From 4891eb093f61d37056c50c572e669349dd49a65a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 31 May 2016 19:33:33 +0000
Subject: [PATCH] Nucleus translates with the vesicle. Dump and restore includes optional <nucleus> tag within <trisurf> tag if the nucleus is present at all.
---
src/main.c | 1 +
src/snapshot.c | 8 +++++++-
src/general.h | 1 +
src/restore.h | 2 +-
src/frame.c | 4 ++++
src/restore.c | 15 +++++++++++++++
src/snapshot.h | 2 +-
7 files changed, 30 insertions(+), 3 deletions(-)
diff --git a/src/frame.c b/src/frame.c
index b29d3e3..d81ba7e 100644
--- a/src/frame.c
+++ b/src/frame.c
@@ -42,6 +42,10 @@
vesicle->filament_list->poly[i]->vlist->vtx[j]->z-=vesicle->cm[2];
}
}
+//move nucleus for the same vector as we moved vesicle
+ vesicle->nucleus_center[0]-=vesicle->cm[0];
+ vesicle->nucleus_center[1]-=vesicle->cm[1];
+ vesicle->nucleus_center[2]-=vesicle->cm[2];
vesicle->cm[0]=0.0;
vesicle->cm[1]=0.0;
diff --git a/src/general.h b/src/general.h
index dccee34..a6f5114 100644
--- a/src/general.h
+++ b/src/general.h
@@ -313,6 +313,7 @@
ts_double R_nucleusX;
ts_double R_nucleusY;
ts_double R_nucleusZ;
+ ts_double nucleus_center[3];
ts_double area;
} ts_vesicle;
diff --git a/src/main.c b/src/main.c
index ac92fd5..1fe6618 100644
--- a/src/main.c
+++ b/src/main.c
@@ -55,6 +55,7 @@
}
fclose(fd);
start_iteration++;
+ printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
}
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 14586c6..196df76 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -165,6 +165,9 @@
if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
parseTrisurfTristar(vesicle, doc, child);
}
+ if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
+ parseTrisurfNucleus(vesicle, doc, child);
+ }
child = child->next;
}
@@ -179,6 +182,18 @@
/* Low level tags parsers */
+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){
diff --git a/src/restore.h b/src/restore.h
index 821f5a2..934d6e8 100644
--- a/src/restore.h
+++ b/src/restore.h
@@ -11,5 +11,5 @@
ts_bool parseTrisurfTristar(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);
#endif
diff --git a/src/snapshot.c b/src/snapshot.c
index cabb1f8..8b71e83 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -32,6 +32,7 @@
xml_trisurf_tria_neigh(data,vesicle->tlist);
xml_trisurf_vtx_neigh(data,vesicle->vlist);
xml_trisurf_vtx_tristar(data,vesicle->vlist);
+ xml_trisurf_nucleus(data,vesicle);
#ifdef COMPRESSION
char *compressed;
ts_uint nbytes=ts_compress_string64(data->string, data->beg-1, &compressed); //suppress null character at the end with by substracting 1
@@ -124,7 +125,12 @@
return TS_SUCCESS;
}
-
+ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle){
+ if(vesicle->R_nucleus>0.0 || (vesicle->R_nucleusX>0.0 && vesicle->R_nucleusY>0.0 && vesicle->R_nucleusZ>0.0)){
+ ts_sprintf(data,"<nucleus>%.17e %.17e %.7e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
+ }
+ return TS_SUCCESS;
+}
/* UTILITIES */
diff --git a/src/snapshot.h b/src/snapshot.h
index e4642e9..0db57f4 100644
--- a/src/snapshot.h
+++ b/src/snapshot.h
@@ -18,7 +18,7 @@
ts_bool xml_trisurf_tria_neigh(ts_string *data, ts_triangle_list *tlist);
ts_bool xml_trisurf_vtx_neigh(ts_string *data, ts_vertex_list *vlist);
ts_bool xml_trisurf_vtx_tristar(ts_string *data, ts_vertex_list *vlist);
-
+ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle);
/* UTILITIES */
char *base64_encode(const unsigned char *data, size_t input_length, size_t *output_length);
unsigned char *base64_decode(const char *data, size_t input_length, size_t *output_length);
--
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