From 579fbdf994b239ddcf68b1364fa3c84b2837d5c8 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Sat, 19 Oct 2019 16:05:49 +0000 Subject: [PATCH] Restore seems to be working, however... --- src/restore.c | 268 +++++++++++++++++++++++++++++++++++++++++----------- 1 files changed, 209 insertions(+), 59 deletions(-) diff --git a/src/restore.c b/src/restore.c index bf9877f..9f9c3f4 100644 --- a/src/restore.c +++ b/src/restore.c @@ -1,3 +1,4 @@ +/* vim: set ts=4 sts=4 sw=4 noet : */ #include <stdio.h> #include <string.h> #include <stdlib.h> @@ -6,21 +7,23 @@ #include <general.h> #include <restore.h> #include <snapshot.h> -#include <zlib.h> +#include <b64zlib_compression.h> #include "vesicle.h" #include "vertex.h" #include "triangle.h" #include "bond.h" #include "energy.h" +#include "poly.h" #include "initial_distribution.h" +#include "io.h" +#include <math.h> -ts_bool parseDump(char *dumpfname) { +ts_vesicle *parseDump(char *dumpfname) { xmlDocPtr doc; xmlNodePtr cur, cur1,cur2; ts_vesicle *vesicle=NULL; - doc = xmlParseFile(dumpfname); - + int i; if (doc == NULL ) { fatal("Dump file could not be found or parsed. It is correct file?",1); } @@ -37,6 +40,11 @@ cur = cur->xmlChildrenNode; while (cur != NULL) { + + if ((!xmlStrcmp(cur->name, (const xmlChar *)"tape"))){ + setGlobalTapeTXTfromTapeTag(doc, cur); + } + if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){ vesicle=parseTrisurfTag(doc, cur); } @@ -47,13 +55,18 @@ if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){ cur2=cur1->xmlChildrenNode; while(cur2!=NULL){ - if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){ - fprintf(stderr,"Found point data\n"); + if ((!xmlStrcmp(cur2->name, (const xmlChar *)"PointData"))){ if(vesicle!=NULL) + parseXMLPointData(vesicle,doc,cur2); + } + if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){ + //fprintf(stderr,"Found point data\n"); + if(vesicle!=NULL) + //fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono); parseXMLVertexPosition(vesicle, doc, cur2); } if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){ - fprintf(stderr,"Found cell(Bonds) data\n"); + //fprintf(stderr,"Found cell(Bonds) data\n"); if(vesicle!=NULL) parseXMLBonds(vesicle, doc, cur2); } @@ -66,25 +79,39 @@ // END Point Position data & Bonds cur = cur->next; } - xmlFreeDoc(doc); + +// vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle); + set_vesicle_values_from_tape(vesicle); init_normal_vectors(vesicle->tlist); mean_curvature_and_energy(vesicle); + sweep_attraction_bond_energy(vesicle); + if(vesicle->tape->stretchswitch==1){ + vesicle->tlist->a0=sqrt(3)/4.0*pow((vesicle->tape->dmax+1.0)/2.0,2); + for(i=0;i<vesicle->tlist->n;i++){ + stretchenergy(vesicle, vesicle->tlist->tria[i]); + } + } +/* TODO: filaments */ -/* TODO: cells, polymeres, filaments, core, tape */ +// ts_fprintf(stdout,"Restoration completed\n"); +// write_vertex_xml_file(vesicle,999); +// vesicle_free(vesicle); +// exit(0); + return vesicle; +} - fprintf(stderr,"Restoration completed\n"); - write_vertex_xml_file(vesicle,999); - vesicle_free(vesicle); - exit(0); +ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){ + xmlChar *tape = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); + strcpy(tapetxt,(char *)tape); + xmlFree(tape); return TS_SUCCESS; } - /* this is a parser of additional data in xml */ ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){ - fprintf(stderr,"Parsing trisurf tag\n"); + //fprintf(stderr,"Parsing trisurf tag\n"); xmlNodePtr child; #ifdef COMPRESS @@ -114,23 +141,26 @@ inflateInit(&infstream); inflate(&infstream, Z_NO_FLUSH); inflateEnd(&infstream); - fprintf(stderr,"%lu\n",cLen); + //fprintf(stderr,"%lu\n",cLen); subtree[infstream.total_out]='\0'; //zero terminate string - fprintf(stderr,"%s\n",subtree); + //fprintf(stderr,"%s\n",subtree); free(subtree); #endif /*parse xml subtree */ - xmlChar *nvtx, *npoly, *nfono; + xmlChar *nvtx, *npoly, *nmono; nvtx = xmlGetProp(cur, (xmlChar *)"nvtx"); npoly=xmlGetProp(cur, (xmlChar *)"npoly"); - nfono=xmlGetProp(cur, (xmlChar *)"nfono"); - fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx)); - ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),10,10,10,0.1); - //vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle); + nmono=xmlGetProp(cur, (xmlChar *)"nmono"); + ts_tape *tape=parsetapebuffer(tapetxt); + //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx)); + //TODO: check if nvtx is in agreement with nshell from tape + ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize); +// vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle); + vesicle->poly_list=init_empty_poly_list(atoi((char *)npoly),atoi((char *)nmono)); xmlFree(nvtx); xmlFree(npoly); - xmlFree(nfono); + xmlFree(nmono); child = cur->xmlChildrenNode; while (child != NULL) { @@ -146,18 +176,55 @@ if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){ parseTrisurfTristar(vesicle, doc, child); } + if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){ + parseTrisurfNucleus(vesicle, doc, child); + } + if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){ + parseTrisurfConstantVolume(doc, child); + } + if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){ + parseTrisurfConstantArea(doc, child); + } + child = child->next; } - - + vesicle->tape=tape; +// set_vesicle_values_from_tape(vesicle); return vesicle; } /* Low level tags parsers */ +ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){ + xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); + char *n=(char *)cvol; + V0=atof(n); + xmlFree(cvol); + return TS_SUCCESS; +} +ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){ + xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); + char *n=(char *)carea; + A0=atof(n); + xmlFree(carea); + return TS_SUCCESS; +} + +ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){ + xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1); + char *n=(char *)coords; + char *token=strtok(n," "); + ts_uint i; + for(i=0;i<3;i++){ + vesicle->nucleus_center[i]=atof(token); + token=strtok(NULL," "); + } + xmlFree(coords); + return TS_SUCCESS; +} ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){ @@ -202,7 +269,7 @@ for(i=0;i<3;i++) vtx[i]=strtok(NULL," "); j++; } - fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j); + //fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j); xmlFree(triangles); return TS_SUCCESS; @@ -226,7 +293,7 @@ j++; for(i=0;i<3;i++) ntria[i]=strtok(NULL," "); } - fprintf(stderr,"Parsing triangle neighbors j=%d\n",j); + //fprintf(stderr,"Parsing triangle neighbors j=%d\n",j); xmlFree(triangles); return TS_SUCCESS; @@ -260,62 +327,145 @@ return TS_SUCCESS; } - +/* this parses the data for vertices (like spontaneous curvature, etc.) */ +ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){ + xmlNodePtr child = cur->xmlChildrenNode; + xmlChar *property_name; + xmlChar *values; +// char *vals; +// char *token; + int idx, polyidx, monoidx, filidx, fonoidx; + while (child != NULL) { + if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){ + property_name=xmlGetProp(child, (xmlChar *)"Name"); + // fprintf(stderr,"Name: %s\n", property_name); + if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){ + values=xmlNodeListGetString(doc,child->xmlChildrenNode,1); +// vals=(char *)values; + unsigned long data_len=0; + ts_double *curv_values=(double *)ts_decompress((unsigned char *)values,strlen((char *)values), &data_len); + data_len=data_len/sizeof(ts_double); +// token=strtok(vals," "); + for(idx=0;idx<data_len;idx++){ +// while(token!=NULL){ + if(idx<vesicle->vlist->n){ + vesicle->vlist->vtx[idx]->c=curv_values[idx]; //atof(token); + } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) { + polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono; + monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono; + vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=curv_values[idx];//atof(token); + } else { + filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono; + fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono; + //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=curv_values[idx];//atof(token); + } + //idx++; + //token=strtok(NULL," "); + } + + xmlFree(values); + free(curv_values); + } + xmlFree(property_name); + } + + child=child->next; + } + return TS_SUCCESS; +} /* this is a parser of vertex positions and bonds from main xml data */ ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){ xmlNodePtr child = cur->xmlChildrenNode; xmlChar *points; - char *pts; - int i, idx; - char *token[3]; +// char *pts; + int i,idx, polyidx, monoidx, filidx, fonoidx; +// char *token[3]; while (child != NULL) { if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){ points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1); - pts=(char *)points; - token[0]=strtok(pts," "); - token[1]=strtok(NULL," "); - token[2]=strtok(NULL,"\n"); - idx=0; - while(token[0]!=NULL){ - vesicle->vlist->vtx[idx]->x=atof(token[0]); - vesicle->vlist->vtx[idx]->y=atof(token[1]); - vesicle->vlist->vtx[idx]->z=atof(token[2]); - for(i=0;i<2;i++) token[i]=strtok(NULL," "); - token[2]=strtok(NULL,"\n"); - idx++; + unsigned long data_len=0; + ts_double *coords=(double *)ts_decompress((unsigned char *)points,strlen((char *)points), &data_len); + data_len=data_len/sizeof(ts_double); + //pts=(char *)points; + //token[0]=strtok(pts," "); + //token[1]=strtok(NULL," "); + //token[2]=strtok(NULL,"\n"); + for(i=0,idx=0;i<data_len;i+=3,idx++){ +// while(token[0]!=NULL){ + if(idx<vesicle->vlist->n){ + vesicle->vlist->vtx[idx]->x=coords[i];//atof(token[0]); + vesicle->vlist->vtx[idx]->y=coords[i+1];//atof(token[1]); + vesicle->vlist->vtx[idx]->z=coords[i+2];//atof(token[2]); + } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) { + polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono; + monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono; + vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=coords[i];//atof(token[0]); + vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=coords[i+1];//atof(token[1]); + vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=coords[i+2];//atof(token[2]); + } else { + filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono; + fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono; + //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=coords[i];//atof(token[0]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=coords[i+1];//atof(token[1]); + vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=coords[i+2];//atof(token[2]); + } + //for(i=0;i<2;i++) token[i]=strtok(NULL," "); + //token[2]=strtok(NULL,"\n"); + //idx++; } xmlFree(points); } child=child->next; } - fprintf(stderr,"Vertices position j=%d\n",idx); + //fprintf(stderr,"Came here\n"); + //fprintf(stderr,"Vertices position j=%d\n",idx); return TS_SUCCESS; } ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){ xmlNodePtr child = cur->xmlChildrenNode; - xmlChar *bonds; - char *b; - int idx; - char *token[2]; + xmlChar *bonds, *conname; +// char *b; + int idx, polyidx; +// char *token[2]; +// int temp_cnt=0; while (child != NULL) { - if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(xmlGetProp(child, (xmlChar *)"Name"), (const xmlChar *)"connectivity") ){ + conname=xmlGetProp(child, (xmlChar *)"Name"); + if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){ bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1); - b=(char *)bonds; - token[0]=strtok(b," "); - token[1]=strtok(NULL,"\n"); - idx=0; - while(token[0]!=NULL){ - bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]); - token[0]=strtok(NULL," "); - token[1]=strtok(NULL,"\n"); - idx++; + unsigned long data_len=0; + unsigned long *conn=(unsigned long *)ts_decompress((unsigned char *)bonds,strlen((char *)bonds), &data_len); + data_len=data_len/sizeof(unsigned long); + //token[0]=strtok(b," "); + //token[1]=strtok(NULL,"\n"); + for(idx=0;idx<data_len;idx+=2){ +// while(token[0]!=NULL){ + if(idx<3*(vesicle->vlist->n-2)){ + bond_add(vesicle->blist, vesicle->vlist->vtx[conn[idx]], vesicle->vlist->vtx[conn[idx+1]]); + //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx); + } + else { + //find grafted vtx + if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono) + && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly)){ +// temp_cnt++; + //fprintf(stderr,"%d: Bonds in poly count idx=%d, t1=%s t2=%s\n",temp_cnt,idx, token[0], token[1]); + + polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono); + //fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0])); + vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[conn[idx]]; + vesicle->vlist->vtx[conn[idx]]->grafted_poly=vesicle->poly_list->poly[polyidx]; + } + } } xmlFree(bonds); } + xmlFree(conname); child=child->next; } - fprintf(stderr,"Bond data j=%d\n",idx); + //fprintf(stderr,"Bond data j=%d\n",idx); return TS_SUCCESS; } -- Gitblit v1.9.3