From 5c64e2bc9d28240b5308882af2e6cf7505d444b6 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 07 Jun 2016 19:14:09 +0000
Subject: [PATCH] Fixed energy calculations
---
src/timestep.c | 4 ++--
src/io.c | 29 ++++++++++++++++++++++++++++-
src/tape | 6 ++++--
3 files changed, 34 insertions(+), 5 deletions(-)
diff --git a/src/io.c b/src/io.c
index 39dc1e0..f0207ac 100644
--- a/src/io.c
+++ b/src/io.c
@@ -862,7 +862,7 @@
xml_trisurf_data(fh,vesicle);
fprintf(fh, " <UnstructuredGrid>\n");
fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1));
- fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
+ fprintf(fh,"<PointData Scalars=\"vertices_idx\">\n<DataArray type=\"Int64\" Name=\"vertices_idx\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
@@ -914,6 +914,33 @@
}
fprintf(fh,"</DataArray>\n");
+ //here comes additional data. Energy!
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ fprintf(fh,"%.17e ",vtx[i]->energy*vtx[i]->xk);
+ }
+ //polymeres
+ if(poly){
+ poly_idx=vlist->n;
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->energy* vesicle->poly_list->poly[i]->k);
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ // fprintf(stderr,"was here\n");
+ fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->energy* vesicle->filament_list->poly[i]->k);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
+
+
fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
diff --git a/src/tape b/src/tape
index 59cc09c..0784fac 100644
--- a/src/tape
+++ b/src/tape
@@ -21,7 +21,7 @@
constvolprecision=1e-14
#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea)
-constareaswitch=2
+constareaswitch=0
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
@@ -37,7 +37,7 @@
# nfono is a number of monomers in each filament
nfono=300
# Persistence lenght of the filaments (in units l_min)
-xi=0
+xi=100
####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
@@ -69,6 +69,8 @@
#shut up if we are using cluster!!!
quiet=false
+
+
#what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto)
#currently only none makes sense.
diff --git a/src/timestep.c b/src/timestep.c
index 6972015..6328b0f 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -61,9 +61,9 @@
epochtime=get_epoch();
srand48(epochtime);
/*Nir Gov: randomly add spontaneous curvature for some vertices */
- for(i=0;i<200;i++){
+ for(i=0;i<20;i++){
int b=rand() % vesicle->vlist->n;
- vesicle->vlist->vtx[b]->c=-0.1;
+ vesicle->vlist->vtx[b]->c=-0.5;
}
centermass(vesicle);
cell_occupation(vesicle);
--
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