From dd4e182bc818974b3ad529422e631aa6a0764f2f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 05 Jul 2016 10:18:24 +0000
Subject: [PATCH] Merge branch 'nirgov' of bitbucket.org:samop/trisurf-ng into nirgov
---
src/restore.c | 199 +++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 166 insertions(+), 33 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index bf9877f..a490d53 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>
@@ -12,13 +13,14 @@
#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, cur1,cur2;
ts_vesicle *vesicle=NULL;
-
doc = xmlParseFile(dumpfname);
if (doc == NULL ) {
@@ -37,6 +39,11 @@
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);
}
@@ -47,13 +54,18 @@
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 ((!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"))){
- fprintf(stderr,"Found cell(Bonds) data\n");
+ //fprintf(stderr,"Found cell(Bonds) data\n");
if(vesicle!=NULL)
parseXMLBonds(vesicle, doc, cur2);
}
@@ -68,23 +80,33 @@
}
xmlFreeDoc(doc);
+
+// vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);
+
init_normal_vectors(vesicle->tlist);
mean_curvature_and_energy(vesicle);
+ sweep_attraction_bond_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);
+// 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
@@ -114,23 +136,25 @@
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) {
@@ -146,18 +170,56 @@
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;
}
-
+ 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){
@@ -202,7 +264,7 @@
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;
@@ -226,7 +288,7 @@
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;
@@ -260,13 +322,54 @@
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;
+ int i, idx, polyidx, monoidx, filidx, fonoidx;
char *token[3];
while (child != NULL) {
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -277,9 +380,24 @@
token[2]=strtok(NULL,"\n");
idx=0;
while(token[0]!=NULL){
- vesicle->vlist->vtx[idx]->x=atof(token[0]);
- vesicle->vlist->vtx[idx]->y=atof(token[1]);
- vesicle->vlist->vtx[idx]->z=atof(token[2]);
+ 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++;
@@ -288,34 +406,49 @@
}
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;
}
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
xmlNodePtr child = cur->xmlChildrenNode;
- xmlChar *bonds;
+ xmlChar *bonds, *conname;
char *b;
- int idx;
+ int idx, polyidx;
char *token[2];
while (child != NULL) {
- if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(xmlGetProp(child, (xmlChar *)"Name"), (const xmlChar *)"connectivity") ){
+ 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){
- bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
+ 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);
+ //fprintf(stderr,"Bond data j=%d\n",idx);
return TS_SUCCESS;
}
--
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