From def8b5262e183297ccee42ebbf9ebdb89c10f44c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 03 Jul 2016 18:21:13 +0000
Subject: [PATCH] restoring vertices with spontaneous curvatures seems to work, however, the dumped energy differs on last few decimal places
---
src/main.c | 1
src/initial_distribution.h | 2 +
src/initial_distribution.c | 17 +++++---
src/restore.h | 1
src/restore.c | 47 +++++++++++++++++++++++
5 files changed, 60 insertions(+), 8 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index d8e917f..dbdd0c4 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -44,6 +44,7 @@
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
vesicle->tape=tape;
set_vesicle_values_from_tape(vesicle);
+ initial_population_with_c0(vesicle,tape);
return vesicle;
}
@@ -111,7 +112,14 @@
vesicle->sphHarmonics=NULL;
}
- int rndvtx;
+
+ return TS_SUCCESS;
+
+}
+
+
+ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
+ int rndvtx,i,j;
if(tape->number_of_vertices_with_c0>0){
ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
j=0;
@@ -133,13 +141,8 @@
sweep_attraction_bond_energy(vesicle);
}
}
-
- return TS_SUCCESS;
-
+ return TS_SUCCESS;
}
-
-
-
ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
diff --git a/src/initial_distribution.h b/src/initial_distribution.h
index b1a20e1..e54ee08 100644
--- a/src/initial_distribution.h
+++ b/src/initial_distribution.h
@@ -15,6 +15,8 @@
ts_vesicle *create_vesicle_from_tape(ts_tape *tape);
ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle);
+
+ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape);
/** Sets the initial position of the vertexes to dipyramid
*
* @param *vlist is a pointer to list of vertices
diff --git a/src/main.c b/src/main.c
index 7c1ff29..8ef8904 100644
--- a/src/main.c
+++ b/src/main.c
@@ -58,6 +58,7 @@
}
fclose(fd);
start_iteration++;
+ write_vertex_xml_file(vesicle,1000);
}
else
ts_fprintf(stdout,"No .status file. The iteration count will start from 0");
diff --git a/src/restore.c b/src/restore.c
index 3a93d3f..24f98fb 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -54,6 +54,10 @@
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)
@@ -318,7 +322,48 @@
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;
diff --git a/src/restore.h b/src/restore.h
index cfc6b66..b05c6a8 100644
--- a/src/restore.h
+++ b/src/restore.h
@@ -9,6 +9,7 @@
ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
+ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
--
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