sph->Ylmi=(ts_double *)calloc(l,sizeof(ts_double ));
5bb11d	15	for(i=0;i<l;i++){
SP	16	sph->Ylmi[i]=(ts_double *)calloc(2i+1,sizeof(ts_double *));
	17	for(j=0;j<(2*i+1);j++){
eb8605	18	sph->Ylmi[i][j]=(ts_double *)calloc(vlist->n,sizeof(ts_double));
074a17	19	}
SP	20	}
	21
	22	/* lets initialize ulm */
	23	sph->ulm=(ts_double *)calloc(l,sizeof(ts_double ));
	24	for(j=0;j<l;j++){
	25	sph->ulm[j]=(ts_double )calloc(2j+1,sizeof(ts_double));
	26	}
	27
262607	28	/* lets initialize sum of Ulm2 */
SP	29	sph->sumUlm2=(ts_double *)calloc(l,sizeof(ts_double ));
	30	for(j=0;j<l;j++){
	31	sph->sumUlm2[j]=(ts_double )calloc(2j+1,sizeof(ts_double));
	32	}
074a17	33
SP	34	/* lets initialize co */
79fc9c	35	//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 2j+2 instead of 2j+2. elements starting with 0 are useles and should be ignored!
SP	36	sph->co=(ts_double *)calloc(l+1,sizeof(ts_double ));
	37	for(j=0;j<=l;j++){
	38	sph->co[j]=(ts_double )calloc(2j+2,sizeof(ts_double));
074a17	39	}
SP	40
5bb11d	41	sph->l=l;
SP	42
	43	/* Calculate coefficients that will remain constant during all the simulation */
	44	precomputeShCoeff(sph);
	45
074a17	46	return sph;
SP	47	}
	48
	49
eb8605	50	ts_bool sph_free(ts_spharm *sph){
SP	51	int i,j;
632960	52	if(sph==NULL) return TS_FAIL;
074a17	53	for(i=0;i<sph->l;i++){
SP	54	if(sph->ulm[i]!=NULL) free(sph->ulm[i]);
262607	55	if(sph->sumUlm2[i]!=NULL) free(sph->sumUlm2[i]);
074a17	56	if(sph->co[i]!=NULL) free(sph->co[i]);
SP	57	}
79fc9c	58	if(sph->co[sph->l]!=NULL) free(sph->co[sph->l]);
074a17	59	if(sph->co != NULL) free(sph->co);
SP	60	if(sph->ulm !=NULL) free(sph->ulm);
	61
eb8605	62	if(sph->Ylmi!=NULL) {
074a17	63	for(i=0;i<sph->l;i++){
eb8605	64	if(sph->Ylmi[i]!=NULL){
5bb11d	65	for(j=0;j<i*2+1;j++){
eb8605	66	if(sph->Ylmi[i][j]!=NULL) free (sph->Ylmi[i][j]);
SP	67	}
	68	free(sph->Ylmi[i]);
	69	}
074a17	70	}
eb8605	71	free(sph->Ylmi);
074a17	72	}
eb8605	73
074a17	74	free(sph);
SP	75	return TS_SUCCESS;
	76	}
	77
88f451	78	/* Gives you legendre polynomials. Taken from NR, p. 254 */
3b3902	79	ts_double plgndr(ts_int l, ts_int m, ts_double x){
88f451	80	ts_double fact, pll, pmm, pmmp1, somx2;
SP	81	ts_int i,ll;
	82
	83	#ifdef TS_DOUBLE_DOUBLE
	84	if(m<0 \|\| m>l \|\| fabs(x)>1.0)
	85	fatal("Bad arguments in routine plgndr",1);
	86	#endif
	87	#ifdef TS_DOUBLE_FLOAT
	88	if(m<0 \|\| m>l \|\| fabsf(x)>1.0)
	89	fatal("Bad arguments in routine plgndr",1);
	90	#endif
	91	#ifdef TS_DOUBLE_LONGDOUBLE
	92	if(m<0 \|\| m>l \|\| fabsl(x)>1.0)
	93	fatal("Bad arguments in routine plgndr",1);
	94	#endif
	95	pmm=1.0;
	96	if (m>0) {
	97	#ifdef TS_DOUBLE_DOUBLE
	98	somx2=sqrt((1.0-x)*(1.0+x));
	99	#endif
	100	#ifdef TS_DOUBLE_FLOAT
	101	somx2=sqrtf((1.0-x)*(1.0+x));
	102	#endif
	103	#ifdef TS_DOUBLE_LONGDOUBLE
	104	somx2=sqrtl((1.0-x)*(1.0+x));
	105	#endif
	106	fact=1.0;
	107	for (i=1; i<=m;i++){
	108	pmm = -factsomx2;
	109	fact +=2.0;
	110	}
	111	}
	112
	113	if (l == m) return pmm;
	114	else {
	115	pmmp1=x(2m+1)*pmm;
	116	if(l==(m+1)) return(pmmp1);
	117	else {
	118	pll=0; /* so it can not be uninitialized */
	119	for(ll=m+2;ll<=l;ll++){
	120	pll=(x(2ll-1)pmmp1-(ll+m-1)pmm)/(ll-m);
	121	pmm=pmmp1;
	122	pmmp1=pll;
	123	}
	124	return(pll);
	125	}
	126	}
	127	}
	128
	129
9bf6ee	130	/** @brief: Precomputes coefficients that are required for spherical harmonics computations.
523bf1	131
9bf6ee	132	*/
523bf1	133	ts_bool precomputeShCoeff(ts_spharm *sph){
074a17	134	ts_int i,j,al,am;
SP	135	ts_double **co=sph->co;
79fc9c	136	for(i=1;i<=sph->l;i++){
SP	137	al=i;
074a17	138	sph->co[i][i+1]=sqrt((2.0*al+1.0)/2.0/M_PI);
79fc9c	139	for(j=1;j<=i-1;j++){
SP	140	am=j;
008026	141	sph->co[i][i+1+j]=co[i][i+j]*sqrt(1.0/(al-am+1.0)/(al+am));
074a17	142	sph->co[i][i+1-j]=co[i][i+1+j];
523bf1	143	}
79fc9c	144	co[i][2i+1]=co[i][2i]sqrt(1.0/(2.0al));
SP	145	co[i][1]=co[i][2*i+1];
074a17	146	co[i][i+1]=sqrt((2.0*al+1.0)/4.0/M_PI);
523bf1	147	}
SP	148	return TS_SUCCESS;
	149
	150	}
	151
	152
c9d07c	153	/** @brief: Computes Y(l,m,theta,fi)
SP	154	*
	155	* Function calculates Y^l_m for vertex with given (\theta, \fi) coordinates in
	156	* spherical coordinate system.
	157	* @param l is an ts_int argument.
	158	* @param m is an ts_int argument.
	159	* @param theta is ts_double argument.
	160	* @param fi is a ts_double argument.
	161	*
	162	* (Miha's definition that is different from common definition for factor srqt(1/(2pi)) /
88f451	163	ts_double shY(ts_int l,ts_int m,ts_double theta,ts_double fi){
SP	164	ts_double fac1, fac2, K;
	165	int i;
	166
	167	if(l<0 \|\| m>l \|\| m<-l)
	168	fatal("Error using shY function!",1);
	169
	170	fac1=1.0;
af3bad	171	for(i=1; i<=l-abs(m);i++){
88f451	172	fac1 *= i;
SP	173	}
	174	fac2=1.0;
af3bad	175	for(i=1; i<=l+abs(m);i++){
88f451	176	fac2 *= i;
SP	177	}
	178
	179	if(m==0){
	180	K=sqrt(1.0/(2.0*M_PI));
	181	}
	182	else if (m>0) {
	183	K=sqrt(1.0/(M_PI))cos(mfi);
	184	}
	185	else {
	186	//K=pow(-1.0,abs(m))sqrt(1.0/(2.0M_PI))cos(mfi);
	187	if(abs(m)%2==0)
af3bad	188	K=sqrt(1.0/(M_PI))cos(mfi);
88f451	189	else
af3bad	190	K=-sqrt(1.0/(M_PI))cos(mfi);
88f451	191	}
SP	192
632960	193	return Ksqrt((2.0l+1.0)/2.0(ts_double)(fac1/fac2))plgndr(l,abs(m),cos(theta));
88f451	194	}
523bf1	195
SP	196
	197	/* Function transforms coordinates from cartesian to spherical coordinates
	198	* (r,phi, theta). */
	199	ts_bool cart2sph(ts_coord coord, ts_double x, ts_double y, ts_double z){
	200	coord->coord_type=TS_COORD_SPHERICAL;
	201	#ifdef TS_DOUBLE_DOUBLE
	202	coord->e1=sqrt(xx+yy+z*z);
	203	if(z==0) coord->e3=M_PI/2.0;
e9c87e	204	else coord->e3=atan2(sqrt(xx+yy),z);
523bf1	205	coord->e2=atan2(y,x);
SP	206	#endif
	207	#ifdef TS_DOUBLE_FLOAT
	208	coord->e1=sqrtf(xx+yy+z*z);
	209	if(z==0) coord->e3=M_PI/2.0;
	210	else coord->e3=atanf(sqrtf(xx+yy)/z);
	211	coord->e2=atan2f(y,x);
	212	#endif
	213	#ifdef TS_DOUBLE_LONGDOUBLE
	214	coord->e1=sqrtl(xx+yy+z*z);
	215	if(z==0) coord->e3=M_PI/2.0;
	216	else coord->e3=atanl(sqrtl(xx+yy)/z);
	217	coord->e2=atan2l(y,x);
	218	#endif
	219
	220	return TS_SUCCESS;
	221	}
	222
e9c87e	223
SP	224	ts_bool sph2cart(ts_coord *coord){
	225	coord->coord_type=TS_COORD_CARTESIAN;
	226	ts_double x,y,z;
	227
	228	x=coord->e1cos(coord->e2)sin(coord->e3);
	229	y=coord->e1sin(coord->e2)sin(coord->e3);
	230	z=coord->e1*cos(coord->e3);
	231
	232	coord->e1=x;
	233	coord->e2=y;
	234	coord->e3=z;
	235
	236	return TS_SUCCESS;
	237	}
	238
	239
523bf1	240	/* Function returns radius of the sphere with the same volume as vesicle (r0) */
SP	241	ts_double getR0(ts_vesicle *vesicle){
	242	ts_double r0;
	243	#ifdef TS_DOUBLE_DOUBLE
	244	r0=pow(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	245	#endif
	246	#ifdef TS_DOUBLE_FLOAT
	247	r0=powf(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	248	#endif
	249	#ifdef TS_DOUBLE_LONGDOUBLE
	250	r0=powl(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	251	#endif
	252	return r0;
	253	}
	254
	255
	256	ts_bool preparationSh(ts_vesicle *vesicle, ts_double r0){
	257	//TODO: before calling or during the call calculate area of each triangle! Can
	258	//be also done after vertexmove and bondflip //
919555	259	//DONE: in energy calculation! //
523bf1	260	ts_uint i,j;
SP	261	ts_vertex **vtx=vesicle->vlist->vtx;
	262	ts_vertex *cvtx;
	263	ts_triangle *ctri;
	264	ts_double centroid[3];
	265	ts_double r;
	266	for (i=0; i<vesicle->vlist->n; i++){
	267	cvtx=vtx[i];
	268	//cvtx->projArea=4.0M_PI/1447.0(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z)/r0/r0;
	269	cvtx->projArea=0.0;
	270
	271	/* go over all triangles that have a common vertex i */
	272	for(j=0; j<cvtx->tristar_no; j++){
	273	ctri=cvtx->tristar[j];
	274	centroid[0]=(ctri->vertex[0]->x + ctri->vertex[1]->x + ctri->vertex[2]->x)/3.0;
	275	centroid[1]=(ctri->vertex[0]->y + ctri->vertex[1]->y + ctri->vertex[2]->y)/3.0;
	276	centroid[2]=(ctri->vertex[0]->z + ctri->vertex[1]->z + ctri->vertex[2]->z)/3.0;
	277	/* calculating projArea+= area(triangle)cos(theta) /
	278	#ifdef TS_DOUBLE_DOUBLE
	279	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrt(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	280	#endif
	281	#ifdef TS_DOUBLE_FLOAT
	282	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrtf(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	283	#endif
	284	#ifdef TS_DOUBLE_LONGDOUBLE
	285	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrtl(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	286	#endif
	287	}
	288
	289	cvtx->projArea=cvtx->projArea/3.0;
	290	//we dont store spherical coordinates of vertex, so we have to calculate
	291	//r(i) at this point.
	292	#ifdef TS_DOUBLE_DOUBLE
	293	r=sqrt(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	294	#endif
	295	#ifdef TS_DOUBLE_FLOAT
	296	r=sqrtf(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	297	#endif
	298	#ifdef TS_DOUBLE_LONGDOUBLE
	299	r=sqrtl(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	300	#endif
	301	cvtx->relR=(r-r0)/r0;
3b3902	302	cvtx->solAngle=cvtx->projArea/r/r;
523bf1	303	}
SP	304	return TS_SUCCESS;
	305	}
	306
	307
	308
	309	ts_bool calculateYlmi(ts_vesicle *vesicle){
3b3902	310	ts_int i,j,k;
523bf1	311	ts_spharm *sph=vesicle->sphHarmonics;
SP	312	ts_coord coord=(ts_coord )malloc(sizeof(ts_coord));
	313	ts_double fi, theta;
79048f	314	ts_int m;
074a17	315	ts_vertex *cvtx;
523bf1	316	for(k=0;k<vesicle->vlist->n;k++){
074a17	317	cvtx=vesicle->vlist->vtx[k];
eb8605	318	sph->Ylmi[0][0][k]=sqrt(1.0/4.0/M_PI);
074a17	319	cart2sph(coord,cvtx->x, cvtx->y, cvtx->z);
523bf1	320	fi=coord->e2;
SP	321	theta=coord->e3;
79048f	322	for(i=1; i<sph->l; i++){
523bf1	323	for(j=0;j<i;j++){
79048f	324	m=j+1;
3b3902	325	//Nastudiraj!!!!!
79048f	326	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));
3b3902	327	if(i==2 && j==0){
SP	328	/* fprintf(stderr," ** vtx %d **\n", k+1);
	329	fprintf(stderr,"m-i-1 =%d\n",m-i-1);
	330	fprintf(stderr,"fi =%e\n",fi);
	331	fprintf(stderr,"(m-i-1)fi =%e\n",((ts_double)(m-i-1))fi);
	332	fprintf(stderr,"-2fi =%e\n",-2fi);
	333	fprintf(stderr,"m =%d\n",m);
	334
	335	fprintf(stderr," cos(m-i-1)=%e\n",cos((m-i-1)*fi));
	336	fprintf(stderr," cos(-2fi)=%e\n",cos(-2fi));
	337	fprintf(stderr," sph->co[i][m]=%e\n",sph->co[i][m]);
	338	fprintf(stderr," plgndr(i,abs(m-i-1),cos(theta))=%e\n",plgndr(i,abs(m-i-1),cos(theta)));
	339	*/
	340	}
523bf1	341	}
3b3902	342	//Nastudiraj!!!!!
SP	343	j=i;
	344	m=j+1;
	345	sph->Ylmi[i][j][k]=sph->co[i][m]*plgndr(i,0,cos(theta));
	346	for(j=i+1;j<2*i+1;j++){
79048f	347	m=j+1;
3b3902	348	//Nastudiraj!!!!!
79048f	349	sph->Ylmi[i][j][k]=sph->co[i][m]sin((m-i-1)fi)*plgndr(i,m-i-1,cos(theta));
523bf1	350	}
SP	351	}
	352
	353	}
	354	free(coord);
	355	return TS_SUCCESS;
	356	}
	357
	358
	359
	360	ts_bool calculateUlm(ts_vesicle *vesicle){
	361	ts_uint i,j,k;
	362	ts_vertex *cvtx;
	363	for(i=0;i<vesicle->sphHarmonics->l;i++){
8e58b4	364	for(j=0;j<2*i+1;j++) vesicle->sphHarmonics->ulm[i][j]=0.0;
523bf1	365	}
SP	366
	367	//TODO: call calculateYlmi !!!
	368
	369
	370	for(k=0;k<vesicle->vlist->n; k++){
	371	cvtx=vesicle->vlist->vtx[k];
	372	for(i=0;i<vesicle->sphHarmonics->l;i++){
3b3902	373	for(j=0;j<2*i+1;j++){
eb8605	374	vesicle->sphHarmonics->ulm[i][j]+= cvtx->solAnglecvtx->relRvesicle->sphHarmonics->Ylmi[i][j][k];
523bf1	375	}
SP	376
	377	}
	378	}
	379
	380	return TS_SUCCESS;
	381	}
262607	382
SP	383
	384
	385
	386
	387	ts_bool storeUlm2(ts_vesicle *vesicle){
	388
	389	ts_spharm *sph=vesicle->sphHarmonics;
	390	ts_int i,j;
	391	for(i=0;i<sph->l;i++){
	392	for(j=0;j<2*i+1;j++){
8e58b4	393	/* DEBUG fprintf(stderr,"sph->sumUlm2[%d][%d]=%e\n",i,j,sph->ulm[i][j]* sph->ulm[i][j]); */
443ba1	394	sph->sumUlm2[i][j]+=sph->ulm[i][j]* sph->ulm[i][j];
262607	395	}
SP	396	}
	397	sph->N++;
	398	return TS_SUCCESS;
	399	}
dc77e8	400
SP	401
	402	ts_bool saveAvgUlm2(ts_vesicle *vesicle){
	403
	404	FILE *fh;
	405
	406	fh=fopen("sph2out.dat", "w");
	407	if(fh==NULL){
	408	err("Cannot open file %s for writing");
	409	return TS_FAIL;
	410	}
	411
	412	ts_spharm *sph=vesicle->sphHarmonics;
	413	ts_int i,j;
	414	fprintf(fh,"l,\tm,\tulm^2avg\n");
	415	for(i=0;i<sph->l;i++){
	416	for(j=0;j<2*i+1;j++){
	417	fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2[i][j]/(ts_double)sph->N);
	418
	419	}
	420	fprintf(fh,"\n");
	421	}
	422	fclose(fh);
	423	return TS_SUCCESS;
	424	}