From e9eab4fb2f72383a1a2adbe5f09f7bbd1fd45768 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Wed, 05 Mar 2014 16:00:30 +0000
Subject: [PATCH] First step in dump and restore. Grafted vtx still missing in the process
---
src/main.c | 11 +
src/io.c | 322 +++++++++++++++++++++++++++++++++++++++++++++++++++++
src/io.h | 2
3 files changed, 335 insertions(+), 0 deletions(-)
diff --git a/src/io.c b/src/io.c
index 8b51793..8ebfb97 100644
--- a/src/io.c
+++ b/src/io.c
@@ -11,6 +11,328 @@
#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;
+ ts_ulong off;
+ 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++){
+ off=(ts_ulong)(vesicle->vlist->vtx[i]->neigh[j]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->bond_no;j++){
+ off=(ts_ulong)(vesicle->vlist->vtx[i]->bond[j]-vesicle->blist->bond[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ off=(ts_ulong)(vesicle->vlist->vtx[i]->tristar[j]-vesicle->tlist->tria[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+// off=(ts_ulong)(vesicle->vlist->vtx[i]->cell-vesicle->clist->cell[0]);
+// fwrite(&off,sizeof(ts_ulong),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(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->blist->bond[i]->vtx2-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),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 */
+ off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[0]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[1]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->tlist->tria[i]->vertex[2]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ /* dump pointer offsets for neigh */
+ for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
+ off=(ts_ulong)(vesicle->tlist->tria[i]->neigh[j]-vesicle->tlist->tria[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ }
+
+ /*dump cells and its contents is not dumped but recalculated on restore*/
+
+/* for(i=0;i<vesicle->clist->cellno;i++){
+ fwrite(vesicle->clist->cell[i],sizeof(ts_cell),1,fh);
+ for(j=0;j<vesicle->clist->cell[i]->nvertex;j++){
+ off=(ts_ulong)(vesicle->clist->cell[i]->vertex[j]-vesicle->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),1,fh);
+ }
+ }
+*/
+
+
+ /*dump polymeres */
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i],sizeof(ts_poly),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(&off,sizeof(ts_ulong),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(&off,sizeof(ts_ulong),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(&off,sizeof(ts_ulong),1,fh);
+ off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]);
+ fwrite(&off,sizeof(ts_ulong),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->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
+ fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
+ fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
+ fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),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_ulong off;
+
+/* 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 */
+
+ /*restore vertices*/
+ 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));
+ 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(&off,sizeof(ts_ulong),1,fh);
+ vesicle->vlist->vtx[i]->neigh[j]=vesicle->vlist->vtx[0]+off;
+ }
+ 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(&off,sizeof(ts_ulong),1,fh);
+ vesicle->vlist->vtx[i]->bond[j]=vesicle->blist->bond[0]+off;
+ }
+
+ 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(&off,sizeof(ts_ulong),1,fh);
+ vesicle->vlist->vtx[i]->tristar[j]=vesicle->tlist->tria[0]+off;
+ }
+
+ }
+
+ /*restore bonds*/
+ 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));
+ retval=fread(vesicle->blist->bond[i],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->blist->bond[i]->vtx1=vesicle->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->blist->bond[i]->vtx2=vesicle->vlist->vtx[0]+off;
+ }
+
+ /*restore triangles*/
+ 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));
+ retval=fread(vesicle->tlist->tria[i],sizeof(ts_triangle),1,fh);
+ /* restore pointers for vertices */
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->vertex[0]=vesicle->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->vertex[1]=vesicle->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->vertex[2]=vesicle->vlist->vtx[0]+off;
+ /* restore pointers for neigh */
+ for(j=0;j<vesicle->tlist->tria[i]->neigh_no;j++){
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->tlist->tria[i]->neigh[j]=vesicle->tlist->tria[0]+off;
+ }
+
+ }
+
+ /*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);
+ }
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ vesicle->poly_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->poly_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ 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));
+ 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(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ }
+ 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(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->poly_list->poly[i]->blist->bond[0]+off;
+ }
+
+ }
+ }
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->poly_list->n;i++){
+ 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]->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(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ retval=fread(&off,sizeof(ts_ulong),1,fh);
+ vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[0]+off;
+ }
+ }
+
+
+ /* recalculate pointers using saved information on pointer addresses */
+ /* following pointers need to be recalculated:
+ all vtx->neigh
+ all vtx->tristar
+ all vtx->bond
+ vtx->cell
+ vtx->grafted_poly
+ bond->vtx1
+ bond->vtx2
+ tria->vertex[*]
+ tria->neigh
+ cell->vertex
+ poly->grafted_vtx
+ poly->vlist->vtx->neigh
+ poly->vlist->vtx->bond
+ poly->vlist->vtx->cell
+ */
+
+ /* read pointers from disk */
+/* fwrite(vesicle->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->blist->bond, sizeof(ts_bond *),1,fh);
+ fwrite(vesicle->tlist->tria, sizeof(ts_triangle *),1,fh);
+ fwrite(vesicle->clist->cell, sizeof(ts_cell *),1,fh);
+ fwrite(vesicle->poly_list->poly, sizeof(ts_poly *),1,fh);
+ for(i=0;i<vesicle->poly_list->n;i++){
+ fwrite(vesicle->poly_list->poly[i]->vlist->vtx, sizeof(ts_vertex *),1,fh);
+ fwrite(vesicle->poly_list->poly[i]->blist->bond, sizeof(ts_bond *),1,fh);
+ }
+*/
+
+
+ if(retval);
+ fclose(fh);
+ return vesicle;
+}
+
+
+
ts_bool print_vertex_list(ts_vertex_list *vlist){
ts_uint i;
printf("Number of vertices: %u\n",vlist->n);
diff --git a/src/io.h b/src/io.h
index 20eab38..7ac2160 100644
--- a/src/io.h
+++ b/src/io.h
@@ -50,4 +50,6 @@
ts_bool write_master_xml_file(ts_char *filename);
ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations);
+ts_bool dump_state(ts_vesicle *vesicle);
+ts_vesicle *restore_state();
#endif
diff --git a/src/main.c b/src/main.c
index 53f4b0e..941daaf 100644
--- a/src/main.c
+++ b/src/main.c
@@ -71,6 +71,17 @@
//poly_list_free(vesicle->poly_list);
/*End testing*/
+printf("Vertex %d ima x komponento %e\n",123,vesicle->vlist->vtx[123]->x);
+dump_state(vesicle);
+vesicle->vlist->vtx[123]->x=123.0;
+printf("Vertex %d ima x komponento %e\n",123,vesicle->vlist->vtx[123]->x);
+write_vertex_xml_file(vesicle,0);
+vesicle=restore_state();
+printf("Stevilo vertexov je %d\n",vesicle->vlist->n);
+printf("Vertex %d ima x komponento %e\n",123,vesicle->vlist->vtx[123]->x);
+write_vertex_xml_file(vesicle,1);
+write_master_xml_file("test.pvd");
+return 0;
run_simulation(vesicle, mcsweeps, inititer, iterations);
--
Gitblit v1.9.3