From 06afc729f9061c1cfa14c78728d61d518324c2f0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 04 May 2022 05:46:43 +0000
Subject: [PATCH] Moved all global variables to separate file and defined extern keyword where appropriate

---
 src/restore.c |  287 +++++++++++++++++++++++++++++++++++++++++++++++++--------
 1 files changed, 247 insertions(+), 40 deletions(-)

diff --git a/src/restore.c b/src/restore.c
index 94e2621..1d4d7f8 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>
@@ -12,15 +13,18 @@
 #include "triangle.h"
 #include "bond.h"
 #include "energy.h"
+#include "poly.h"
 #include "initial_distribution.h"
+#include "io.h"
+#include <math.h>
+#include "globals.h"
 
-ts_bool parseDump(char *dumpfname) {
+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);
 	}
@@ -37,6 +41,11 @@
 	
 	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);
 		}
@@ -47,15 +56,20 @@
 				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)
-								parseXMLVertexPosition(vesicle, doc, cur);
+								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, cur);
+								parseXMLBonds(vesicle, doc, cur2);
 						}
 						cur2=cur2->next;
 					}	
@@ -66,24 +80,39 @@
 		// 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 */
 
-/* TODO: cells, polymeres, filaments, core, tape */
+//	ts_fprintf(stdout,"Restoration completed\n");
+//	write_vertex_xml_file(vesicle,999);
+//	vesicle_free(vesicle);
+//	exit(0);
+	return vesicle;
+}
 
-	fprintf(stderr,"Restoration completed\n");
-	exit(0);
-	vesicle_free(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
@@ -113,23 +142,26 @@
     	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);
-	//vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
+	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);
+	vesicle->poly_list=init_empty_poly_list(atoi((char *)npoly),atoi((char *)nmono));
 	xmlFree(nvtx);
 	xmlFree(npoly);
-	xmlFree(nfono);
+	xmlFree(nmono);
 
 	child = cur->xmlChildrenNode;
 	while (child != NULL) {
@@ -139,21 +171,61 @@
 		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);
 		}
+		 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){
 
@@ -187,14 +259,42 @@
 	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;
@@ -228,54 +328,161 @@
 	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);		
+			}
+			if(!xmlStrcmp(property_name,(const xmlChar *)"direct_interaction_force")){
+				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]->direct_interaction_force=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]->direct_interaction_force=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]->direct_interaction_force=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"))){
 			points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
 			pts=(char *)points;
-			for(i=0;i<3;i++)	token[i]=strtok(pts," ");
+			token[0]=strtok(pts," ");
+			token[1]=strtok(NULL," ");
+			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]);
-				for(i=0;i<3;i++)	token[i]=strtok(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;
+	xmlChar *bonds, *conname;
 	char *b;
-	int i, idx;
+	int idx, polyidx;
 	char *token[2];
+	int temp_cnt=0;
 	while (child != NULL) {
-		if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
+		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;
-			for(i=0;i<2;i++)	token[i]=strtok(b," ");
+			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])]);
-				for(i=0;i<2;i++)	token[i]=strtok(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->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])];
+						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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