From a6b1b556b6c8c8da22c5f322b57ccc1528578e10 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo@andromeda>
Date: Sat, 04 Dec 2010 21:47:44 +0000
Subject: [PATCH] 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 | 2
src/main.c | 5 +
src/io.c | 117 ++++++++++++++++++++------------------
src/tape | 23 +++++++
src/io.h | 3
5 files changed, 91 insertions(+), 59 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index b2da64f..024f250 100644
--- a/src/Makefile.am
+++ b/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
diff --git a/src/io.c b/src/io.c
index 064155c..86d5d02 100644
--- a/src/io.c
+++ b/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;
diff --git a/src/io.h b/src/io.h
index a0d27c6..0dab974 100644
--- a/src/io.h
+++ b/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);
diff --git a/src/main.c b/src/main.c
index b0886f6..a66e81b 100644
--- a/src/main.c
+++ b/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.
diff --git a/src/tape b/src/tape
new file mode 100644
index 0000000..26b4d44
--- /dev/null
+++ b/src/tape
@@ -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
--
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