From bfa6c4d2d234dac214ae05855669844255a32979 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 03 Jul 2016 20:46:31 +0000
Subject: [PATCH] Merge branch 'paraview'. This enables view of triangles in paraview.

---
 src/initial_distribution.c |  135 +++++++++++++++++++++++++++++++++++---------
 1 files changed, 107 insertions(+), 28 deletions(-)

diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 382750b..45a4124 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>
@@ -9,34 +10,112 @@
 #include "triangle.h"
 #include "initial_distribution.h"
 #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(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
+	ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
 	ts_bool retval;
-    ts_uint no_vertices=5*nshell*nshell+2;
-
-
-	
-    ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
-
-//TODO: debugging only. Please remove ASAP!
-	vesicle->bending_rigidity=25.0;
-
-    vesicle->nshell=nshell;
-    retval = vtx_set_global_values(vesicle);
-    retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
-    retval = init_vertex_neighbours(vesicle->vlist);
-    vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
+	ts_uint no_vertices=5*nshell*nshell+2;	
+	ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
+	vesicle->nshell=nshell;
+	//retval = vtx_set_global_values(vesicle);
+	retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
+	retval = init_vertex_neighbours(vesicle->vlist);
+	vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
    // retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
-    retval = init_triangles(vesicle);
-    retval = init_triangle_neighbours(vesicle);
-    retval = init_common_vertex_triangle_neighbours(vesicle);
-    retval = init_normal_vectors(vesicle->tlist);
-    retval = mean_curvature_and_energy(vesicle);
- ts_fprintf(stderr,"initial_distribution finished!\n");
+	retval = init_triangles(vesicle);
+	retval = init_triangle_neighbours(vesicle);
+	retval = init_common_vertex_triangle_neighbours(vesicle);
+	retval = init_normal_vectors(vesicle->tlist);
+	retval = mean_curvature_and_energy(vesicle);
+	ts_fprintf(stdout,"initial_distribution finished!\n");
 	if(retval);
 	return vesicle;
 } 
+
+
+
+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:
+	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);
+	poly_assign_filament_xi(vesicle,tape);
+
+	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);
+
+	
+	vesicle->nshell=tape->nshell;
+	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);
+	vesicle->stepsize=tape->stepsize;
+	vesicle->clist->ncmax[0]=tape->ncxmax;
+	vesicle->clist->ncmax[1]=tape->ncymax;
+	vesicle->clist->ncmax[2]=tape->nczmax;
+	vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
+
+	vesicle->pressure= tape->pressure;
+	vesicle->pswitch=tape->pswitch;
+    if(tape->shc>0){
+	    vesicle->sphHarmonics=complex_sph_init(vesicle->vlist,tape->shc);
+    }
+    else {
+        vesicle->sphHarmonics=NULL;
+    }
+    return TS_SUCCESS;
+
+}
+
+
+
 
 
 ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
@@ -47,15 +126,15 @@
 	const ts_double c2= cos(4.0*M_PI/5.0);
 
 	/* Calculates projection lenght of an edge bond to pentagram plane */
-	const ts_double xl0=A0/(2.0*sin(M_PI/5.0));
+	const ts_double xl0=DEF_A0/(2.0*sin(M_PI/5.0));
 #ifdef TS_DOUBLE_DOUBLE
-	const ts_double z0=sqrt(pow(A0,2)-pow(xl0,2));
+	const ts_double z0=sqrt(pow(DEF_A0,2)-pow(xl0,2));
 #endif
 #ifdef TS_DOUBLE_FLOAT
-	const ts_double z0=sqrtf(powf(A0,2)-powf(xl0,2));
+	const ts_double z0=sqrtf(powf(DEF_A0,2)-powf(xl0,2));
 #endif
 #ifdef TS_DOUBLE_LONGDOUBLE
-	const ts_double z0=sqrtl(powl(A0,2)-powl(xl0,2));
+	const ts_double z0=sqrtl(powl(DEF_A0,2)-powl(xl0,2));
 #endif
 //	const z0=sqrt(A0*A0 -xl0*xl0); /* I could use pow function but if pow is used make a check on the float type. If float then powf, if long double use powl */
 
@@ -147,7 +226,7 @@
 	for(i=1;i<=vlist->n;i++){
 		for(j=1;j<=vlist->n;j++){
 			dist2=vtx_distance_sq(vtx[i],vtx[j]);
-			if( (dist2>eps) && (dist2<(A0*A0+eps))){ 
+			if( (dist2>eps) && (dist2<(DEF_A0*DEF_A0+eps))){ 
 	//if it is close enough, but not too much close (solves problem of comparing when i==j)
 				vtx_add_neighbour(vtx[i],vtx[j]);
 			}
@@ -180,7 +259,7 @@
                	dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
                	direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
 // TODO: check if fabs can be used with all floating point types!!
-               	if( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
+               	if( (fabs(dist2-DEF_A0*DEF_A0)<=eps) && (direct>0.0) && (j!=jjj) ){
            			vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
            			jjj=jj;
            			jj=j;
@@ -246,7 +325,7 @@
 				dist=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
 				direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);				
 // TODO: same as above				
-				if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
+				if(fabs(dist-DEF_A0*DEF_A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
 					triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
 				}	
 			}	

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