From 82a8abcddd62838bfcd06b6081042caf4d385a88 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 21:37:13 +0000
Subject: [PATCH] Seems that the bugs are fixed. Pegs are self avoidant now
---
src/restore.c | 88 ++++++++++++++++++++++++++++++++++----------
1 files changed, 68 insertions(+), 20 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index a3196bd..3a93d3f 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>
@@ -16,7 +17,7 @@
#include "initial_distribution.h"
#include "io.h"
-ts_bool parseDump(char *dumpfname) {
+ts_vesicle *parseDump(char *dumpfname) {
xmlDocPtr doc;
xmlNodePtr cur, cur1,cur2;
ts_vesicle *vesicle=NULL;
@@ -54,12 +55,13 @@
cur2=cur1->xmlChildrenNode;
while(cur2!=NULL){
if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
- fprintf(stderr,"Found point data\n");
+ //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);
}
@@ -80,13 +82,13 @@
init_normal_vectors(vesicle->tlist);
mean_curvature_and_energy(vesicle);
-/* TODO: cells, polymeres, filaments, core, tape */
+/* TODO: filaments */
- fprintf(stderr,"Restoration completed\n");
- write_vertex_xml_file(vesicle,999);
- vesicle_free(vesicle);
- exit(0);
- return TS_SUCCESS;
+// ts_fprintf(stdout,"Restoration completed\n");
+// write_vertex_xml_file(vesicle,999);
+// vesicle_free(vesicle);
+// exit(0);
+ return vesicle;
}
ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){
@@ -99,7 +101,7 @@
/* 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
@@ -129,9 +131,9 @@
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
@@ -163,6 +165,16 @@
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;
}
@@ -177,6 +189,33 @@
/* 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){
@@ -221,7 +260,7 @@
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;
@@ -245,7 +284,7 @@
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;
@@ -285,7 +324,7 @@
xmlNodePtr child = cur->xmlChildrenNode;
xmlChar *points;
char *pts;
- int i, idx, polyidx, monoidx;
+ int i, idx, polyidx, monoidx, filidx, fonoidx;
char *token[3];
while (child != NULL) {
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -300,12 +339,19 @@
vesicle->vlist->vtx[idx]->x=atof(token[0]);
vesicle->vlist->vtx[idx]->y=atof(token[1]);
vesicle->vlist->vtx[idx]->z=atof(token[2]);
- } else {
+ } 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=atof(token[0]);
vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=atof(token[1]);
vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=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=atof(token[0]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=atof(token[1]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=atof(token[2]);
}
for(i=0;i<2;i++) token[i]=strtok(NULL," ");
token[2]=strtok(NULL,"\n");
@@ -315,7 +361,8 @@
}
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;
}
@@ -339,9 +386,10 @@
}
else {
//find grafted vtx
- if((vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)){
+ 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+vesicle->tape->npoly)){
polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
- fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
+ //fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])];
vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
}
@@ -355,7 +403,7 @@
xmlFree(conname);
child=child->next;
}
- fprintf(stderr,"Bond data j=%d\n",idx);
+ //fprintf(stderr,"Bond data j=%d\n",idx);
return TS_SUCCESS;
}
--
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