From b14a8d3d373ab1682a8a713e4f2a3795934d6b26 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 20 Oct 2013 13:36:53 +0000
Subject: [PATCH] Program parameters are finally read from tape. Initial tests are removed
---
src/io.c | 193 ++++++++++++++++++++++++++++++++---------------
1 files changed, 131 insertions(+), 62 deletions(-)
diff --git a/src/io.c b/src/io.c
index 064155c..2127796 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,29 +1,34 @@
-#include<general.h>
+#include "general.h"
#include<stdio.h>
#include "io.h"
-#include "confuse.h"
+#include <confuse.h>
+#include "vertex.h"
+#include "bond.h"
#include<string.h>
+#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>
-
+#include "initial_distribution.h"
ts_bool print_vertex_list(ts_vertex_list *vlist){
ts_uint i;
printf("Number of vertices: %u\n",vlist->n);
for(i=0;i<vlist->n;i++){
- printf("%u: %f %f %f\n", vlist->vertex[i].idx,vlist->vertex[i].x, vlist->vertex[i].y, vlist->vertex[i].z);
+ printf("%u: %f %f %f\n",
+vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
}
return TS_SUCCESS;
}
ts_bool print_vertex_neighbours(ts_vertex_list *vlist){
ts_uint i,j;
- ts_vertex *vtx=vlist->vertex;
+ 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].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("%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");
}
@@ -32,7 +37,7 @@
}
ts_bool write_vertex_fcompat_file(ts_vertex_list *vlist,ts_char *filename){
- ts_vertex *vtx=vlist->vertex;
+ ts_vertex **vtx=vlist->vtx;
ts_uint i;
FILE *fh;
@@ -42,7 +47,7 @@
return TS_FAIL;
}
for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i].x,vtx[i].y, vtx[i].z);
+ fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
fclose(fh);
return TS_SUCCESS;
@@ -52,10 +57,12 @@
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->vertex[i].x,
- vlist->vertex[i].y, vlist->vertex[i].z, vlist->vertex[i].neigh_no);
- for(j=0;j<vlist->vertex[i].neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vlist->vertex[i].neigh[j]-vlist->vertex+1));
+ 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");
}
@@ -64,10 +71,10 @@
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.vertex[i].tristar_no);
- for(j=0;j<vesicle->vlist.vertex[i].tristar_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist.vertex[i].tristar[j]-vesicle->tlist.triangle+1));
+ for(i=0;i<vesicle->vlist->n;i++){
+ 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");
}
@@ -75,20 +82,20 @@
}
ts_bool fprint_triangle_list(FILE *fh, ts_vesicle *vesicle){
- ts_triangle_list *tlist=&vesicle->tlist;
+ ts_triangle_list *tlist=vesicle->tlist;
ts_uint i,j;
for(i=0;i<tlist->n;i++){
- fprintf(fh,"\t%u",tlist->triangle[i].neigh_no);
- for(j=0;j<tlist->triangle[i].neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].neigh[j]-tlist->triangle+1));
+ fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
+ for(j=0;j<tlist->tria[i]->neigh_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1));
}
fprintf(fh,"\n");
for(j=0;j<3;j++){
- fprintf(fh,"\t%u",(ts_uint)(tlist->triangle[i].vertex[j]-vesicle->vlist.vertex+1));
+ fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1));
}
fprintf(fh,"\n");
- fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->triangle[i].xnorm,
-tlist->triangle[i].ynorm,tlist->triangle[i].znorm);
+ fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
+tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
}
return TS_SUCCESS;
@@ -98,14 +105,14 @@
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->vertex[i].xk,vlist->vertex[i].c,vlist->vertex[i].energy,
- vlist->vertex[i].energy_h, vlist->vertex[i].curvature, 0);
- for(j=0;j<vlist->vertex[i].neigh_no;j++){
- fprintf(fh," %.17E", vlist->vertex[i].bond_length_dual[j]);
+ 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->vertex[i].neigh_no;j++){
- fprintf(fh," %.17E", vlist->vertex[i].bond_length[j]);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
}
@@ -114,8 +121,11 @@
ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
ts_uint i;
- for(i=0;i<vesicle->blist.n;i++){
- fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist.bond[i].vtx1-vesicle->vlist.vertex+1),(ts_uint)(vesicle->blist.bond[i].vtx2-vesicle->vlist.vertex+1));
+ for(i=0;i<vesicle->blist->n;i++){
+ fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
+//-vesicle->vlist->vtx+1),
+ (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
+ //-vesicle->vlist.vtx+1));
}
return TS_SUCCESS;
}
@@ -123,17 +133,16 @@
ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
FILE *fh;
- ts_uint i,j;
fh=fopen(filename, "w");
if(fh==NULL){
err("Cannot open file %s for writing");
return TS_FAIL;
}
fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
- fprint_vertex_list(fh,&vesicle->vlist);
+ fprint_vertex_list(fh,vesicle->vlist);
fprint_tristar(fh,vesicle);
fprint_triangle_list(fh,vesicle);
- fprint_vertex_data(fh,&vesicle->vlist);
+ fprint_vertex_data(fh,vesicle->vlist);
fprint_bonds(fh,vesicle);
fclose(fh);
return TS_SUCCESS;
@@ -147,7 +156,7 @@
err("Cannot open file for reading... Nonexistant file?");
return TS_FAIL;
}
- ts_uint retval;
+ ts_uint retval=1;
while(retval!=EOF){
retval=fscanf(fh,"%s",line);
@@ -181,22 +190,23 @@
j=rindex(ent->d_name,'_');
if(j==NULL) continue;
number=strndup(j+1,j-i);
- fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atol(number),ent->d_name);
+ fprintf(fh,"<DataSet timestep=\"%u\" group=\"\" part=\"0\" file=\"%s\"/>\n",atoi(number),ent->d_name);
tstep++;
free(number);
}
}
}
+ free(dir);
fprintf(fh,"</Collection>\n</VTKFile>\n");
fclose(fh);
return TS_SUCCESS;
}
ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno){
- ts_vertex_list *vlist=&vesicle->vlist;
- ts_bond_list *blist=&vesicle->blist;
- ts_vertex *vtx=vlist->vertex;
- ts_uint i,j;
+ ts_vertex_list *vlist=vesicle->vlist;
+ ts_bond_list *blist=vesicle->blist;
+ ts_vertex **vtx=vlist->vtx;
+ ts_uint i;
char filename[255];
FILE *fh;
@@ -211,17 +221,17 @@
fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%u ",vlist->vertex[i].idx);
+ fprintf(fh,"%u ",vtx[i]->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);
+ fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->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);
+ fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
}
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
for (i=2;i<blist->n*2+1;i+=2){
@@ -240,10 +250,10 @@
}
ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text){
- ts_vertex_list *vlist=&vesicle->vlist;
- ts_bond_list *blist=&vesicle->blist;
- ts_vertex *vtx=vlist->vertex;
- ts_uint i,j;
+ ts_vertex_list *vlist=vesicle->vlist;
+ ts_bond_list *blist=vesicle->blist;
+ ts_vertex **vtx=vlist->vtx;
+ ts_uint i;
FILE *fh;
fh=fopen(filename, "w");
@@ -260,12 +270,12 @@
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].x,vtx[i].y, vtx[i].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);
for(i=0;i<blist->n;i++){
- fprintf(fh,"2 %u %u\n",blist->bond[i].vtx1->idx,blist->bond[i].vtx2->idx);
+ fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
}
fprintf(fh,"CELL_TYPES %u\n",blist->n);
for(i=0;i<blist->n;i++)
@@ -276,7 +286,7 @@
fprintf(fh,"LOOKUP_TABLE default\n");
for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i].idx);
+ fprintf(fh,"%u\n",vtx[i]->idx);
fclose(fh);
return TS_SUCCESS;
@@ -284,8 +294,12 @@
-ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
+ts_vesicle *parsetape(ts_uint *iterations){
long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // 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;
*iterations=1000;
cfg_opt_t opts[] = {
@@ -298,28 +312,83 @@
CFG_SIMPLE_INT("nzmax", &nczmax),
CFG_SIMPLE_INT("iterations",iterations),
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;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, "tape_new");
+ retval=cfg_parse(cfg, "tape");
if(retval==CFG_FILE_ERROR){
- fatal("No tape_new file.",100);
+ fatal("No tape file.",100);
}
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
+ ts_vesicle *vesicle;
+ vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
vesicle->nshell=nshell;
vesicle->dmax=dmax*dmax;
vesicle->bending_rigidity=xk0;
vesicle->stepsize=stepsize;
- vesicle->clist.ncmax[0]=ncxmax;
- 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;
+ vesicle->clist->ncmax[0]=ncxmax;
+ vesicle->clist->ncmax[1]=ncymax;
+ vesicle->clist->ncmax[2]=nczmax;
+ vesicle->clist->max_occupancy=8;
+ cfg_free(cfg);
+ free(buf);
+ // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
+ return vesicle;
+
+}
+
+
+ts_bool read_geometry_file(char *fname, ts_vesicle *vesicle){
+ FILE *fh;
+ ts_uint i, nvtx,nedges,ntria;
+ ts_uint vtxi1,vtxi2;
+ float x,y,z;
+ ts_vertex_list *vlist;
+ fh=fopen(fname, "r");
+ if(fh==NULL){
+ err("Cannot open file for reading... Nonexistant file?");
+ return TS_FAIL;
+ }
+ ts_uint retval;
+ retval=fscanf(fh,"%u %u %u",&nvtx, &nedges, &ntria);
+ vesicle->vlist=init_vertex_list(nvtx);
+ vlist=vesicle->vlist;
+ for(i=0;i<nvtx;i++){
+ // 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]->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);
+ bond_add(vesicle->blist,vesicle->vlist->vtx[vtxi1-1],vesicle->vlist->vtx[vtxi2-1]);
+ }
+ //TODO: neighbours from bonds,
+ //TODO: triangles from neigbours
+
+// Don't need to read triangles. Already have enough data
+ /*
+ for(i=0;i<ntria;i++){
+ retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
+ vtxi1=vesicle->blist->vertex1->idx;
+ vtxi2=vesicle->blist->vertex1->idx;
+
+ }
+ */
+ if(retval);
+ fclose(fh);
+
+
+
+ return TS_SUCCESS;
}
--
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