From a37ba25eb9dc4b99ced8e8dcc3c36b9ed434a262 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 06 Mar 2014 07:58:36 +0000
Subject: [PATCH] Fixed a bug in vertex reinit. Still buggy.
---
src/io.c | 461 ++++++++++++++++++++++++++++++++++++++++++++++++++++-----
1 files changed, 421 insertions(+), 40 deletions(-)
diff --git a/src/io.c b/src/io.c
index 8688067..d022d89 100644
--- a/src/io.c
+++ b/src/io.c
@@ -8,6 +8,314 @@
#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>
+#include "initial_distribution.h"
+#include "poly.h"
+
+
+
+/** DUMP STATE TO DISK DRIVE **/
+
+ts_bool dump_state(ts_vesicle *vesicle){
+
+ /* save current state with wrong pointers. Will fix that later */
+ ts_uint i,j,k;
+ FILE *fh=fopen("dump.bin","wb");
+
+ /* dump vesicle */
+ fwrite(vesicle, sizeof(vesicle),1,fh);
+ /* dump vertex list */
+ fwrite(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
+ /* dump bond list */
+ fwrite(vesicle->blist, sizeof(ts_bond_list),1,fh);
+ /* dump triangle list */
+ fwrite(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
+ /* dump cell list */
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
+ /* dump poly list */
+ fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* level 1 complete */
+
+ /*dump vertices*/
+ for(i=0;i<vesicle->vlist->n;i++){
+ fwrite(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
+ /* dump pointer offsets for:
+ neigh
+ bond
+ tria
+ cell is ignored
+ */
+ for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
+ fwrite(&vesicle->vlist->vtx[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
+ fwrite(&vesicle->vlist->vtx[i]->bond[j]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ fwrite(&vesicle->vlist->vtx[i]->tristar[j]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+
+ /*dump bonds*/
+ for(i=0;i<vesicle->blist->n;i++){
+ fwrite(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
+ /* dump pointer offsets for vtx1 and vtx2 */
+ //off=(ts_ulong)(vesicle->blist->bond[i]->vtx1-vesicle->vlist->vtx[0]);
+ fwrite(&vesicle->blist->bond[i]->vtx1->idx,sizeof(ts_uint),1,fh);
+ //off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
+ fwrite(&vesicle->blist->bond[i]->vtx2->idx,sizeof(ts_uint),1,fh);
+ }
+
+ /*dump triangles*/
+ for(i=0;i<vesicle->tlist->n;i++){
+ fwrite(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
+ /* dump pointer offsets for vertex */
+ fwrite(&vesicle->tlist->tria[i]->vertex[0]->idx,sizeof(ts_uint),1,fh);
+ fwrite(&vesicle->tlist->tria[i]->vertex[1]->idx,sizeof(ts_uint),1,fh);
+ fwrite(&vesicle->tlist->tria[i]->vertex[2]->idx,sizeof(ts_uint),1,fh);
+ /* dump pointer offsets for neigh */
+ for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
+ fwrite(&vesicle->tlist->tria[i]->neigh[j]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+
+
+ /*dump polymeres */
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ }
+
+ /* dump poly vertex(monomer) list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fwrite(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+ /* dump offset for neigh and bond */
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]);
+ fwrite(&vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+ // grafted vtx on vesicle data dump
+ fwrite(&vesicle->poly_list->poly[i]->grafted_vtx->idx, sizeof(ts_uint),1,fh);
+ }
+ /* dump poly bonds between monomers list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ fwrite(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* dump vtx1 and vtx2 offsets */
+ //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh);
+// off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+
+/* pointer offsets for fixing the restored pointers */
+/* need pointers for
+ vlist->vtx
+ blist->bond
+ tlist->tria
+ clist->cell
+ poly_list->poly
+ and for each poly:
+ poly_list->poly->vtx
+ poly_list->poly->bond
+*/
+
+ fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
+
+ fclose(fh);
+ return TS_SUCCESS;
+}
+
+
+/** RESTORE DUMP FROM DISK **/
+ts_vesicle *restore_state(){
+ ts_uint i,j,k;
+ FILE *fh=fopen("dump.bin","rb");
+ ts_uint retval;
+ ts_uint idx;
+
+/* we restore all the data from the dump */
+ /* restore vesicle */
+ ts_vesicle *vesicle=(ts_vesicle *)calloc(1,sizeof(ts_vesicle));
+ retval=fread(vesicle, sizeof(vesicle),1,fh);
+ /* restore vertex list */
+ vesicle->vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
+ retval=fread(vesicle->vlist, sizeof(ts_vertex_list),1,fh);
+ /* restore bond list */
+ vesicle->blist=(ts_bond_list *)malloc(sizeof(ts_bond_list));
+ retval=fread(vesicle->blist, sizeof(ts_bond_list),1,fh);
+ /* restore triangle list */
+ vesicle->tlist=(ts_triangle_list *)malloc(sizeof(ts_triangle_list));
+ retval=fread(vesicle->tlist, sizeof(ts_triangle_list),1,fh);
+ /* restore cell list */
+ vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
+ retval=fread(vesicle->clist, sizeof(ts_cell_list),1,fh);
+ /* restore poly list */
+ vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* level 1 complete */
+
+/* prerequisity. Bonds must be malloced before vertexes are recreated */
+ vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *));
+ for(i=0;i<vesicle->blist->n;i++){
+ vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+/* prerequisity. Triangles must be malloced before vertexes are recreated */
+ vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *));
+ for(i=0;i<vesicle->tlist->n;i++){
+ vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
+}
+/* prerequisity. Vertices must be malloced before vertexes are recreated */
+ vesicle->vlist->vtx=(ts_vertex **)calloc(vesicle->vlist->n,sizeof(ts_vertex *));
+ for(i=0;i<vesicle->vlist->n;i++){
+ vesicle->vlist->vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ /*restore vertices*/
+ for(i=0;i<vesicle->vlist->n;i++){
+ retval=fread(vesicle->vlist->vtx[i],sizeof(ts_vertex),1,fh);
+ /*restore neigh, bond, tristar. Ignoring cell */
+ vesicle->vlist->vtx[i]->neigh=(ts_vertex **)calloc(vesicle->vlist->vtx[i]->neigh_no, sizeof(ts_vertex *));
+ for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[idx];
+ }
+ vesicle->vlist->vtx[i]->bond=(ts_bond **)calloc(vesicle->vlist->vtx[i]->bond_no, sizeof(ts_bond *));
+ for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+/* pointer can be assigned only when list of bonds is fully initialized in memory. Thus bondlist popularization must be done before vertex can reference to it */
+ vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[idx];
+ }
+
+ vesicle->vlist->vtx[i]->tristar=(ts_triangle **)calloc(vesicle->vlist->vtx[i]->tristar_no, sizeof(ts_triangle *));
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+/* same comment as above */
+ vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[idx];
+ }
+
+ }
+
+ /*restore bonds*/
+ // vesicle->blist->bond=(ts_bond **)calloc(vesicle->blist->n,sizeof(ts_bond *)); // done before.
+ for(i=0;i<vesicle->blist->n;i++){
+ // vesicle->blist->bond[i]=(ts_bond *)malloc(sizeof(ts_bond)); //done before.
+ retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[idx];
+ }
+
+ /*restore triangles*/
+// vesicle->tlist->tria=(ts_triangle **)calloc(vesicle->tlist->n,sizeof(ts_triangle *)); // done before
+ for(i=0;i<vesicle->tlist->n;i++){
+ // vesicle->tlist->tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle)); // done before
+ retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
+ /* restore pointers for vertices */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[idx];
+ /* restore pointers for neigh */
+ vesicle->tlist->tria[i]->neigh=(ts_triangle **)malloc(vesicle->tlist->tria[i]->neigh_no*sizeof(ts_triangle *));
+ for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[idx];
+ }
+
+ }
+
+ /*restore cells */
+/*TODO: do we need to recalculate cells here? */
+/* vesicle->clist->cell=(ts_cell **)malloc(vesicle->clist->cellno*sizeof(ts_cell *));
+ for(i=0;i<vesicle->clist->cellno;i++){
+ vesicle->clist->cell[i]=(ts_cell *)malloc(sizeof(ts_cell));
+ retval=fread(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
+ }
+*/
+ /*restore polymeres */
+ vesicle->poly_list->poly = (ts_poly **)calloc(vesicle->poly_list->n,sizeof(ts_poly *));
+ for(i=0;i<vesicle->poly_list->n;i++){
+ vesicle->poly_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
+ retval=fread(vesicle->poly_list->poly[i],sizeof(ts_poly),1,fh);
+ vesicle->poly_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+ retval=fread(vesicle->poly_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ vesicle->poly_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
+ retval=fread(vesicle->poly_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
+ vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ vesicle->poly_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ vesicle->poly_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+
+ }
+
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ retval=fread(vesicle->poly_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+
+ /* restore neigh and bonds */
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[idx];
+ }
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
+ for(k=0;k<vesicle->poly_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[idx];
+ }
+
+ }
+ /* restore grafted vtx on vesicle and grafted_poly */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->vlist->vtx[idx]->grafted_poly=vesicle->poly_list->poly[i];
+ vesicle->poly_list->poly[i]->grafted_vtx=vesicle->vlist->vtx[idx];
+ }
+
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->poly_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx];
+ }
+ }
+
+// recreating space for cells //
+ vesicle->clist=(ts_cell_list *)malloc(sizeof(ts_cell_list));
+ retval=fread(vesicle->clist, sizeof(ts_cell_list), 1,fh);
+ vesicle->clist->cell=(ts_cell **)malloc(sizeof(ts_cell *)*vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2]);
+ for(i=0;i<vesicle->clist->ncmax[0]*vesicle->clist->ncmax[1]*vesicle->clist->ncmax[2];i++){
+ vesicle->clist->cell[i]=(ts_cell *)calloc(1,sizeof(ts_cell));
+ vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
+ }
+
+ if(retval);
+ fclose(fh);
+ return vesicle;
+}
+
ts_bool print_vertex_list(ts_vertex_list *vlist){
@@ -15,7 +323,7 @@
printf("Number of vertices: %u\n",vlist->n);
for(i=0;i<vlist->n;i++){
printf("%u: %f %f %f\n",
-vlist->vtx[i]->idx,vlist->vtx[i]->data->x, vlist->vtx[i]->data->y, vlist->vtx[i]->data->z);
+vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
}
return TS_SUCCESS;
}
@@ -25,10 +333,10 @@
ts_vertex **vtx=vlist->vtx;
printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
for(i=0;i<vlist->n;i++){
- printf("%u(%u): ",vtx[i]->idx,vtx[i]->data->neigh_no);
- for(j=0;j<vtx[i]->data->neigh_no;j++){
- printf("(%f,%f,%f)",vtx[i]->data->neigh[j]->data->x,
-vtx[i]->data->neigh[j]->data->y,vtx[i]->data->neigh[j]->data->z);
+ printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
+ for(j=0;j<vtx[i]->neigh_no;j++){
+ printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
+vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
}
printf("\n");
}
@@ -47,7 +355,7 @@
return TS_FAIL;
}
for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
fclose(fh);
return TS_SUCCESS;
@@ -57,11 +365,11 @@
ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
ts_uint i,j;
for(i=0;i<vlist->n;i++){
- fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->data->x,
- vlist->vtx[i]->data->y, vlist->vtx[i]->data->z,
- vlist->vtx[i]->data->neigh_no);
- for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->data->neigh[j]->idx));
+ fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
+ vlist->vtx[i]->y, vlist->vtx[i]->z,
+ vlist->vtx[i]->neigh_no);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
//-vlist->vtx+1));
}
fprintf(fh,"\n");
@@ -72,9 +380,9 @@
ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
ts_uint i,j;
for(i=0;i<vesicle->vlist->n;i++){
- fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->data->tristar_no);
- for(j=0;j<vesicle->vlist->vtx[i]->data->tristar_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->data->tristar[j]->idx));//-vesicle->tlist->tria+1));
+ fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
}
fprintf(fh,"\n");
}
@@ -105,14 +413,14 @@
ts_uint i,j;
for(i=0;i<vlist->n;i++){
fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
- vlist->vtx[i]->data->xk,vlist->vtx[i]->data->c,vlist->vtx[i]->data->energy,
- vlist->vtx[i]->data->energy_h, vlist->vtx[i]->data->curvature, 0);
- for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->bond_length_dual);
+ vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
+ vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
}
fprintf(fh,"\n");
- for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->bond_length);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
}
@@ -206,7 +514,7 @@
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;
@@ -217,29 +525,72 @@
return TS_FAIL;
}
/* Here comes header of the file */
+
+ //find number of extra vtxs and bonds of polymeres
+ ts_uint monono=0, polyno=0, poly_idx=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){
+ poly_idx=vlist->n;
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%u ", poly_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]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ 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){
+ poly_idx=vlist->n;
+ 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);
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+i*monono,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+i*monono);
+ }
+ //grafted bonds
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx+vlist->n+i*monono);
+ }
+
+ }
+
+
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 ");
}
@@ -270,7 +621,7 @@
fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
fprintf(fh,"POINTS %u double\n", vlist->n);
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
@@ -286,7 +637,7 @@
fprintf(fh,"LOOKUP_TABLE default\n");
for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i]->data->idx);
+ fprintf(fh,"%u\n",vtx[i]->idx);
fclose(fh);
return TS_SUCCESS;
@@ -294,20 +645,35 @@
-ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
- long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
- ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
- *iterations=1000;
+ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
+ long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20; // THIS IS DUE TO CONFUSE BUG!
+ char *buf=malloc(255*sizeof(char));
+ long int brezveze0=1;
+ long int brezveze1=1;
+ long int brezveze2=1;
+ ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
+ long int iter=1000, init=1000, mcsw=1000;
+
+
cfg_opt_t opts[] = {
CFG_SIMPLE_INT("nshell", &nshell),
+ CFG_SIMPLE_INT("npoly", &npoly),
+ CFG_SIMPLE_INT("nmono", &nmono),
CFG_SIMPLE_FLOAT("dmax", &dmax),
CFG_SIMPLE_FLOAT("xk0",&xk0),
+ CFG_SIMPLE_FLOAT("k_spring",&kspring),
CFG_SIMPLE_FLOAT("stepsize",&stepsize),
CFG_SIMPLE_INT("nxmax", &ncxmax),
CFG_SIMPLE_INT("nymax", &ncymax),
CFG_SIMPLE_INT("nzmax", &nczmax),
- CFG_SIMPLE_INT("iterations",iterations),
+ CFG_SIMPLE_INT("iterations",&iter),
+ CFG_SIMPLE_INT("mcsweeps",&mcsw),
+ CFG_SIMPLE_INT("inititer", &init),
CFG_SIMPLE_BOOL("quiet",&quiet),
+ CFG_SIMPLE_STR("multiprocessing",buf),
+ CFG_SIMPLE_INT("smp_cores",&brezveze0),
+ CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
+ CFG_SIMPLE_INT("distributed_processes",&brezveze2),
CFG_END()
};
cfg_t *cfg;
@@ -320,6 +686,16 @@
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
+ ts_vesicle *vesicle;
+ *iterations=iter;
+ *inititer=init;
+ *mcsweeps=mcsw;
+ vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
+ vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
+ vesicle->spring_constant=kspring;
+ poly_assign_spring_const(vesicle);
+
+
vesicle->nshell=nshell;
vesicle->dmax=dmax*dmax;
vesicle->bending_rigidity=xk0;
@@ -328,9 +704,14 @@
vesicle->clist->ncmax[1]=ncymax;
vesicle->clist->ncmax[2]=nczmax;
vesicle->clist->max_occupancy=8;
+
cfg_free(cfg);
-// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
- return TS_SUCCESS;
+ free(buf);
+ // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
+
+
+
+ return vesicle;
}
@@ -351,11 +732,11 @@
vesicle->vlist=init_vertex_list(nvtx);
vlist=vesicle->vlist;
for(i=0;i<nvtx;i++){
- // fscanf(fh,"%F %F %F",&vlist->vtx[i]->data->x,&vlist->vtx[i]->data->y,&vlist->vtx[i]->data->z);
+ // fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
retval=fscanf(fh,"%F %F %F",&x,&y,&z);
- vlist->vtx[i]->data->x=x;
- vlist->vtx[i]->data->y=y;
- vlist->vtx[i]->data->z=z;
+ vlist->vtx[i]->x=x;
+ vlist->vtx[i]->y=y;
+ vlist->vtx[i]->z=z;
}
for(i=0;i<nedges;i++){
retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
@@ -368,8 +749,8 @@
/*
for(i=0;i<ntria;i++){
retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
- vtxi1=vesicle->blist->data->vertex1->idx;
- vtxi2=vesicle->blist->data->vertex1->idx;
+ vtxi1=vesicle->blist->vertex1->idx;
+ vtxi2=vesicle->blist->vertex1->idx;
}
*/
--
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