From 40aa5b1bea828225a582b191600996f0674b2760 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 07 Dec 2013 14:14:28 +0000
Subject: [PATCH] Finished io.c. Changes made also in poly.c to accomodate unique indexing of all vertices for purpose of visualization
---
src/poly.c | 19 +++++++--
src/io.c | 53 ++++++++++++++++++++++++--
src/tape | 8 ++--
3 files changed, 68 insertions(+), 12 deletions(-)
diff --git a/src/io.c b/src/io.c
index aaac102..81ab298 100644
--- a/src/io.c
+++ b/src/io.c
@@ -207,7 +207,7 @@
ts_vertex_list *vlist=vesicle->vlist;
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
- ts_uint i;
+ ts_uint i,j;
char filename[255];
FILE *fh;
@@ -218,29 +218,69 @@
return TS_FAIL;
}
/* Here comes header of the file */
+
+ //find number of extra vtxs and bonds of polymeres
+ ts_uint monono=0, polyno=0;
+ ts_bool poly=0;
+ if(vesicle->poly_list!=NULL){
+ if(vesicle->poly_list->poly[0]!=NULL){
+ polyno=vesicle->poly_list->n;
+ monono=vesicle->poly_list->poly[0]->vlist->n;
+ poly=1;
+ }
+ }
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
+ }
+ }
+ }
fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ }
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ }
+ }
}
fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
for(i=0;i<blist->n;i++){
fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
}
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
+ }
+ //grafted bonds
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
+ }
+
+ }
+
+
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<blist->n*2+1;i+=2){
+ for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n;i++){
+ for (i=0;i<blist->n+monono*polyno;i++){
fprintf(fh,"3 ");
}
@@ -303,6 +343,8 @@
long int brezveze2=1;
ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
long int iter=1000, init=1000, mcsw=1000;
+
+
cfg_opt_t opts[] = {
CFG_SIMPLE_INT("nshell", &nshell),
CFG_SIMPLE_INT("npoly", &npoly),
@@ -352,6 +394,9 @@
cfg_free(cfg);
free(buf);
// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
+
+
+
return vesicle;
}
diff --git a/src/poly.c b/src/poly.c
index 20529e2..05566d0 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -26,7 +26,7 @@
ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist){
ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
- ts_uint i=0,j=0;
+ ts_uint i=0,j=0, idx;
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
@@ -49,9 +49,9 @@
ynorm=0.0;
znorm=0.0;
for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
- xnorm+=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
- ynorm+=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
- znorm+=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
+ xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
+ ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
+ znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
}
normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
xnorm=xnorm/normlength;
@@ -65,6 +65,17 @@
}
}
+ //index correction for polymeres. Important, since each vtx has to have unique id
+ idx=vlist->n;
+ for(i=0;i<n_poly;i++){
+ for(j=0;j<n_mono;j++,idx++){
+
+ poly_list->poly[i]->vlist->vtx[j]->idx=idx;
+
+ }
+ }
+
+
return poly_list;
}
diff --git a/src/tape b/src/tape
index e0d0dee..55973b6 100644
--- a/src/tape
+++ b/src/tape
@@ -10,7 +10,7 @@
####### Polymer definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=1000
+npoly=10
# nmono is a number of monomers in each polymere
nmono=15
@@ -22,11 +22,11 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
-mcsweeps=100
+mcsweeps=10
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
-inititer=100
+inititer=1
#how many records do you want on the disk iteration are there in a run?
-iterations=1000
+iterations=100
#shut up if we are using cluster!!!
--
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