trisurf-ng.git - Gitblit

Changed bondflip. lm, lp found before and only once

mihaf

2014-03-07 b866cf902b92a94fb438e40a24dae0a89fa2afec

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>
b14a8d	11	#include "initial_distribution.h"
a2db52	12	#include "poly.h"
d7639a	13
SP	14	ts_bool print_vertex_list(ts_vertex_list *vlist){
	15	ts_uint i;
	16	printf("Number of vertices: %u\n",vlist->n);
	17	for(i=0;i<vlist->n;i++){
a6b1b5	18	printf("%u: %f %f %f\n",
8f6a69	19	vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
d7639a	20	}
SP	21	return TS_SUCCESS;
	22	}
	23
	24	ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
	25	ts_uint i,j;
a6b1b5	26	ts_vertex **vtx=vlist->vtx;
d7639a	27	printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
SP	28	for(i=0;i<vlist->n;i++){
8f6a69	29	printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
SP	30	for(j=0;j<vtx[i]->neigh_no;j++){
	31	printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
	32	vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
d7639a	33	}
SP	34	printf("\n");
	35	}
	36
	37	return TS_SUCCESS;
	38	}
	39
	40	ts_bool write_vertex_fcompat_file(ts_vertex_list vlist,ts_char filename){
a6b1b5	41	ts_vertex **vtx=vlist->vtx;
d7639a	42	ts_uint i;
SP	43	FILE *fh;
	44
	45	fh=fopen(filename, "w");
	46	if(fh==NULL){
	47	err("Cannot open file %s for writing");
	48	return TS_FAIL;
	49	}
	50	for(i=0;i<vlist->n;i++)
8f6a69	51	fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	52
SP	53	fclose(fh);
	54	return TS_SUCCESS;
	55	}
	56
	57
	58	ts_bool fprint_vertex_list(FILE fh,ts_vertex_list vlist){
	59	ts_uint i,j;
	60	for(i=0;i<vlist->n;i++){
8f6a69	61	fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
SP	62	vlist->vtx[i]->y, vlist->vtx[i]->z,
	63	vlist->vtx[i]->neigh_no);
	64	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	65	fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
a6b1b5	66	//-vlist->vtx+1));
d7639a	67	}
SP	68	fprintf(fh,"\n");
	69	}
	70	return TS_SUCCESS;
	71	}
	72
	73	ts_bool fprint_tristar(FILE fh, ts_vesicle vesicle){
	74	ts_uint i,j;
a6b1b5	75	for(i=0;i<vesicle->vlist->n;i++){
8f6a69	76	fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
SP	77	for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
	78	fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
d7639a	79	}
SP	80	fprintf(fh,"\n");
	81	}
	82	return TS_SUCCESS;
	83	}
	84
	85	ts_bool fprint_triangle_list(FILE fh, ts_vesicle vesicle){
a6b1b5	86	ts_triangle_list *tlist=vesicle->tlist;
d7639a	87	ts_uint i,j;
SP	88	for(i=0;i<tlist->n;i++){
41a035	89	fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
SP	90	for(j=0;j<tlist->tria[i]->neigh_no;j++){
	91	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
d7639a	92	}
SP	93	fprintf(fh,"\n");
	94	for(j=0;j<3;j++){
41a035	95	fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
d7639a	96	}
SP	97	fprintf(fh,"\n");
41a035	98	fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
SP	99	tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
d7639a	100	fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
SP	101	}
	102	return TS_SUCCESS;
	103	}
	104
	105	ts_bool fprint_vertex_data(FILE fh,ts_vertex_list vlist){
	106	ts_uint i,j;
	107	for(i=0;i<vlist->n;i++){
	108	fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
8f6a69	109	vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
SP	110	vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
	111	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
	112	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
d7639a	113	}
SP	114	fprintf(fh,"\n");
8f6a69	115	for(j=0;j<vlist->vtx[i]->neigh_no;j++){
SP	116	fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
d7639a	117	}
SP	118	fprintf(fh,"\n");
	119	}
	120	return TS_SUCCESS;
	121	}
	122
	123	ts_bool fprint_bonds(FILE fh,ts_vesicle vesicle){
	124	ts_uint i;
a6b1b5	125	for(i=0;i<vesicle->blist->n;i++){
e016c4	126	fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
a6b1b5	127	//-vesicle->vlist->vtx+1),
e016c4	128	(ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
a6b1b5	129	//-vesicle->vlist.vtx+1));
d7639a	130	}
SP	131	return TS_SUCCESS;
	132	}
	133
	134
	135	ts_bool write_dout_fcompat_file(ts_vesicle vesicle, ts_char filename){
	136	FILE *fh;
	137	fh=fopen(filename, "w");
	138	if(fh==NULL){
	139	err("Cannot open file %s for writing");
	140	return TS_FAIL;
	141	}
	142	fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
a6b1b5	143	fprint_vertex_list(fh,vesicle->vlist);
d7639a	144	fprint_tristar(fh,vesicle);
SP	145	fprint_triangle_list(fh,vesicle);
a6b1b5	146	fprint_vertex_data(fh,vesicle->vlist);
d7639a	147	fprint_bonds(fh,vesicle);
SP	148	fclose(fh);
	149	return TS_SUCCESS;
	150	}
	151
	152	ts_bool read_tape_fcompat_file(ts_vesicle vesicle, ts_char filename){
	153	FILE *fh;
	154	char line[255];
	155	fh=fopen(filename, "r");
	156	if(fh==NULL){
	157	err("Cannot open file for reading... Nonexistant file?");
	158	return TS_FAIL;
	159	}
a6b1b5	160	ts_uint retval=1;
d7639a	161	while(retval!=EOF){
SP	162	retval=fscanf(fh,"%s",line);
	163
	164	fprintf(stderr,"%s",line);
	165	}
	166	fclose(fh);
	167	return TS_SUCCESS;
	168	}
	169
	170	ts_bool write_master_xml_file(ts_char *filename){
	171	FILE *fh;
	172	ts_char i,j;
	173	ts_uint tstep;
	174	ts_char *number;
	175	fh=fopen(filename, "w");
	176	if(fh==NULL){
	177	err("Cannot open file %s for writing");
	178	return TS_FAIL;
	179	}
	180
	181	fprintf(fh,"<?xml version=\"1.0\"?>\n<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n<Collection>");
	182	DIR *dir = opendir(".");
	183	if(dir){
	184	struct dirent *ent;
	185	tstep=0;
	186	while((ent = readdir(dir)) != NULL)
	187	{
	188	i=rindex(ent->d_name,'.');
	189	if(i==NULL) continue;
	190	if(strcmp(i+1,"vtu")==0){
	191	j=rindex(ent->d_name,'_');
	192	if(j==NULL) continue;
	193	number=strndup(j+1,j-i);
a6b1b5	194	fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
d7639a	195	tstep++;
SP	196	free(number);
	197	}
	198	}
	199	}
f74313	200	free(dir);
d7639a	201	fprintf(fh,"</Collection>\n</VTKFile>\n");
SP	202	fclose(fh);
	203	return TS_SUCCESS;
	204	}
	205
	206	ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
a6b1b5	207	ts_vertex_list *vlist=vesicle->vlist;
SP	208	ts_bond_list *blist=vesicle->blist;
	209	ts_vertex **vtx=vlist->vtx;
40aa5b	210	ts_uint i,j;
d7639a	211	char filename[255];
SP	212	FILE *fh;
	213
	214	sprintf(filename,"timestep_%.6u.vtu",timestepno);
	215	fh=fopen(filename, "w");
	216	if(fh==NULL){
	217	err("Cannot open file %s for writing");
	218	return TS_FAIL;
	219	}
	220	/* Here comes header of the file */
40aa5b	221
SP	222	//find number of extra vtxs and bonds of polymeres
	223	ts_uint monono=0, polyno=0;
	224	ts_bool poly=0;
	225	if(vesicle->poly_list!=NULL){
	226	if(vesicle->poly_list->poly[0]!=NULL){
	227	polyno=vesicle->poly_list->n;
	228	monono=vesicle->poly_list->poly[0]->vlist->n;
	229	poly=1;
	230	}
	231	}
d7639a	232	fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
40aa5b	233	fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+mononopolyno, blist->n+mononopolyno);
d7639a	234	fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
SP	235	for(i=0;i<vlist->n;i++){
a6b1b5	236	fprintf(fh,"%u ",vtx[i]->idx);
d7639a	237	}
40aa5b	238	//polymeres
SP	239	if(poly){
	240	for(i=0;i<vesicle->poly_list->n;i++){
	241	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	242	fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
	243	}
	244	}
	245	}
d7639a	246
SP	247	fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
	248	for(i=0;i<vlist->n;i++){
8f6a69	249	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
40aa5b	250	}
SP	251	//polymeres
	252	if(poly){
	253	for(i=0;i<vesicle->poly_list->n;i++){
	254	for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
	255	fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
	256	}
	257	}
d7639a	258	}
SP	259
	260	fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
	261	for(i=0;i<blist->n;i++){
e016c4	262	fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	263	}
40aa5b	264	//polymeres
SP	265	if(poly){
	266	for(i=0;i<vesicle->poly_list->n;i++){
	267	for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
	268	fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
	269	}
	270	//grafted bonds
	271	fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
	272	}
	273
	274	}
	275
	276
d7639a	277	fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
40aa5b	278	for (i=2;i<(blist->n+mononopolyno)2+1;i+=2){
d7639a	279	fprintf(fh,"%u ",i);
SP	280	}
	281	fprintf(fh,"\n");
	282	fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
40aa5b	283	for (i=0;i<blist->n+monono*polyno;i++){
d7639a	284	fprintf(fh,"3 ");
SP	285	}
	286
	287	fprintf(fh,"</DataArray>\n</Cells>\n</Piece>\n</UnstructuredGrid>\n</VTKFile>\n");
	288	fclose(fh);
	289	return TS_SUCCESS;
	290
	291	}
	292
	293	ts_bool write_vertex_vtk_file(ts_vesicle vesicle,ts_char filename, ts_char *text){
a6b1b5	294	ts_vertex_list *vlist=vesicle->vlist;
SP	295	ts_bond_list *blist=vesicle->blist;
	296	ts_vertex **vtx=vlist->vtx;
	297	ts_uint i;
d7639a	298	FILE *fh;
SP	299
	300	fh=fopen(filename, "w");
	301	if(fh==NULL){
	302	err("Cannot open file %s for writing");
	303	return TS_FAIL;
	304	}
	305	/* Here comes header of the file */
	306	// fprintf(stderr,"NSHELL=%u\n",nshell);
	307	fprintf(fh, "# vtk DataFile Version 2.0\n");
	308	/* TODO: Do a sanity check on text. Max 255 char, must not me \n terminated */
	309	fprintf(fh, "%s\n", text);
	310	fprintf(fh,"ASCII\n");
	311	fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
	312	fprintf(fh,"POINTS %u double\n", vlist->n);
	313	for(i=0;i<vlist->n;i++){
8f6a69	314	fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
d7639a	315	}
SP	316
	317	fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
	318	for(i=0;i<blist->n;i++){
e016c4	319	fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
d7639a	320	}
SP	321	fprintf(fh,"CELL_TYPES %u\n",blist->n);
	322	for(i=0;i<blist->n;i++)
	323	fprintf(fh,"3\n");
	324
	325	fprintf(fh,"POINT_DATA %u\n", vlist->n);
	326	fprintf(fh,"SCALARS scalars long 1\n");
	327	fprintf(fh,"LOOKUP_TABLE default\n");
	328
	329	for(i=0;i<vlist->n;i++)
8f6a69	330	fprintf(fh,"%u\n",vtx[i]->idx);
d7639a	331
SP	332	fclose(fh);
	333	return TS_SUCCESS;
	334	}
	335
	336
	337
d7a113	338	ts_vesicle parsetape(ts_uint mcsweeps, ts_uint inititer, ts_uint iterations){
b866cf	339	long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
b14a8d	340	char buf=malloc(255sizeof(char));
SP	341	long int brezveze0=1;
	342	long int brezveze1=1;
	343	long int brezveze2=1;
e86357	344	ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0,pressure=0.0;
d7a113	345	long int iter=1000, init=1000, mcsw=1000;
40aa5b	346
SP	347
d7639a	348	cfg_opt_t opts[] = {
SP	349	CFG_SIMPLE_INT("nshell", &nshell),
a2db52	350	CFG_SIMPLE_INT("npoly", &npoly),
SP	351	CFG_SIMPLE_INT("nmono", &nmono),
d7639a	352	CFG_SIMPLE_FLOAT("dmax", &dmax),
SP	353	CFG_SIMPLE_FLOAT("xk0",&xk0),
b866cf	354	CFG_SIMPLE_INT("pswitch",&pswitch),
e86357	355	CFG_SIMPLE_FLOAT("pressure",&pressure),
M	356	CFG_SIMPLE_FLOAT("k_spring",&kspring),
d7639a	357	CFG_SIMPLE_FLOAT("stepsize",&stepsize),
SP	358	CFG_SIMPLE_INT("nxmax", &ncxmax),
	359	CFG_SIMPLE_INT("nymax", &ncymax),
	360	CFG_SIMPLE_INT("nzmax", &nczmax),
d7a113	361	CFG_SIMPLE_INT("iterations",&iter),
SP	362	CFG_SIMPLE_INT("mcsweeps",&mcsw),
	363	CFG_SIMPLE_INT("inititer", &init),
d7639a	364	CFG_SIMPLE_BOOL("quiet",&quiet),
314f2d	365	CFG_SIMPLE_STR("multiprocessing",buf),
b14a8d	366	CFG_SIMPLE_INT("smp_cores",&brezveze0),
SP	367	CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
	368	CFG_SIMPLE_INT("distributed_processes",&brezveze2),
d7639a	369	CFG_END()
SP	370	};
	371	cfg_t *cfg;
	372	ts_uint retval;
	373	cfg = cfg_init(opts, 0);
a6b1b5	374	retval=cfg_parse(cfg, "tape");
d7639a	375	if(retval==CFG_FILE_ERROR){
a6b1b5	376	fatal("No tape file.",100);
d7639a	377	}
SP	378	else if(retval==CFG_PARSE_ERROR){
	379	fatal("Invalid tape!",100);
	380	}
b14a8d	381	ts_vesicle *vesicle;
d7a113	382	*iterations=iter;
SP	383	*inititer=init;
	384	*mcsweeps=mcsw;
b14a8d	385	vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
a2db52	386	vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
48bb92	387	vesicle->spring_constant=kspring;
M	388	poly_assign_spring_const(vesicle);
	389
a2db52	390
d7639a	391	vesicle->nshell=nshell;
SP	392	vesicle->dmax=dmax*dmax;
	393	vesicle->bending_rigidity=xk0;
e86357	394	vtx_set_global_values(vesicle); //copies xk0 to every vertex
M	395
	396
d7639a	397	vesicle->stepsize=stepsize;
a6b1b5	398	vesicle->clist->ncmax[0]=ncxmax;
SP	399	vesicle->clist->ncmax[1]=ncymax;
	400	vesicle->clist->ncmax[2]=nczmax;
	401	vesicle->clist->max_occupancy=8;
e86357	402	vesicle->pressure=pressure/vesicle->bending_rigidity; //all energy contributions need to be divided by bending_rigidity!
b866cf	403	vesicle->pswitch=pswitch;
d7639a	404	cfg_free(cfg);
b14a8d	405	free(buf);
SP	406	// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
40aa5b	407
SP	408
	409
b14a8d	410	return vesicle;
d7639a	411
SP	412	}
f74313	413
SP	414
	415	ts_bool read_geometry_file(char fname, ts_vesicle vesicle){
	416	FILE *fh;
	417	ts_uint i, nvtx,nedges,ntria;
	418	ts_uint vtxi1,vtxi2;
	419	float x,y,z;
	420	ts_vertex_list *vlist;
	421	fh=fopen(fname, "r");
	422	if(fh==NULL){
	423	err("Cannot open file for reading... Nonexistant file?");
	424	return TS_FAIL;
	425	}
	426	ts_uint retval;
	427	retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
	428	vesicle->vlist=init_vertex_list(nvtx);
	429	vlist=vesicle->vlist;
	430	for(i=0;i<nvtx;i++){
8f6a69	431	// fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
f74313	432	retval=fscanf(fh,"%F %F %F",&x,&y,&z);
8f6a69	433	vlist->vtx[i]->x=x;
SP	434	vlist->vtx[i]->y=y;
	435	vlist->vtx[i]->z=z;
f74313	436	}
SP	437	for(i=0;i<nedges;i++){
	438	retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
	439	bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
	440	}
	441	//TODO: neighbours from bonds,
	442	//TODO: triangles from neigbours
	443
	444	// Don't need to read triangles. Already have enough data
	445	/*
	446	for(i=0;i<ntria;i++){
	447	retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
8f6a69	448	vtxi1=vesicle->blist->vertex1->idx;
SP	449	vtxi2=vesicle->blist->vertex1->idx;
f74313	450
SP	451	}
	452	*/
41a035	453	if(retval);
f74313	454	fclose(fh);
SP	455
	456
	457
	458	return TS_SUCCESS;
	459	}