From 314f2dd60176b0f378baa66f5a5514fb15dddabc Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 23 Feb 2012 19:29:55 +0000
Subject: [PATCH] Debugging, but not finished yet! There are still problems in vertex move and extreme points that remain sharp edged.
---
src/main.c | 16 +++++++++++++---
src/io.c | 6 ++++++
src/initial_distribution.c | 6 ++++++
src/vertexmove.c | 12 ++++++------
4 files changed, 31 insertions(+), 9 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index a7a8202..382750b 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -14,8 +14,14 @@
ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
ts_bool retval;
ts_uint no_vertices=5*nshell*nshell+2;
+
+
ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
+
+//TODO: debugging only. Please remove ASAP!
+ vesicle->bending_rigidity=25.0;
+
vesicle->nshell=nshell;
retval = vtx_set_global_values(vesicle);
retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
diff --git a/src/io.c b/src/io.c
index 7421f0d..f993e72 100644
--- a/src/io.c
+++ b/src/io.c
@@ -296,6 +296,8 @@
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!
+ char buf[255];
+ long int brezveze=1;
ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
*iterations=1000;
cfg_opt_t opts[] = {
@@ -308,6 +310,10 @@
CFG_SIMPLE_INT("nzmax", &nczmax),
CFG_SIMPLE_INT("iterations",iterations),
CFG_SIMPLE_BOOL("quiet",&quiet),
+ CFG_SIMPLE_STR("multiprocessing",buf),
+ CFG_SIMPLE_INT("smp_cores",&brezveze),
+ CFG_SIMPLE_INT("cluster_nodes",&brezveze),
+ CFG_SIMPLE_INT("distributed_processes",&brezveze),
CFG_END()
};
cfg_t *cfg;
diff --git a/src/main.c b/src/main.c
index b846658..9112278 100644
--- a/src/main.c
+++ b/src/main.c
@@ -60,13 +60,23 @@
vtx_list_free(vlist1);
printf("Tests complete.\n");
-vesicle=initial_distribution_dipyramid(17,60,60,60,0.15);
+vesicle=initial_distribution_dipyramid(8,60,60,60,0.15);
+//parsetape(vesicle,&i);
+
+//these four must come from parsetype!
+vesicle->dmax=1.67;
+vesicle->stepsize=0.15;
+vesicle->clist->max_occupancy=8;
+vesicle->bending_rigidity=25.0;
+fprintf(stderr,"xk=%f",vesicle->bending_rigidity);
centermass(vesicle);
cell_occupation(vesicle);
-for(i=0;i<100;i++){
+for(i=0;i<10000;i++){
single_timestep(vesicle);
-write_vertex_xml_file(vesicle,i);
+if(i%100==0){
+write_vertex_xml_file(vesicle,i/100);
+}
}
write_master_xml_file("test.pvd");
write_dout_fcompat_file(vesicle,"dout");
diff --git a/src/vertexmove.c b/src/vertexmove.c
index c8ce697..c62aeda 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -16,16 +16,15 @@
*rn){
ts_uint i;
ts_double dist;
- ts_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
-// tvtx->data=init_vertex_data();
ts_bool retval;
ts_uint cellidx;
ts_double xold,yold,zold;
ts_double delta_energy,oenergy;
ts_vertex *ovtx;
+ ts_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
//randomly we move the temporary vertex
- tvtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
+ tvtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
tvtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
tvtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
//check we if some length to neighbours are too much
@@ -33,16 +32,17 @@
dist=vtx_distance_sq(tvtx,vtx->neigh[i]);
if(dist<1.0 || dist>vesicle->dmax) {
vtx_free(tvtx);
+// fprintf(stderr,"Fail 1, dist=%f, vesicle->dmax=%f\n", dist, vesicle->dmax);
return TS_FAIL;
}
}
-//fprintf(stderr,"Was here!\n");
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, tvtx);
//check occupation number
retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
if(retval==TS_FAIL){
vtx_free(tvtx);
+// fprintf(stderr,"Fail 2\n");
return TS_FAIL;
}
@@ -68,7 +68,7 @@
energy_vertex(vtx->neigh[i]);
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
-// fprintf(stderr, "DE=%f\n",delta_energy);
+// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
@@ -101,7 +101,7 @@
//END MONTE CARLOOOOOOO
//TODO: change cell occupation if necessary!
-
+// fprintf(stderr,"Success!!\n");
free(ovtx->bond_length);
free(ovtx->bond_length_dual);
free(ovtx);
--
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