From a2db521649cdcdfef3bdf6b306e05228a01498c0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 07 Dec 2013 09:45:07 +0000
Subject: [PATCH] Added poly information to tape& parsing function. Also, poly_list is freed in vesicle_free
---
src/io.c | 102 +++++++++++++++++++++++++++++++--------------------
1 files changed, 62 insertions(+), 40 deletions(-)
diff --git a/src/io.c b/src/io.c
index d062137..aaac102 100644
--- a/src/io.c
+++ b/src/io.c
@@ -8,14 +8,15 @@
#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>
-
+#include "initial_distribution.h"
+#include "poly.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;
}
@@ -25,10 +26,10 @@
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");
}
@@ -47,7 +48,7 @@
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;
@@ -57,11 +58,11 @@
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");
@@ -72,9 +73,9 @@
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");
}
@@ -105,14 +106,14 @@
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");
}
@@ -122,9 +123,9 @@
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;
@@ -226,12 +227,12 @@
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){
@@ -270,12 +271,12 @@
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++)
@@ -286,7 +287,7 @@
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;
@@ -294,20 +295,32 @@
-ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
- long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
+ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
+ long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20; // 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_INT("npoly", &npoly),
+ CFG_SIMPLE_INT("nmono", &nmono),
CFG_SIMPLE_FLOAT("dmax", &dmax),
CFG_SIMPLE_FLOAT("xk0",&xk0),
CFG_SIMPLE_FLOAT("stepsize",&stepsize),
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;
@@ -320,6 +333,13 @@
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->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
+
vesicle->nshell=nshell;
vesicle->dmax=dmax*dmax;
vesicle->bending_rigidity=xk0;
@@ -328,9 +348,11 @@
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;
+ free(buf);
+ // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
+ return vesicle;
}
@@ -351,11 +373,11 @@
vesicle->vlist=init_vertex_list(nvtx);
vlist=vesicle->vlist;
for(i=0;i<nvtx;i++){
- // fscanf(fh,"%F %F %F",&vlist->vtx[i]->data->x,&vlist->vtx[i]->data->y,&vlist->vtx[i]->data->z);
+ // 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]->data->x=x;
- vlist->vtx[i]->data->y=y;
- vlist->vtx[i]->data->z=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);
@@ -368,8 +390,8 @@
/*
for(i=0;i<ntria;i++){
retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
- vtxi1=vesicle->blist->data->vertex1->idx;
- vtxi2=vesicle->blist->data->vertex1->idx;
+ vtxi1=vesicle->blist->vertex1->idx;
+ vtxi2=vesicle->blist->vertex1->idx;
}
*/
--
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