Finished rewriting io.c. Output for paraview works. Tape parser doesn't wor...

Samo Penic

2010-12-04 a6b1b556b6c8c8da22c5f322b57ccc1528578e10

Finished rewriting io.c. Output for paraview works. Tape parser doesn't work
because of problems in some function declaration. Will repair tomorrow.

 src/Makefile.am

@@ -1,5 +1,5 @@
trisurfdir=../
trisurf_PROGRAMS=trisurf
trisurf_SOURCES=general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c main.c
trisurf_SOURCES=general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c main.c
trisurf_LDFLAGS = -lm -lconfuse
trisurf_CFLAGS = -Wall -Werror

 src/io.c

@@ -3,6 +3,7 @@
#include "io.h"
#include "confuse.h"
#include<string.h>
#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>

@@ -11,19 +12,21 @@
    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]->data->x, vlist->vtx[i]->data->y, vlist->vtx[i]->data->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]->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("\n");
    }
@@ -32,7 +35,7 @@
}

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 +45,7 @@
        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]->data->x,vtx[i]->data->y, vtx[i]->data->z);

    fclose(fh);
return TS_SUCCESS;
@@ -52,10 +55,12 @@
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]->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));
        //-vlist->vtx+1));
        }
        fprintf(fh,"\n");
    }
@@ -64,10 +69,10 @@

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]->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,"\n");
    }
@@ -75,20 +80,20 @@
}

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]->data->neigh_no);
        for(j=0;j<tlist->tria[i]->data->neigh_no;j++){
            fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->data->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]->data->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]->data->xnorm,
tlist->tria[i]->data->ynorm,tlist->tria[i]->data->znorm);
        fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
    }
    return TS_SUCCESS;
@@ -98,14 +103,14 @@
    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]->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]->data->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]->data->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->data->bond_length);
        }
            fprintf(fh,"\n");
    }
@@ -114,8 +119,11 @@

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]->data->vtx1->idx),
//-vesicle->vlist->vtx+1),
        (ts_uint)(vesicle->blist->bond[i]->data->vtx2->idx));
    //-vesicle->vlist.vtx+1));
    }
    return TS_SUCCESS;
}
@@ -123,17 +131,16 @@

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 +154,7 @@
                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);
        
@@ -181,7 +188,7 @@
                    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);
            }  
@@ -193,10 +200,10 @@
}

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 +218,17 @@
    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]->data->x,vtx[i]->data->y, vtx[i]->data->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]->data->vtx1->idx,blist->bond[i]->data->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 +247,10 @@
}

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 +267,12 @@
    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]->data->x,vtx[i]->data->y, vtx[i]->data->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]->data->vtx1->idx,blist->bond[i]->data->vtx2->idx);
    }
    fprintf(fh,"CELL_TYPES %u\n",blist->n);
    for(i=0;i<blist->n;i++)
@@ -276,7 +283,7 @@
    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]->data->idx);

    fclose(fh);
    return TS_SUCCESS;
@@ -303,9 +310,9 @@
    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);
@@ -314,10 +321,10 @@
    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;
    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;

 src/io.h

@@ -46,7 +46,8 @@
 *    @param *text is a description line (max. 255 characters) to be included in the file
 */
ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text);

ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno);
ts_bool write_master_xml_file(ts_char *filename);
ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations);



 src/main.c

@@ -6,7 +6,7 @@
#include "triangle.h"
#include "cell.h"
#include "vesicle.h"
//#include "io.h"
#include "io.h"
#include "initial_distribution.h"

/** Entrance function to the program
@@ -56,7 +56,8 @@
printf("Tests complete.\n");

vesicle=initial_distribution_dipyramid(7,10,10,10,0.3);

write_vertex_xml_file(vesicle,0);
write_master_xml_file("test.pvd");
vesicle_free(vesicle);

return 0; //program finished perfectly ok. We return 0.

 src/tape

New file
@@ -0,0 +1,23 @@
####### Vesicle definitions ###########
# nshell is a number of divisions of dipyramid
nshell=20
# dmax is the square of the bond length 
dmax=1.67
# bending rigidity of the membrane 
xk0=25.0
# max step size 
stepsize=0.15


#######  Cell definitions ############
nxmax=60
nymax=60
nzmax=60


####### Program Control ############
#how many iteration are there in a run?
iterations=20000

#shut up if we are using cluster!!!
quiet=false