| commit | author | age | ||
| ee84bd | 1 | #include <string.h> |
| SP | 2 | #include "general.h" |
| 3 | #include <stdio.h> | |
| 4 | #include "initial_distribution.h" | |
| 5 | #include "vesicle.h" | |
| 6 | #include "dumpstate.h" | |
| 7 | #include <libxml/parser.h> | |
| 8 | #include <libxml/tree.h> | |
| 43e534 | 9 | #include "vertex.h" |
| SP | 10 | #include "energy.h" |
| fda1ab | 11 | #include "sh.h" |
| SP | 12 | #include "cell.h" |
| 13 | #include "frame.h" | |
| ee84bd | 14 | ts_vesicle *vtk2vesicle(char *filename, ts_tape *tape){ |
| SP | 15 | |
| 16 | ts_uint nshell=tape->nshell; | |
| 17 | ts_uint ncmax1=tape->ncxmax; | |
| 18 | ts_uint ncmax2=tape->ncymax; | |
| 19 | ts_uint ncmax3=tape->nczmax; | |
| 20 | ts_double stepsize=tape->stepsize; | |
| 21 | ||
| 22 | ts_uint no_vertices=5*nshell*nshell+2; | |
| 23 | ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize); | |
| 24 | vesicle->nshell=nshell; | |
| 25 | parse_vtk(filename, vesicle); | |
| fda1ab | 26 | |
| SP | 27 | //we have vertices and neighbour relations all set, but unordered. Let's do bonds, ordering, triangles... |
| 28 | vesicle->vlist = vtk_sort_neighbours(vesicle->blist,vesicle->vlist); | |
| 29 | init_triangles(vesicle); | |
| 30 | init_triangle_neighbours(vesicle); | |
| 31 | init_common_vertex_triangle_neighbours(vesicle); | |
| 32 | init_normal_vectors(vesicle->tlist); | |
| 33 | mean_curvature_and_energy(vesicle); | |
| 34 | ||
| 35 | ||
| 36 | //preliminaries for spherical harmonics... | |
| 37 | centermass(vesicle); | |
| 38 | cell_occupation(vesicle); | |
| 39 | vesicle_volume(vesicle); //needed for constant volume at this moment | |
| 40 | vesicle_area(vesicle); //needed for constant area at this moment | |
| 41 | ts_double v0=vesicle->volume; | |
| 42 | ts_double a0=vesicle->area; | |
| 43 | ts_double r0=getR0(vesicle); | |
| 44 | if(r0&&v0&&a0); | |
| ee84bd | 45 | exit(1); |
| SP | 46 | return vesicle; |
| 47 | } | |
| 48 | ||
| 49 | ||
| 50 | ts_bool parse_vtk(char *filename, ts_vesicle *vesicle){ | |
| 51 | xmlDoc *doc; | |
| 52 | xmlNode *root_element=NULL; | |
| 53 | xmlNode *cur_node = NULL; | |
| 54 | doc = xmlReadFile(filename, NULL, 0); | |
| 55 | root_element=xmlDocGetRootElement(doc); | |
| 56 | cur_node=root_element->children; | |
| 57 | while(cur_node!=NULL){ | |
| 58 | // fprintf(stderr,"Node name is: %s\n",cur_node->name); | |
| 59 | if(strcmp((char *)cur_node->name,"UnstructuredGrid")==0) break; | |
| 60 | cur_node=cur_node->next; | |
| 61 | } | |
| 62 | ||
| 63 | cur_node=cur_node->children; | |
| 64 | while(cur_node!=NULL){ | |
| 65 | // fprintf(stderr,"Node name is: %s\n",cur_node->name); | |
| 66 | cur_node=cur_node->next; | |
| 67 | if(strcmp((char *)cur_node->name,"Piece")==0) break; | |
| 68 | } | |
| 69 | ||
| 70 | cur_node=cur_node->children; | |
| 71 | while(cur_node!=NULL){ | |
| 43e534 | 72 | //fprintf(stderr,"Node name is: %s\n",cur_node->name); |
| ee84bd | 73 | cur_node=cur_node->next; |
| SP | 74 | if(strcmp((char *)cur_node->name,"PointData")==0) vtk_index2vesicle(cur_node->children->next->children, vesicle); |
| 43e534 | 75 | if(strcmp((char *)cur_node->name,"Points")==0) vtk_coordinates(cur_node->children->next->children,vesicle); |
| SP | 76 | if(strcmp((char *)cur_node->name,"Cells")==0) { |
| 77 | vtk_neighbours(cur_node->children->next->children,vesicle); | |
| 78 | break; //segfaults, because it finds another cells. Why? | |
| 79 | } | |
| ee84bd | 80 | } |
| 43e534 | 81 | ts_fprintf(stdout,"restoring from vtk dump finished!\n"); |
| ee84bd | 82 | return TS_SUCCESS; |
| SP | 83 | } |
| 84 | ||
| 85 | ||
| 86 | ts_bool vtk_index2vesicle(xmlNode *node, ts_vesicle *vesicle){ | |
| 87 | //fprintf(stderr, "vsebina: %s\n",node->content); | |
| 88 | ts_uint i; | |
| 89 | char *token; | |
| 90 | token = strtok((char *)node->content, " "); | |
| 91 | for(i=0;i<vesicle->vlist->n;i++){ | |
| 92 | vesicle->vlist->vtx[i]->idx=atoi(token); | |
| 93 | token=strtok(NULL," "); | |
| 94 | } | |
| 95 | //fprintf(stderr,"idx[11]=%d\n",vesicle->vlist->vtx[11]->idx); | |
| 96 | return TS_SUCCESS; | |
| 97 | } | |
| 43e534 | 98 | |
| SP | 99 | ts_bool vtk_coordinates(xmlNode *node, ts_vesicle *vesicle){ |
| 100 | //fprintf(stderr, "vsebina: %s\n",node->content); | |
| 101 | ts_uint i; | |
| 102 | char *token; | |
| 103 | token = strtok((char *)node->content, " "); | |
| 104 | for(i=0;i<vesicle->vlist->n;i++){ | |
| 105 | vesicle->vlist->vtx[i]->x=atof(token); | |
| 106 | // fprintf(stderr,"%e, ",atof(token)); | |
| 107 | token=strtok(NULL," "); | |
| 108 | vesicle->vlist->vtx[i]->y=atof(token); | |
| 109 | token=strtok(NULL,"\n"); | |
| 110 | vesicle->vlist->vtx[i]->z=atof(token); | |
| 111 | if(i>0) token=strtok(NULL," "); | |
| 112 | } | |
| 113 | return TS_SUCCESS; | |
| 114 | ||
| 115 | } | |
| 116 | ||
| 117 | ts_bool vtk_neighbours(xmlNode *node, ts_vesicle *vesicle){ | |
| 118 | // fprintf(stderr, "vsebina: %s\n",node->content); | |
| 119 | ts_uint i; | |
| 120 | ts_uint idx1, idx2; | |
| 121 | char *token; | |
| 122 | token = strtok((char *)node->content, " "); | |
| 123 | for(i=0;i<3*(vesicle->vlist->n-2);i++){ | |
| 124 | idx1=atoi(token); | |
| 125 | token=strtok(NULL,"\n"); | |
| 126 | idx2=atoi(token); | |
| 127 | vtx_add_neighbour(vesicle->vlist->vtx[idx1], vesicle->vlist->vtx[idx2]); | |
| 128 | vtx_add_neighbour(vesicle->vlist->vtx[idx2], vesicle->vlist->vtx[idx1]); | |
| 129 | fprintf(stderr, "%d. povezujem %d in %d\n",i,idx1,idx2); | |
| 130 | if(i>0) token=strtok(NULL," "); | |
| 131 | } | |
| 132 | return TS_SUCCESS; | |
| 133 | } | |
| 134 | ||
| 135 | /* this is almost exact copy of init_sort_neighbours */ | |
| 136 | ts_vertex_list *vtk_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist){ | |
| 137 | ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment. | |
| 138 | ts_uint i,l,j,jj,jjj,k=0; | |
| 139 | ts_double eps=0.001; // Take a look if EPS from math.h can be used | |
| 140 | ||
| 141 | /*lets initialize memory for temporary vertex_list. Should we write a function instead */ | |
| 142 | ts_vertex_list *tvlist=vertex_list_copy(vlist); | |
| 143 | ts_vertex **tvtx=tvlist->vtx -1; /* again to compensate for 0-indexing */ | |
| 144 | ||
| 145 | ts_double dist2; // Square of distance of neighbours | |
| 146 | ts_double direct; // Something, dont know what, but could be normal of some kind | |
| 147 | for(i=1;i<=vlist->n;i++){ | |
| 148 | k++; // WHY i IS NOT GOOD?? | |
| 149 | vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st | |
| 150 | jjj=1; | |
| 151 | jj=1; | |
| 152 | for(l=2;l<=vtx[i]->neigh_no;l++){ | |
| 153 | for(j=2;j<=vtx[i]->neigh_no;j++){ | |
| 154 | dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]); | |
| 155 | direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]); | |
| 156 | // TODO: check if fabs can be used with all floating point types!! | |
| 157 | if( (direct>0.0) && (j!=jjj) ){ | |
| 158 | vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]); | |
| 159 | jjj=jj; | |
| 160 | jj=j; | |
| 161 | // break; | |
| 162 | } | |
| 163 | } | |
| 164 | } | |
| 165 | if(vtx[i]->neigh_no!=tvtx[i]->neigh_no){ | |
| 166 | fprintf(stderr,"Hej! pri vtx=%d se razikuje stevilo sosedov (prej=%d, potem=%d)\n",i, vtx[i]->neigh_no, tvtx[i]->neigh_no); | |
| 167 | } | |
| 168 | } | |
| 169 | if(eps>dist2); | |
| 170 | /* We use the temporary vertex for our main vertices and we abandon main | |
| 171 | * vertices, because their neighbours are not correctly ordered */ | |
| 172 | // tvtx=vlist->vtx; | |
| 173 | // vlist->vtx=tvtx; | |
| 174 | // tvlist->vtx=vtx; | |
| 175 | vtx_list_free(vlist); | |
| 176 | /* Let's make a check if the number of bonds is correct */ | |
| 177 | if((blist->n)!=3*(tvlist->n-2)){ | |
| 178 | ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2)); | |
| 179 | fatal("Number of bonds is not 3*(no_vertex-2).",4); | |
| 180 | } | |
| 181 | ||
| 182 | return tvlist; | |
| 183 | } | |
| 184 | ||
| 185 | ||
