trisurf-ng.git - Gitblit

Samo Penic

2012-06-07 008026f5162bf79e75565548c1bbe5ca3a8fc248

commit \| author \| age
f74313	1	#include "general.h"
d7639a	2	#include<stdio.h>
SP	3	#include "io.h"
f74313	4	#include <confuse.h>
SP	5	#include "vertex.h"
	6	#include "bond.h"
d7639a	7	#include<string.h>
a6b1b5	8	#include<stdlib.h>
d7639a	9	#include <sys/types.h>
SP	10	#include <dirent.h>
	11
	12
	13	ts_bool print_vertex_list(ts_vertex_list *vlist){
	14	ts_uint i;
	15	printf("Number of vertices: %u\n",vlist->n);
	16	for(i=0;i<vlist->n;i++){
a6b1b5	17	printf("%u: %f %f %f\n",
8f6a69	18	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	19	}
SP	20	return TS_SUCCESS;
	21	}
	22
	23	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	24	ts_uint i,j;
a6b1b5	25	ts_vertex **vtx=vlist->vtx;
d7639a	26	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	27	for(i=0;i<vlist->n;i++){
8f6a69	28	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	29	for(j=0;j<vtx[i]->neigh_no;j++){
	30	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	31	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	32	}
SP	33	printf("\n");
	34	}
	35
	36	return TS_SUCCESS;
	37	}
	38
	39	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	40	ts_vertex **vtx=vlist->vtx;
d7639a	41	ts_uint i;
SP	42	FILE *fh;
	43
	44	fh=fopen(filename, "w");
	45	if(fh==NULL){
	46	err("Cannot open file %s for writing");
	47	return TS_FAIL;
	48	}
	49	for(i=0;i<vlist->n;i++)
8f6a69	50	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	51
SP	52	fclose(fh);
	53	return TS_SUCCESS;
	54	}
	55
	56
	57	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	58	ts_uint i,j;
	59	for(i=0;i<vlist->n;i++){
8f6a69	60	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	61	vlist->vtx[i]->y, vlist->vtx[i]->z,
	62	vlist->vtx[i]->neigh_no);
	63	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	64	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	65	//-vlist->vtx+1));
d7639a	66	}
SP	67	fprintf(fh,"\n");
	68	}
	69	return TS_SUCCESS;
	70	}
	71
	72	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	73	ts_uint i,j;
a6b1b5	74	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	75	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	76	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	77	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	78	}
SP	79	fprintf(fh,"\n");
	80	}
	81	return TS_SUCCESS;
	82	}
	83
	84	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	85	ts_triangle_list *tlist=vesicle->tlist;
d7639a	86	ts_uint i,j;
SP	87	for(i=0;i<tlist->n;i++){
41a035	88	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	89	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	90	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	91	}
SP	92	fprintf(fh,"\n");
	93	for(j=0;j<3;j++){
41a035	94	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	95	}
SP	96	fprintf(fh,"\n");
41a035	97	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	98	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	99	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	100	}
	101	return TS_SUCCESS;
	102	}
	103
	104	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	105	ts_uint i,j;
	106	for(i=0;i<vlist->n;i++){
	107	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	108	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	109	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
	110	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	111	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	112	}
SP	113	fprintf(fh,"\n");
8f6a69	114	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
SP	115	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	116	}
SP	117	fprintf(fh,"\n");
	118	}
	119	return TS_SUCCESS;
	120	}
	121
	122	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	123	ts_uint i;
a6b1b5	124	for(i=0;i<vesicle->blist->n;i++){
e016c4	125	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	126	//-vesicle->vlist->vtx+1),
e016c4	127	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	128	//-vesicle->vlist.vtx+1));
d7639a	129	}
SP	130	return TS_SUCCESS;
	131	}
	132
	133
	134	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	135	FILE *fh;
	136	fh=fopen(filename, "w");
	137	if(fh==NULL){
	138	err("Cannot open file %s for writing");
	139	return TS_FAIL;
	140	}
	141	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	142	fprint_vertex_list(fh,vesicle->vlist);
d7639a	143	fprint_tristar(fh,vesicle);
SP	144	fprint_triangle_list(fh,vesicle);
a6b1b5	145	fprint_vertex_data(fh,vesicle->vlist);
d7639a	146	fprint_bonds(fh,vesicle);
SP	147	fclose(fh);
	148	return TS_SUCCESS;
	149	}
	150
	151	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	152	FILE *fh;
	153	char line[255];
	154	fh=fopen(filename, "r");
	155	if(fh==NULL){
	156	err("Cannot open file for reading... Nonexistant file?");
	157	return TS_FAIL;
	158	}
a6b1b5	159	ts_uint retval=1;
d7639a	160	while(retval!=EOF){
SP	161	retval=fscanf(fh,"%s",line);
	162
	163	fprintf(stderr,"%s",line);
	164	}
	165	fclose(fh);
	166	return TS_SUCCESS;
	167	}
	168
	169	ts_bool write_master_xml_file(ts_char *filename){
	170	FILE *fh;
	171	ts_char i,j;
	172	ts_uint tstep;
	173	ts_char *number;
	174	fh=fopen(filename, "w");
	175	if(fh==NULL){
	176	err("Cannot open file %s for writing");
	177	return TS_FAIL;
	178	}
	179
	180	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	181	DIR *dir = opendir(".");
	182	if(dir){
	183	struct dirent *ent;
	184	tstep=0;
	185	while((ent = readdir(dir)) != NULL)
	186	{
	187	i=rindex(ent->d_name,'.');
	188	if(i==NULL) continue;
	189	if(strcmp(i+1,"vtu")==0){
	190	j=rindex(ent->d_name,'_');
	191	if(j==NULL) continue;
	192	number=strndup(j+1,j-i);
a6b1b5	193	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	194	tstep++;
SP	195	free(number);
	196	}
	197	}
	198	}
f74313	199	free(dir);
d7639a	200	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	201	fclose(fh);
	202	return TS_SUCCESS;
	203	}
	204
	205	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	206	ts_vertex_list *vlist=vesicle->vlist;
SP	207	ts_bond_list *blist=vesicle->blist;
	208	ts_vertex **vtx=vlist->vtx;
	209	ts_uint i;
d7639a	210	char filename[255];
SP	211	FILE *fh;
	212
	213	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	214	fh=fopen(filename, "w");
	215	if(fh==NULL){
	216	err("Cannot open file %s for writing");
	217	return TS_FAIL;
	218	}
	219	/* Here comes header of the file */
	220	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
	221	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
	222	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
	223	for(i=0;i<vlist->n;i++){
a6b1b5	224	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	225	}
SP	226
	227	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	228	for(i=0;i<vlist->n;i++){
8f6a69	229	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	230	}
SP	231
	232	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	233	for(i=0;i<blist->n;i++){
e016c4	234	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	235	}
SP	236	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
	237	for (i=2;i<blist->n*2+1;i+=2){
	238	fprintf(fh,"%u ",i);
	239	}
	240	fprintf(fh,"\n");
	241	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
	242	for (i=0;i<blist->n;i++){
	243	fprintf(fh,"3 ");
	244	}
	245
	246	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	247	fclose(fh);
	248	return TS_SUCCESS;
	249
	250	}
	251
	252	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	253	ts_vertex_list *vlist=vesicle->vlist;
SP	254	ts_bond_list *blist=vesicle->blist;
	255	ts_vertex **vtx=vlist->vtx;
	256	ts_uint i;
d7639a	257	FILE *fh;
SP	258
	259	fh=fopen(filename, "w");
	260	if(fh==NULL){
	261	err("Cannot open file %s for writing");
	262	return TS_FAIL;
	263	}
	264	/* Here comes header of the file */
	265	// fprintf(stderr,"NSHELL=%u\n",nshell);
	266	fprintf(fh, "# vtk DataFile Version 2.0\n");
	267	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	268	fprintf(fh, "%s\n", text);
	269	fprintf(fh,"ASCII\n");
	270	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	271	fprintf(fh,"POINTS %u double\n", vlist->n);
	272	for(i=0;i<vlist->n;i++){
8f6a69	273	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	274	}
SP	275
	276	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	277	for(i=0;i<blist->n;i++){
e016c4	278	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	279	}
SP	280	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	281	for(i=0;i<blist->n;i++)
	282	fprintf(fh,"3\n");
	283
	284	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	285	fprintf(fh,"SCALARS scalars long 1\n");
	286	fprintf(fh,"LOOKUP_TABLE default\n");
	287
	288	for(i=0;i<vlist->n;i++)
8f6a69	289	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	290
SP	291	fclose(fh);
	292	return TS_SUCCESS;
	293	}
	294
	295
	296
	297	ts_bool parsetape(ts_vesicle vesicle,ts_uint iterations){
	298	long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
314f2d	299	char buf[255];
SP	300	long int brezveze=1;
d7639a	301	ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
SP	302	*iterations=1000;
	303	cfg_opt_t opts[] = {
	304	CFG_SIMPLE_INT("nshell", &nshell),
	305	CFG_SIMPLE_FLOAT("dmax", &dmax),
	306	CFG_SIMPLE_FLOAT("xk0",&xk0),
	307	CFG_SIMPLE_FLOAT("stepsize",&stepsize),
	308	CFG_SIMPLE_INT("nxmax", &ncxmax),
	309	CFG_SIMPLE_INT("nymax", &ncymax),
	310	CFG_SIMPLE_INT("nzmax", &nczmax),
	311	CFG_SIMPLE_INT("iterations",iterations),
	312	CFG_SIMPLE_BOOL("quiet",&quiet),
314f2d	313	CFG_SIMPLE_STR("multiprocessing",buf),
SP	314	CFG_SIMPLE_INT("smp_cores",&brezveze),
	315	CFG_SIMPLE_INT("cluster_nodes",&brezveze),
	316	CFG_SIMPLE_INT("distributed_processes",&brezveze),
d7639a	317	CFG_END()
SP	318	};
	319	cfg_t *cfg;
	320	ts_uint retval;
	321	cfg = cfg_init(opts, 0);
a6b1b5	322	retval=cfg_parse(cfg, "tape");
d7639a	323	if(retval==CFG_FILE_ERROR){
a6b1b5	324	fatal("No tape file.",100);
d7639a	325	}
SP	326	else if(retval==CFG_PARSE_ERROR){
	327	fatal("Invalid tape!",100);
	328	}
	329	vesicle->nshell=nshell;
	330	vesicle->dmax=dmax*dmax;
	331	vesicle->bending_rigidity=xk0;
	332	vesicle->stepsize=stepsize;
a6b1b5	333	vesicle->clist->ncmax[0]=ncxmax;
SP	334	vesicle->clist->ncmax[1]=ncymax;
	335	vesicle->clist->ncmax[2]=nczmax;
	336	vesicle->clist->max_occupancy=8;
d7639a	337	cfg_free(cfg);
SP	338	// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
	339	return TS_SUCCESS;
	340
	341	}
f74313	342
SP	343
	344	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	345	FILE *fh;
	346	ts_uint i, nvtx,nedges,ntria;
	347	ts_uint vtxi1,vtxi2;
	348	float x,y,z;
	349	ts_vertex_list *vlist;
	350	fh=fopen(fname, "r");
	351	if(fh==NULL){
	352	err("Cannot open file for reading... Nonexistant file?");
	353	return TS_FAIL;
	354	}
	355	ts_uint retval;
	356	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	357	vesicle->vlist=init_vertex_list(nvtx);
	358	vlist=vesicle->vlist;
	359	for(i=0;i<nvtx;i++){
8f6a69	360	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	361	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	362	vlist->vtx[i]->x=x;
SP	363	vlist->vtx[i]->y=y;
	364	vlist->vtx[i]->z=z;
f74313	365	}
SP	366	for(i=0;i<nedges;i++){
	367	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	368	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	369	}
	370	//TODO: neighbours from bonds,
	371	//TODO: triangles from neigbours
	372
	373	// Don't need to read triangles. Already have enough data
	374	/*
	375	for(i=0;i<ntria;i++){
	376	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	377	vtxi1=vesicle->blist->vertex1->idx;
SP	378	vtxi2=vesicle->blist->vertex1->idx;
f74313	379
SP	380	}
	381	*/
41a035	382	if(retval);
f74313	383	fclose(fh);
SP	384
	385
	386
	387	return TS_SUCCESS;
	388	}