From cc95bd1ca5e69ce13766ca0acea11560531ed620 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 24 May 2016 08:01:55 +0000
Subject: [PATCH] From snapshots, raw tape configuration is extracted and written into tape file and not the rendered one
---
src/initial_distribution.c | 55 +++++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 47 insertions(+), 8 deletions(-)
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index c7eed90..ae7de0b 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include<stdio.h>
@@ -11,6 +12,8 @@
#include "energy.h"
#include "poly.h"
#include "io.h"
+#include "sh.h"
+#include "shcomplex.h"
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
@@ -37,22 +40,53 @@
ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
ts_vesicle *vesicle;
+
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
+ vesicle->tape=tape;
+ set_vesicle_values_from_tape(vesicle);
+ return vesicle;
+}
+
+ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle){
// Nucleus:
- vesicle->R_nucleus=tape->R_nucleus;
+ ts_vertex *vtx;
+ ts_tape *tape=vesicle->tape;
+ vesicle->R_nucleus=tape->R_nucleus*tape->R_nucleus;
+ vesicle->R_nucleusX=tape->R_nucleusX*tape->R_nucleusX;
+ vesicle->R_nucleusY=tape->R_nucleusY*tape->R_nucleusY;
+ vesicle->R_nucleusZ=tape->R_nucleusZ*tape->R_nucleusZ;
+ vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
+
//Initialize grafted polymers (brush):
vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
vesicle->spring_constant=tape->kspring;
poly_assign_spring_const(vesicle);
+
//Initialize filaments (polymers inside the vesicle):
vesicle->filament_list=init_poly_list(tape->nfil,tape->nfono, NULL, vesicle);
-ts_uint i,j;
- for(i=0;i<vesicle->filament_list->n;i++){
- for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ poly_assign_filament_xi(vesicle,tape);
- fprintf(stderr,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z );
+ ts_uint i,j;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){
+ bond_vector(vesicle->filament_list->poly[i]->blist->bond[j]);
+ vesicle->filament_list->poly[i]->blist->bond[j]->bond_length = sqrt(vtx_distance_sq(vesicle->filament_list->poly[i]->blist->bond[j]->vtx1,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2));
+ }
}
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
+ vtx = vesicle->filament_list->poly[i]->vlist->vtx[j];
+ if(vtx->bond_no == 2){
+ vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+ }
+ }
}
+
+ 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);
@@ -61,7 +95,7 @@
vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
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);
+// ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
vesicle->stepsize=tape->stepsize;
vesicle->clist->ncmax[0]=tape->ncxmax;
vesicle->clist->ncmax[1]=tape->ncymax;
@@ -70,8 +104,13 @@
vesicle->pressure= tape->pressure;
vesicle->pswitch=tape->pswitch;
-
- return vesicle;
+ if(tape->shc>0){
+ vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
+ }
+ else {
+ vesicle->sphHarmonics=NULL;
+ }
+ return TS_SUCCESS;
}
--
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