From 201659654a328f84c229d16fe85d8709a4183957 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 19 Oct 2019 15:53:42 +0000
Subject: [PATCH] Fixed most problems, some still persists.
---
src/restore.c | 124 ++++++++++++++++++++++------------------
1 files changed, 68 insertions(+), 56 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index c89ff6d..7079960 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -7,7 +7,7 @@
#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"
@@ -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);
}
@@ -78,15 +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");
@@ -151,7 +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);
@@ -184,9 +190,8 @@
child = child->next;
}
-
vesicle->tape=tape;
- set_vesicle_values_from_tape(vesicle);
+// set_vesicle_values_from_tape(vesicle);
return vesicle;
}
@@ -327,8 +332,8 @@
xmlNodePtr child = cur->xmlChildrenNode;
xmlChar *property_name;
xmlChar *values;
- char *vals;
- char *token;
+// char *vals;
+// char *token;
int idx, polyidx, monoidx, filidx, fonoidx;
while (child != NULL) {
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -336,26 +341,31 @@
// 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){
+// 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=atof(token);
+ 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=atof(token);
+ 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=atof(token);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=curv_values[idx];//atof(token);
}
- idx++;
- token=strtok(NULL," ");
+ //idx++;
+ //token=strtok(NULL," ");
}
+
xmlFree(values);
+ free(curv_values);
}
xmlFree(property_name);
}
@@ -368,39 +378,42 @@
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];
+// 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){
+ 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=atof(token[0]);
- vesicle->vlist->vtx[idx]->y=atof(token[1]);
- vesicle->vlist->vtx[idx]->z=atof(token[2]);
+ vesicle->vlist->vtx[idx]->x=coords[idx];//atof(token[0]);
+ vesicle->vlist->vtx[idx]->y=coords[idx+1];//atof(token[1]);
+ vesicle->vlist->vtx[idx]->z=coords[idx+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=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]);
+ vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=coords[idx];//atof(token[0]);
+ vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=coords[idx+1];//atof(token[1]);
+ vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=coords[idx+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=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]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=coords[idx];//atof(token[0]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=coords[idx+1];//atof(token[1]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=coords[idx+2];//atof(token[2]);
}
- for(i=0;i<2;i++) token[i]=strtok(NULL," ");
- token[2]=strtok(NULL,"\n");
- idx++;
+ //for(i=0;i<2;i++) token[i]=strtok(NULL," ");
+ //token[2]=strtok(NULL,"\n");
+ //idx++;
}
xmlFree(points);
}
@@ -414,39 +427,38 @@
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];
- int temp_cnt=0;
+// char *b;
+ int i,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") ){
bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
- b=(char *)bonds;
- token[0]=strtok(b," ");
- token[1]=strtok(NULL,"\n");
- idx=0;
- while(token[0]!=NULL){
+ 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(i=0,idx=0;i<data_len;i+=2,idx++){
+// 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])]);
+ 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++;
+// 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])];
- vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
+ vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[conn[idx]];
+ vesicle->vlist->vtx[conn[idx]]->grafted_poly=vesicle->poly_list->poly[polyidx];
}
}
- token[0]=strtok(NULL," ");
- token[1]=strtok(NULL,"\n");
- idx++;
}
xmlFree(bonds);
}
--
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