From e5858ff1dcf5cecfcfe81602f52d255de9d508f4 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 21 Jun 2016 10:49:57 +0000
Subject: [PATCH] Change in location of setting spontaneous curvature. Now it is done in initial_distribution.c, in function set_vesicle_values_from_tape. Also, energy assigning function is done and sweeping of the whole vesicle aswell.
---
src/timestep.c | 5 --
src/io.c | 3 +
src/tape | 10 +++++
src/energy.c | 22 +++++++++++
src/initial_distribution.c | 15 +++++++
src/general.h | 3 +
src/energy.h | 4 ++
src/vertexmove.c | 1
8 files changed, 58 insertions(+), 5 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 4f2b386..cc5ccde 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -185,3 +185,25 @@
return TS_SUCCESS;
}
+
+
+
+ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle){
+ int i;
+ for(i=0;i<vesicle->blist->n;i++){
+ attraction_bond_energy(vesicle->blist->bond[i], vesicle->tape->w);
+ }
+ return TS_SUCCESS;
+}
+
+
+inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w){
+
+ if(fabs(bond->vtx1->c)>1e-16 && fabs(bond->vtx2->c)>1e-16){
+ bond->energy=w;
+ }
+ else {
+ bond->energy=0.0;
+ }
+ return TS_SUCCESS;
+}
diff --git a/src/energy.h b/src/energy.h
index e463815..4d51b24 100644
--- a/src/energy.h
+++ b/src/energy.h
@@ -4,4 +4,8 @@
ts_bool mean_curvature_and_energy(ts_vesicle *vesicle);
inline ts_bool energy_vertex(ts_vertex *vtx);
inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly);
+
+ts_bool sweep_attraction_bond_energy(ts_vesicle *vesicle);
+inline ts_bool attraction_bond_energy(ts_bond *bond, ts_double w);
+
#endif
diff --git a/src/general.h b/src/general.h
index a6f5114..31de50a 100644
--- a/src/general.h
+++ b/src/general.h
@@ -283,6 +283,9 @@
long int mcsweeps;
long int quiet;
long int shc;
+ long int number_of_vertices_with_c0;
+ ts_double c0;
+ ts_double w;
} ts_tape;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 45a4124..0f04e5f 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -110,6 +110,21 @@
else {
vesicle->sphHarmonics=NULL;
}
+
+ int rndvtx;
+ if(tape->number_of_vertices_with_c0>0){
+ ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
+ for(i=0;i<tape->number_of_vertices_with_c0;i++){
+ rndvtx=rand() % vesicle->vlist->n;
+ vesicle->vlist->vtx[rndvtx]->c=tape->c0;
+ }
+ mean_curvature_and_energy(vesicle);
+ if(fabs(tape->w)>1e-16){ //if nonzero energy
+ ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
+ sweep_attraction_bond_energy(vesicle);
+ }
+ }
+
return TS_SUCCESS;
}
diff --git a/src/io.c b/src/io.c
index f0207ac..9c0bb75 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1140,6 +1140,9 @@
CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
CFG_SIMPLE_INT("spherical_harmonics_coefficients",&tape->shc),
+ CFG_SIMPLE_INT("number_of_vertices_with_c0", &tape->number_of_vertices_with_c0),
+ CFG_SIMPLE_FLOAT("c0",&tape->c0),
+ CFG_SIMPLE_FLOAT("w",&tape->w),
CFG_END()
};
cfg_t *cfg;
diff --git a/src/tape b/src/tape
index 0784fac..206d649 100644
--- a/src/tape
+++ b/src/tape
@@ -82,3 +82,13 @@
#max number of processes in distributed (voluntary) environment
distributed_processes=50
#cuda options???
+
+
+#NirGov branch only!
+#number of vertices with spontaneous curvature (integer)
+number_of_vertices_with_c0=200
+#spontaneous curvature (float)
+c0=2.0
+#energy of attraction of vertices with spontaneous curvature
+w=1.0
+
diff --git a/src/timestep.c b/src/timestep.c
index 6328b0f..be14619 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -60,11 +60,6 @@
/* RANDOM SEED SET BY CURRENT TIME */
epochtime=get_epoch();
srand48(epochtime);
-/*Nir Gov: randomly add spontaneous curvature for some vertices */
- for(i=0;i<20;i++){
- int b=rand() % vesicle->vlist->n;
- vesicle->vlist->vtx[b]->c=-0.5;
- }
centermass(vesicle);
cell_occupation(vesicle);
vesicle_volume(vesicle); //needed for constant volume at this moment
diff --git a/src/vertexmove.c b/src/vertexmove.c
index fb74a06..0b6f50a 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -198,6 +198,7 @@
*/
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
+// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
if(exp(-delta_energy)< drand48())
--
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