From 301c87b8a0ae31d97adf840d90dd241ffb3328b6 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 24 May 2016 17:02:48 +0000
Subject: [PATCH] A fix in restoring from snapshot when filaments are used
---
src/tape | 8 ++++----
src/restore.c | 15 ++++++++++++---
2 files changed, 16 insertions(+), 7 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index 643188b..545cc84 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -286,7 +286,7 @@
xmlNodePtr child = cur->xmlChildrenNode;
xmlChar *points;
char *pts;
- int i, idx, polyidx, monoidx;
+ int i, idx, polyidx, monoidx, filidx, fonoidx;
char *token[3];
while (child != NULL) {
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -301,12 +301,19 @@
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 {
+ } 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");
@@ -316,6 +323,7 @@
}
child=child->next;
}
+ fprintf(stderr,"Came here\n");
//fprintf(stderr,"Vertices position j=%d\n",idx);
return TS_SUCCESS;
@@ -340,7 +348,8 @@
}
else {
//find grafted vtx
- if((vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)){
+ 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])];
diff --git a/src/tape b/src/tape
index 620a4a3..12f88cd 100644
--- a/src/tape
+++ b/src/tape
@@ -1,6 +1,6 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
-nshell=10
+nshell=17
# dmax is the max. bond length (in units l_min)
dmax=1.7
# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
@@ -25,7 +25,7 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=0
+npoly=3
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
@@ -33,7 +33,7 @@
####### Filament (inside the vesicle) definitions ###########
# nfil is a number of filaments inside the vesicle
-nfil=0
+nfil=2
# nfono is a number of monomers in each filament
nfono=300
# Persistence lenght of the filaments (in units l_min)
@@ -54,7 +54,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
-mcsweeps=2000
+mcsweeps=20
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
inititer=0
--
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