From 364c3073f652fbc02a9ddf051a381b3fd5ea48e4 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 08 Jul 2014 16:54:41 +0000
Subject: [PATCH] Fixed max occupancy error
---
src/io.c | 151 +++++++++++++++++++++++++++++++++++++++++++++++---
1 files changed, 141 insertions(+), 10 deletions(-)
diff --git a/src/io.c b/src/io.c
index a47bd9a..afdbfee 100644
--- a/src/io.c
+++ b/src/io.c
@@ -10,7 +10,7 @@
#include <dirent.h>
#include "initial_distribution.h"
#include "poly.h"
-
+#include "cell.h"
#include <getopt.h>
#include <sys/stat.h>
#include <sys/types.h>
@@ -36,6 +36,8 @@
fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh);
/* dump poly list */
fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh);
+ /* dump filament list */
+ fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
/*dump vertices*/
@@ -118,6 +120,43 @@
}
}
+
+ /*dump filamentes grandes svinjas */
+ for(i=0;i<vesicle->filament_list->n;i++){
+ fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ }
+
+ /* dump filamentes vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+ /* dump offset for neigh and bond */
+ for(k=0;k<vesicle->filament_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->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ for(k=0;k<vesicle->filament_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->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh);
+ }
+ }
+ }
+ /* dump poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ fwrite(vesicle->filament_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->filament_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->filament_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
@@ -131,7 +170,8 @@
*/
fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
-
+/* write tape information on vesicle */
+ fwrite(vesicle->tape,sizeof(ts_tape),1,fh);
fwrite(&iteration, sizeof(ts_uint),1,fh);
fclose(fh);
return TS_SUCCESS;
@@ -180,6 +220,9 @@
/* 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);
+ /* restore filament list */
+ vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
+ retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh);
/* level 1 complete */
/* prerequisity. Bonds must be malloced before vertexes are recreated */
@@ -322,15 +365,66 @@
}
}
-// 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!
- }
+ /*restore filaments */
+ vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *));
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly));
+ retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh);
+ vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list));
+ retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh);
+ vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list));
+ retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh);
+ /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *));
+ vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *));
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ }
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ }
+ }
+
+
+ /* restore poly vertex(monomer) list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh);
+
+ /* restore neigh and bonds */
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *));
+ for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx];
+ }
+
+ }
+ }
+
+ /* restore poly bonds between monomers list*/
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond));
+ retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh);
+ /* restore vtx1 and vtx2 */
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ retval=fread(&idx,sizeof(ts_uint),1,fh);
+ vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx];
+ }
+ }
+ vesicle->tape=parsetape("tape");
+// recreating space for cells //
+ vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
+ vesicle->clist->max_occupancy=8;
+// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
+// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
retval=fread(iteration,sizeof(ts_uint),1,fh);
if(retval);
fclose(fh);
@@ -821,6 +915,39 @@
+ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){
+ FILE *fh;
+ ts_uint i;
+
+ fh=fopen(filename, "w");
+ if(fh==NULL){
+ err("Cannot open file %s for writing");
+ return TS_FAIL;
+ }
+
+ for(i=0;i<vesicle->tlist->n;i++){
+
+ fprintf(fh,"\ttriangle {");
+ fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n",
+ vesicle->tlist->tria[i]->vertex[0]->x,
+ vesicle->tlist->tria[i]->vertex[0]->y,
+ vesicle->tlist->tria[i]->vertex[0]->z,
+
+ vesicle->tlist->tria[i]->vertex[1]->x,
+ vesicle->tlist->tria[i]->vertex[1]->y,
+ vesicle->tlist->tria[i]->vertex[1]->z,
+
+ vesicle->tlist->tria[i]->vertex[2]->x,
+ vesicle->tlist->tria[i]->vertex[2]->y,
+ vesicle->tlist->tria[i]->vertex[2]->z
+ );
+ }
+
+ fclose(fh);
+ return TS_SUCCESS;
+}
+
+
ts_tape *parsetape(char *filename){
// long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
@@ -840,8 +967,11 @@
CFG_SIMPLE_INT("nfono",&tape->nfono),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
+ CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
+ CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
CFG_SIMPLE_FLOAT("xi",&tape->xi),
@@ -857,6 +987,7 @@
CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
+ CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
CFG_END()
};
cfg_t *cfg;
--
Gitblit v1.9.3