From ea1cce4c80ddb68c0b46a6873ef3b64cc4a958a1 Mon Sep 17 00:00:00 2001
From: mihaf <miha.fosnaric@gmail.com>
Date: Mon, 24 Mar 2014 16:37:44 +0000
Subject: [PATCH] Added dmin_interspecies.
---
src/cell.c | 6 ++----
src/main.c | 1 +
src/vertex.c | 8 ++++++++
src/io.c | 1 +
src/tape | 10 ++++++----
src/initial_distribution.c | 4 ++++
src/general.h | 3 +++
src/frame.c | 1 +
src/io.h | 1 +
src/vertex.h | 2 ++
10 files changed, 29 insertions(+), 8 deletions(-)
diff --git a/src/cell.c b/src/cell.c
index 97f2fe7..f95ff21 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -44,7 +44,6 @@
}
-//TODO: not debugged at all!
inline ts_uint vertex_self_avoidance(ts_vesicle *vesicle, ts_vertex *vtx){
ts_uint cellidx;
ts_uint ncx, ncy,ncz;
@@ -68,7 +67,6 @@
}
-//TODO: looks ok, but debug anyway in the future
inline ts_bool cell_add_vertex(ts_cell *cell, ts_vertex *vtx){
ts_uint i;
for(i=0;i<cell->nvertex;i++){
@@ -124,7 +122,7 @@
return TS_SUCCESS;
}
-// TODO: compiles ok, but it is completely untested and undebugged. It was debugged before rewrite, but this was long time ago.
+
ts_bool cell_occupation_number_and_internal_proximity(ts_cell_list *clist, ts_uint cellidx, ts_vertex *vtx){
ts_uint ncx,ncy,ncz,remainder,cell_occupation;
ts_uint i,j,k,l,neigh_cidx;
@@ -155,7 +153,7 @@
// fprintf(stderr,"calling dist on vertex %i\n",l);
dist=vtx_distance_sq(clist->cell[neigh_cidx]->vertex[l],vtx);
// fprintf(stderr,"dist was %f\n",dist);
- if(dist<=1.0) return TS_FAIL;
+ if(dist<=1.0 || (dist<=clist->dmin_interspecies && (clist->cell[neigh_cidx]->vertex[l]->id != vtx->id))) return TS_FAIL;
}
}
}
diff --git a/src/frame.c b/src/frame.c
index aeaef21..237aa87 100644
--- a/src/frame.c
+++ b/src/frame.c
@@ -2,6 +2,7 @@
#include "general.h"
#include "cell.h"
#include "frame.h"
+
ts_bool centermass(ts_vesicle *vesicle){
ts_uint i,j, n=vesicle->vlist->n;
ts_vertex **vtx=vesicle->vlist->vtx;
diff --git a/src/general.h b/src/general.h
index 79da2ba..e47ef1c 100644
--- a/src/general.h
+++ b/src/general.h
@@ -48,6 +48,8 @@
/* CONSTANTS */
+#define TS_ID_FILAMENT 1
+
/* DATA TYPES */
/** @brief Sets the default datatype for ts_double
*
@@ -213,6 +215,7 @@
ts_double dcell;
ts_double shift;
ts_double max_occupancy;
+ ts_double dmin_interspecies;
} ts_cell_list;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 3c27e55..a93e2ee 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -69,6 +69,9 @@
}
}
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vertex_list_assign_id(vesicle->filament_list->poly[i]->vlist,TS_ID_FILAMENT);
+ }
// vesicle->spring_constant=tape->kspring;
// poly_assign_spring_const(vesicle);
@@ -76,6 +79,7 @@
vesicle->nshell=tape->nshell;
vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
+ vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
vesicle->bending_rigidity=tape->xk0;
vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
diff --git a/src/io.c b/src/io.c
index 17adda4..a25b16c 100644
--- a/src/io.c
+++ b/src/io.c
@@ -970,6 +970,7 @@
CFG_SIMPLE_INT("nfono",&tape->nfono),
CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus),
CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies),
CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
CFG_SIMPLE_INT("pswitch",&tape->pswitch),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
diff --git a/src/io.h b/src/io.h
index 8118db4..117c9ff 100644
--- a/src/io.h
+++ b/src/io.h
@@ -26,6 +26,7 @@
long int brezveze2;
ts_double xk0;
ts_double dmax;
+ ts_double dmin_interspecies;
ts_double stepsize;
ts_double kspring;
ts_double xi;
diff --git a/src/main.c b/src/main.c
index c052928..fa4b872 100644
--- a/src/main.c
+++ b/src/main.c
@@ -48,6 +48,7 @@
vesicle->pressure=tape->pressure;
vesicle->dmax=tape->dmax*tape->dmax;
poly_assign_filament_xi(vesicle,tape);
+ vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
if(command_line_args.reset_iteration_count) start_iteration=tape->inititer;
else start_iteration++;
diff --git a/src/tape b/src/tape
index bd62b6c..8d589d0 100644
--- a/src/tape
+++ b/src/tape
@@ -3,6 +3,8 @@
nshell=17
# dmax is the max. bond length (in units l_min)
dmax=1.7
+# dmin_interspecies in the min. dist. between different vertex species (in units l_min)
+dmin_interspecies=1
# bending rigidity of the membrane (in units kT)
xk0=10.0
# max step size (in units l_min)
@@ -10,13 +12,13 @@
# Pressure calculations
# (pswitch=1: calc. p*dV energy contribution)
-pswitch = 0
+pswitch = 1
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
-pressure=0.1
+pressure=-2.0
####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=300
+npoly=0
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
@@ -42,7 +44,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
-mcsweeps=500
+mcsweeps=100
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
inititer=0
#how many records do you want on the disk iteration are there in a run?
diff --git a/src/vertex.c b/src/vertex.c
index 38647aa..f733d49 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -6,6 +6,14 @@
#include "bond.h"
#include<stdio.h>
+ts_bool vertex_list_assign_id(ts_vertex_list *vlist, ts_uint id){
+ ts_uint i;
+ for(i=0;i<vlist->n;i++){
+ vlist->vtx[i]->id = id;
+ }
+ return TS_SUCCESS;
+}
+
ts_vertex_list *init_vertex_list(ts_uint N){
ts_int i;
ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
diff --git a/src/vertex.h b/src/vertex.h
index 97775d2..cca12ee 100644
--- a/src/vertex.h
+++ b/src/vertex.h
@@ -1,6 +1,8 @@
#ifndef _VERTEX_H
#define _VERTEX_H
+ts_bool vertex_list_assign_id(ts_vertex_list *vlist, ts_uint id);
+
/** @brief Creates initial vertex list
*
* Allocates memory and initializes the vertices.
--
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