From 6da644f98434d3eac8b4e19981754f6030a315a5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 27 Jun 2018 12:05:32 +0000
Subject: [PATCH] Resolving the issues with restoring vesicles from vtu and fixing the volume. Dump to vtu has been repaired.
---
src/restore.c | 117 +++++++++++++++++++++++++++++++++++++++++++++++++++++++---
1 files changed, 110 insertions(+), 7 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index 643188b..989a87b 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -16,13 +16,14 @@
#include "poly.h"
#include "initial_distribution.h"
#include "io.h"
+#include <math.h>
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);
}
@@ -54,9 +55,14 @@
if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
cur2=cur1->xmlChildrenNode;
while(cur2!=NULL){
+ 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"))){
@@ -80,7 +86,13 @@
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 */
// ts_fprintf(stdout,"Restoration completed\n");
@@ -164,6 +176,16 @@
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;
}
@@ -171,13 +193,39 @@
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){
@@ -280,13 +328,54 @@
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;
+ token=strtok(vals," ");
+ idx=0;
+ while(token!=NULL){
+ if(idx<vesicle->vlist->n){
+ vesicle->vlist->vtx[idx]->c=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=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=atof(token);
+ }
+ idx++;
+ token=strtok(NULL," ");
+ }
+ xmlFree(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, polyidx, monoidx;
+ int i, idx, polyidx, monoidx, filidx, fonoidx;
char *token[3];
while (child != NULL) {
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -301,12 +390,19 @@
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");
@@ -316,6 +412,7 @@
}
child=child->next;
}
+ //fprintf(stderr,"Came here\n");
//fprintf(stderr,"Vertices position j=%d\n",idx);
return TS_SUCCESS;
@@ -326,6 +423,7 @@
char *b;
int idx, polyidx;
char *token[2];
+ int temp_cnt=0;
while (child != NULL) {
conname=xmlGetProp(child, (xmlChar *)"Name");
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
@@ -337,10 +435,15 @@
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])]);
+ //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
}
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)){
+ 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[atoi(token[0])];
--
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