From 6487a03362d35589c286d0660eba123a7ab00535 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 10 May 2021 11:14:04 +0000
Subject: [PATCH] Raj and Yoav session in making multiple protein species
---
src/io.c | 24 ++++++++++++++++++++++++
src/tape | 8 ++++----
src/energy.c | 2 +-
src/initial_distribution.c | 1 +
src/general.h | 1 +
src/restore.c | 23 +++++++++++++++++++++++
6 files changed, 54 insertions(+), 5 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 1dae415..b182a87 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -213,7 +213,7 @@
}
ts_double direct_force_energy(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *vtx_old){
- if(fabs(vtx->c)<1e-15) return 0.0;
+ if(fabs(vtx->direct_interaction_force)<1e-15) return 0.0;
// printf("was here");
if(fabs(vesicle->tape->F)<1e-15) return 0.0;
diff --git a/src/general.h b/src/general.h
index 2dd63d8..d131ca6 100644
--- a/src/general.h
+++ b/src/general.h
@@ -158,6 +158,7 @@
ts_double solAngle;
struct ts_poly *grafted_poly;
struct ts_cluster *cluster;
+ ts_double direct_interaction_force;
};
typedef struct ts_vertex ts_vertex;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 21eda68..756fdae 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -137,6 +137,7 @@
continue;
}
vesicle->vlist->vtx[rndvtx]->c=tape->c0;
+ vesicle->vlist->vtx[rndvtx]->direct_interaction_force=tape->F;
}
mean_curvature_and_energy(vesicle);
if(fabs(tape->w)>1e-16){ //if nonzero energy
diff --git a/src/io.c b/src/io.c
index 8fa652c..034207b 100644
--- a/src/io.c
+++ b/src/io.c
@@ -935,6 +935,30 @@
}
}
fprintf(fh,"</DataArray>\n");
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"direct_interaction_force\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ fprintf(fh,"%.17e ",vtx[i]->direct_interaction_force);
+ }
+ //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]->direct_interaction_force);
+ }
+ }
+ }
+ //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]->direct_interaction_force);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
//here comes additional data. Energy!
fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
diff --git a/src/restore.c b/src/restore.c
index 6e12c1e..9ee9c45 100644
--- a/src/restore.c
+++ b/src/restore.c
@@ -362,6 +362,29 @@
}
xmlFree(values);
}
+ if(!xmlStrcmp(property_name,(const xmlChar *)"direct_interaction_force")){
+ values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
+ vals=(char *)values;
+ token=strtok(vals," ");
+ idx=0;
+ while(token!=NULL){
+ if(idx<vesicle->vlist->n){
+ vesicle->vlist->vtx[idx]->direct_interaction_force=atof(token);
+ } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
+ polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
+ monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
+ vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->direct_interaction_force=atof(token);
+ } else {
+ filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
+ fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
+ //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
+ vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->direct_interaction_force=atof(token);
+ }
+ idx++;
+ token=strtok(NULL," ");
+ }
+ xmlFree(values);
+ }
xmlFree(property_name);
}
diff --git a/src/tape b/src/tape
index d2965a6..f30ddaa 100644
--- a/src/tape
+++ b/src/tape
@@ -30,9 +30,9 @@
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=10
+npoly=0
# nmono is a number of monomers in each polymer
-nmono=20
+nmono=0
# Spring constant between monomers of the polymer
k_spring=800
#set to 1 if half of the polymeres are inside the vesicle
@@ -92,9 +92,9 @@
#number of vertices with spontaneous curvature (integer)
-number_of_vertices_with_c0=0
+number_of_vertices_with_c0=200
#c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float)
-c0=0.5
+c0=1.0
#energy of attraction of vertices with spontaneous curvature (float, positive value for attraction)
w=10.0
#direct force on vesicles with spontaneous curvature (float)
--
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