From 3197854e89eb9ffe5ff3137e274d16806c2028a5 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 27 Jul 2021 12:51:09 +0000
Subject: [PATCH] Found one bug in the code when calculating mprod. Fixed.
---
src/restore.c | 68 +++++++++++++++++++++++++++++----
1 files changed, 59 insertions(+), 9 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index 086bf1c..6e12c1e 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);
}
@@ -54,6 +55,10 @@
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)
@@ -74,14 +79,19 @@
// 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 */
// ts_fprintf(stdout,"Restoration completed\n");
@@ -146,7 +156,8 @@
//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_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(nmono);
@@ -179,10 +190,8 @@
child = child->next;
}
-
vesicle->tape=tape;
- set_vesicle_values_from_tape(vesicle);
-
+// set_vesicle_values_from_tape(vesicle);
return vesicle;
}
@@ -318,7 +327,48 @@
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;
--
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