From 301c87b8a0ae31d97adf840d90dd241ffb3328b6 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 24 May 2016 17:02:48 +0000
Subject: [PATCH] A fix in restoring from snapshot when filaments are used
---
src/restore.c | 213 ++++++++++++++++++++++++++++++++++++++++++++++++----
1 files changed, 195 insertions(+), 18 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index d8542ac..545cc84 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>
@@ -10,12 +11,16 @@
#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"
-ts_bool parseDump(char *dumpfname) {
+ts_vesicle *parseDump(char *dumpfname) {
xmlDocPtr doc;
- xmlNodePtr cur;
- ts_vesicle *vesicle;
-
+ xmlNodePtr cur, cur1,cur2;
+ ts_vesicle *vesicle=NULL;
doc = xmlParseFile(dumpfname);
if (doc == NULL ) {
@@ -34,22 +39,68 @@
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);
}
-
+ // START Point Position data & Bonds
+ if ((!xmlStrcmp(cur->name, (const xmlChar *)"UnstructuredGrid"))){
+ cur1 = cur->xmlChildrenNode;
+ while(cur1!=NULL){
+ 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(vesicle!=NULL)
+ parseXMLVertexPosition(vesicle, doc, cur2);
+ }
+ if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
+ //fprintf(stderr,"Found cell(Bonds) data\n");
+ if(vesicle!=NULL)
+ parseXMLBonds(vesicle, doc, cur2);
+ }
+ cur2=cur2->next;
+ }
+ }
+ cur1 = cur1->next;
+ }
+ }
+ // END Point Position data & Bonds
cur = cur->next;
}
xmlFreeDoc(doc);
- fprintf(stderr,"Restoration completed\n");
- exit(0);
- vesicle_free(vesicle);
+
+// vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);
+
+ init_normal_vectors(vesicle->tlist);
+ mean_curvature_and_energy(vesicle);
+
+/* TODO: filaments */
+
+// 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){
+ 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
@@ -79,23 +130,25 @@
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);
+ 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);
xmlFree(nvtx);
xmlFree(npoly);
- xmlFree(nfono);
+ xmlFree(nmono);
child = cur->xmlChildrenNode;
while (child != NULL) {
@@ -105,6 +158,9 @@
if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){
parseTrisurfTria(vesicle, doc, child);
}
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"trianeigh"))){
+ parseTrisurfTriaNeigh(vesicle, doc, child);
+ }
if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
parseTrisurfTristar(vesicle, doc, child);
}
@@ -113,6 +169,8 @@
}
+ vesicle->tape=tape;
+ set_vesicle_values_from_tape(vesicle);
return vesicle;
}
@@ -153,14 +211,42 @@
char *tria;
char *vtx[3];
- ts_uint i;
+ ts_uint i,j;
triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
tria=(char *)triangles;
- for(i=0;i<3;i++) vtx[i]=strtok(tria," ");
+ vtx[0]=strtok(tria," ");
+ for(i=1;i<3;i++) vtx[i]=strtok(NULL," ");
+ j=0;
while(vtx[2]!=NULL){
triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]);
for(i=0;i<3;i++) vtx[i]=strtok(NULL," ");
+ j++;
}
+ //fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);
+
+ xmlFree(triangles);
+ return TS_SUCCESS;
+}
+
+
+ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
+ xmlChar *triangles;
+ char *tria;
+ char *ntria[3];
+ ts_uint i,j;
+ triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
+ tria=(char *)triangles;
+ ntria[0]=strtok(tria," ");
+ for(i=1;i<3;i++) ntria[i]=strtok(NULL," ");
+ j=0;
+ while(ntria[2]!=NULL){
+ triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[0])]);
+ triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[1])]);
+ triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[2])]);
+ j++;
+ for(i=0;i<3;i++) ntria[i]=strtok(NULL," ");
+ }
+ //fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);
xmlFree(triangles);
return TS_SUCCESS;
@@ -194,3 +280,94 @@
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, 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){
+ if(idx<vesicle->vlist->n){
+ 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 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");
+ idx++;
+ }
+ xmlFree(points);
+ }
+ child=child->next;
+ }
+ 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, *conname;
+ char *b;
+ int idx, polyidx;
+ char *token[2];
+ while (child != NULL) {
+ 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){
+ if(idx<3*(vesicle->vlist->n-2)){
+ bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
+ }
+ 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+vesicle->tape->npoly)){
+ 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[atoi(token[0])];
+ vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
+ }
+ }
+ token[0]=strtok(NULL," ");
+ token[1]=strtok(NULL,"\n");
+ idx++;
+ }
+ xmlFree(bonds);
+ }
+ xmlFree(conname);
+ child=child->next;
+ }
+ //fprintf(stderr,"Bond data j=%d\n",idx);
+ return TS_SUCCESS;
+}
+
+
+
--
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