From f6bc99c334f6481e40f547d0e91f771b9564aa38 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 05 Jul 2016 10:09:08 +0000
Subject: [PATCH] Merge branch 'clustercount' into nirgov
---
src/Makefile.am | 4
src/cluster.c | 155 ++++++++++++++++++++++++++++++++++++++
src/general.h | 17 ++++
src/cluster.h | 8 ++
4 files changed, 181 insertions(+), 3 deletions(-)
diff --git a/src/Makefile.am b/src/Makefile.am
index fb2c46b..04ad1c7 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,5 +1,5 @@
bin_PROGRAMS = trisurf tsmeasure
-trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c
+trisurf_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c main.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c
GITVERSION:=$(shell git --no-pager describe --tags --always --dirty)
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline
AM_CPPFLAGS = ${libxml2_CFLAGS} -fgnu89-inline
@@ -18,7 +18,7 @@
#spherical_trisurf_ff_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c frame.c energy.c timestep.c vertexmove.c spherical_trisurf_ff.c sh.c bondflip.c poly.c stats.c shcomplex.c
-tsmeasure_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c tsmeasure.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c
+tsmeasure_SOURCES = general.c vertex.c bond.c triangle.c cell.c vesicle.c initial_distribution.c io.c dumpstate.c frame.c energy.c timestep.c vertexmove.c bondflip.c tsmeasure.c poly.c stats.c sh.c shcomplex.c constvol.c snapshot.c restore.c cluster.c
tsmeasure_LDADD = ${libcurl_LIBS} ${libxml2_LIBS}
#gitversion.c: .git/HEAD .git/index
# echo "const char *gitversion = \"$(shell git rev-parse HEAD)\";" > $@
diff --git a/src/cluster.c b/src/cluster.c
new file mode 100644
index 0000000..9a43183
--- /dev/null
+++ b/src/cluster.c
@@ -0,0 +1,155 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
+#include<stdlib.h>
+#include "general.h"
+#include "cluster.h"
+#include <math.h>
+
+
+
+
+ts_cluster_list *init_cluster_list(){
+ ts_cluster_list *cstlist=(ts_cluster_list *)malloc(sizeof(ts_cluster_list));
+ cstlist->n=0;
+ cstlist->cluster=NULL;
+ return cstlist;
+}
+
+ts_cluster *new_cluster(ts_cluster_list *cstlist){
+
+ cstlist->n++;
+ cstlist->cluster=(ts_cluster **)realloc(cstlist->cluster,cstlist->n*sizeof(ts_cluster *));
+ if(cstlist->cluster==NULL) fatal("Cannot reallocate memory for additional **ts_cluster.",100);
+ cstlist->cluster[cstlist->n-1]=(ts_cluster *)calloc(1,sizeof(ts_cluster));
+ if(cstlist->cluster[cstlist->n-1]==NULL) fatal("Cannot allocate memory for additional *ts_cluster.",100);
+ return cstlist->cluster[cstlist->n-1];
+}
+
+ts_bool cluster_add_vertex(ts_cluster *cluster, ts_vertex *vtx){
+ cluster->nvtx++;
+ cluster->vtx=(ts_vertex **)realloc(cluster->vtx, cluster->nvtx*sizeof(ts_vertex *));
+ cluster->vtx[cluster->nvtx-1]=vtx;
+ vtx->cluster=cluster;
+ return TS_SUCCESS;
+}
+
+ts_bool cluster_list_compact(ts_cluster_list *cstlist){
+
+
+ ts_uint i,n=cstlist->n;
+
+ for(i=0;i<cstlist->n;i++){
+ if(cstlist->cluster[i]==NULL){
+ do{
+ n--;
+ } while(cstlist->cluster[n]==NULL && n>i);
+ if(i<=n) break;
+ cstlist->cluster[i]=cstlist->cluster[n];
+ cstlist->cluster[n]=NULL;
+ }
+ }
+ cstlist->cluster=(ts_cluster **)realloc(cstlist->cluster,n*sizeof(ts_cluster *));
+ cstlist->n=n;
+ return TS_SUCCESS;
+}
+
+
+ts_bool cluster_join(ts_cluster *cluster1, ts_cluster *cluster2){
+ ts_cluster *master_cluster,*slave_cluster;
+ ts_uint i;
+ if(cluster1->idx<cluster2->idx){
+ master_cluster=cluster1;
+ slave_cluster=cluster2;
+ } else {
+ master_cluster=cluster2;
+ slave_cluster=cluster1;
+ }
+ for(i=0;i<slave_cluster->nvtx;i++){
+ cluster_add_vertex(master_cluster,slave_cluster->vtx[i]);
+ }
+ cluster_free(slave_cluster);
+ slave_cluster=NULL;
+ return TS_SUCCESS;
+}
+
+ts_bool cluster_free(ts_cluster *cluster){
+ if(cluster!=NULL){
+ if(cluster->vtx!=NULL)
+ free(cluster->vtx);
+ free(cluster);
+ }
+ return TS_SUCCESS;
+}
+
+ts_bool cluster_list_free(ts_cluster_list *cstlist){
+ ts_uint i;
+ if(cstlist!=NULL){
+ for(i=0;i<cstlist->n;i++){
+ cluster_free(cstlist->cluster[i]);
+ }
+ free(cstlist->cluster);
+ free(cstlist);
+ }
+ return TS_SUCCESS;
+}
+
+
+/* This is a stub function. User should check whether the vertex is clustering or not. */
+ts_bool is_clusterable(ts_vertex *vtx){
+
+return 1;
+}
+
+
+ts_cluster *cluster_vertex_neighbor(ts_vertex *vtx){
+ int j;
+ for(j=0;j<vtx->neigh_no;j++){
+ if(vtx->neigh[j]->cluster!=NULL)
+ return vtx->neigh[j]->cluster;
+ }
+ return NULL;
+}
+
+ts_bool cluster_vertex_neighbor_check(ts_vertex *vtx){
+
+ int j;
+ for(j=0;j<vtx->neigh_no;j++){
+ if(vtx->neigh[j]->cluster!=NULL){
+ if(vtx->neigh[j]->cluster!=vtx->cluster){
+ cluster_join(vtx->cluster, vtx->neigh[j]->cluster);
+ }
+ }
+ }
+ return TS_SUCCESS;
+}
+
+
+ts_bool clusterize_vesicle(ts_vesicle *vesicle, ts_cluster_list *cstlist){
+
+ int i;
+ ts_vertex *vtx;
+ ts_cluster *cst;
+ for(i=0;i<vesicle->vlist->n;i++){
+ //for each vertex
+ vtx=vesicle->vlist->vtx[i];
+ if(is_clusterable(vtx)){
+ if(vtx->cluster!=NULL){
+ //find first neigbor with cluster index
+ cst=cluster_vertex_neighbor(vtx);
+ if(cst==NULL){
+ //no clusters are around us, vo we are probably lonely vertex or no surronding vertex has been mapped yet.
+ cst=new_cluster(cstlist);
+ cluster_add_vertex(cst,vtx);
+ } else {
+ //we are added to the first cluster found
+ cluster_add_vertex(cst,vtx);
+ cluster_vertex_neighbor_check(vtx);
+ cluster_list_compact(cstlist);
+ }
+
+ }
+ }
+ }
+
+
+ return TS_SUCCESS;
+}
diff --git a/src/cluster.h b/src/cluster.h
new file mode 100644
index 0000000..5250628
--- /dev/null
+++ b/src/cluster.h
@@ -0,0 +1,8 @@
+#ifndef _H_CLUSTER
+#define _H_CLUSTER
+ts_cluster_list *init_cluster_list();
+ts_cluster *new_cluster(ts_cluster_list *cstlist);
+ts_bool cluster_add_vertex(ts_cluster *cluster, ts_vertex *vtx);
+ts_bool cluster_free(ts_cluster *cluster);
+ts_bool cluster_list_free(ts_cluster_list *cstlist);
+#endif
diff --git a/src/general.h b/src/general.h
index 31de50a..9fefc5b 100644
--- a/src/general.h
+++ b/src/general.h
@@ -156,7 +156,8 @@
ts_double projArea;
ts_double relR;
ts_double solAngle;
- struct ts_poly *grafted_poly;
+ struct ts_poly *grafted_poly;
+ struct ts_cluster *cluster;
};
typedef struct ts_vertex ts_vertex;
@@ -322,6 +323,20 @@
+struct ts_cluster{
+ ts_uint nvtx;
+ ts_uint idx;
+ ts_vertex **vtx;
+};
+
+typedef struct ts_cluster ts_cluster;
+
+typedef struct{
+ ts_uint n;
+ ts_cluster **cluster;
+} ts_cluster_list;
+
+
/* GLOBAL VARIABLES */
int quiet;
--
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