From 142a67fe82b830e5c7816914afa62445959c87ca Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 05 Nov 2013 14:04:21 +0000
Subject: [PATCH] changes in bondflip call. No need to bondflip all the bonds, but only as many bonds as there are vertices. Also, rnvec seems to be not needed for bondflip, so it is commented out
---
src/io.c | 151 ++++++++++++++++++++++++++++++++++++--------------
1 files changed, 109 insertions(+), 42 deletions(-)
diff --git a/src/io.c b/src/io.c
index 86d5d02..9e278ec 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,19 +1,21 @@
-#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->vtx[i]->idx,vlist->vtx[i]->data->x, vlist->vtx[i]->data->y, vlist->vtx[i]->data->z);
+vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
}
return TS_SUCCESS;
}
@@ -23,10 +25,10 @@
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]->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("%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");
}
@@ -45,7 +47,7 @@
return TS_FAIL;
}
for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
fclose(fh);
return TS_SUCCESS;
@@ -55,11 +57,11 @@
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->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));
+ 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");
@@ -70,9 +72,9 @@
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->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,"\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");
}
@@ -83,17 +85,17 @@
ts_triangle_list *tlist=vesicle->tlist;
ts_uint i,j;
for(i=0;i<tlist->n;i++){
- 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,"\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->tria[i]->data->vertex[j]->idx));//-vesicle->vlist->vtx+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->tria[i]->data->xnorm,
-tlist->tria[i]->data->ynorm,tlist->tria[i]->data->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;
@@ -103,14 +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->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);
+ 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->vtx[i]->data->neigh_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->data->bond_length);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
}
@@ -120,9 +122,9 @@
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]->data->vtx1->idx),
+ 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]->data->vtx2->idx));
+ (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
//-vesicle->vlist.vtx+1));
}
return TS_SUCCESS;
@@ -194,6 +196,7 @@
}
}
}
+ free(dir);
fprintf(fh,"</Collection>\n</VTKFile>\n");
fclose(fh);
return TS_SUCCESS;
@@ -223,12 +226,12 @@
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]->data->x,vtx[i]->data->y, vtx[i]->data->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]->data->vtx1->idx,blist->bond[i]->data->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){
@@ -267,12 +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]->data->x,vtx[i]->data->y, vtx[i]->data->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]->data->vtx1->idx,blist->bond[i]->data->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++)
@@ -283,7 +286,7 @@
fprintf(fh,"LOOKUP_TABLE default\n");
for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i]->data->idx);
+ fprintf(fh,"%u\n",vtx[i]->idx);
fclose(fh);
return TS_SUCCESS;
@@ -291,10 +294,14 @@
-ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
+ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, 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;
+ long int iter=1000, init=1000, mcsw=1000;
cfg_opt_t opts[] = {
CFG_SIMPLE_INT("nshell", &nshell),
CFG_SIMPLE_FLOAT("dmax", &dmax),
@@ -303,8 +310,14 @@
CFG_SIMPLE_INT("nxmax", &ncxmax),
CFG_SIMPLE_INT("nymax", &ncymax),
CFG_SIMPLE_INT("nzmax", &nczmax),
- CFG_SIMPLE_INT("iterations",iterations),
+ CFG_SIMPLE_INT("iterations",&iter),
+ CFG_SIMPLE_INT("mcsweeps",&mcsw),
+ CFG_SIMPLE_INT("inititer", &init),
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;
@@ -317,6 +330,11 @@
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
+ ts_vesicle *vesicle;
+ *iterations=iter;
+ *inititer=init;
+ *mcsweeps=mcsw;
+ vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
vesicle->nshell=nshell;
vesicle->dmax=dmax*dmax;
vesicle->bending_rigidity=xk0;
@@ -325,8 +343,57 @@
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;
+ 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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