From 60c2b879f26c5f008af0df7d7f159d33077225ac Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:47:16 +0000
Subject: [PATCH] Cleanup of stretching energy plugin
---
src/poly.c | 267 +++++++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 226 insertions(+), 41 deletions(-)
diff --git a/src/poly.c b/src/poly.c
index 1ddcec7..bcf01e5 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include"general.h"
#include"poly.h"
#include<stdlib.h>
@@ -5,6 +6,18 @@
#include"bond.h"
#include<math.h>
#include"energy.h"
+#include"cell.h"
+#include"frame.h"
+ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
+ ts_uint i;
+
+ for(i=0;i<vesicle->filament_list->n;i++){
+ vesicle->filament_list->poly[i]->k = tape->xi;
+ }
+
+ return TS_SUCCESS;
+}
+
ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
ts_uint i;
@@ -20,8 +33,10 @@
ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly));
poly->vlist = init_vertex_list(n);
poly->blist = init_bond_list();
- poly->grafted_vtx = grafted_vtx;
- grafted_vtx->grafted_poly = poly;
+ if (grafted_vtx!=NULL){
+ poly->grafted_vtx = grafted_vtx;
+ grafted_vtx->grafted_poly = poly;
+ }
ts_uint i;
for(i=0;i<n-1;i++){
@@ -33,55 +48,185 @@
poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
bond_energy(poly->blist->bond[i],poly);
}
-
+ vertex_list_assign_id(poly->vlist,TS_ID_FILAMENT);
return poly;
}
-ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist){
+
+ts_bool poly_initial_distribution(ts_poly_list *poly_list, ts_int i, ts_vesicle *vesicle){
+ /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
+ ts_double xnorm,ynorm,znorm,normlength;
+ ts_int intpoly=vesicle->tape->internal_poly;
+ ts_int cellidx;
+ ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
+ ts_bool retval;
+ ts_int j,k,l,m;
+ xnorm=0.0;
+ ynorm=0.0;
+ znorm=0.0;
+ for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
+ xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
+ ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
+ znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
+ }
+ normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ if(intpoly && i%2){
+ normlength=-normlength;
+ }
+ xnorm=xnorm/normlength;
+ ynorm=ynorm/normlength;
+ znorm=znorm/normlength;
+ //prepare starting position for building the polymeres
+ prevPosX=poly_list->poly[i]->grafted_vtx->x;
+ prevPosY=poly_list->poly[i]->grafted_vtx->y;
+ prevPosZ=poly_list->poly[i]->grafted_vtx->z;
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ //if(j==0){
+ posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
+ posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
+ posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
+ //}else{
+ // posX=prevPosX+xnorm;
+ // posY=prevPosY+ynorm;
+ // posZ=prevPosZ+znorm;
+ //}
+ //trying to go towards normal
+ k=0;
+ while(1){
+ poly_list->poly[i]->vlist->vtx[j]->x = posX;
+ poly_list->poly[i]->vlist->vtx[j]->y = posY;
+ poly_list->poly[i]->vlist->vtx[j]->z = posZ;
+ cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[j]);
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);
+ if(retval==TS_SUCCESS){
+ retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
+ break;
+ }
+ else{
+ // printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
+ //randomly change the direction.
+ m=0;
+ //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
+ do{
+ costheta=2.0*drand48()-1.0;
+ sintheta=sqrt(1-pow(costheta,2));
+ phi=drand48()*2.0*M_PI;
+ if(j==0){
+ //for special cases, when we are on the edge of bipyramid the distance od dmin_interspecies is not enough
+ posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
+ posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
+ posZ=prevPosZ+vesicle->dmax*costheta;
+
+ } else {
+ posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
+ posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
+ posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
+ }
+ m++;
+ if(m>1000) {
+ k=9999; //break also ot of the outer loop
+ printf("was here\n");
+ break;
+ }
+ }
+ while((xnorm*(poly_list->poly[i]->grafted_vtx->x-posX)+ynorm*(poly_list->poly[i]->grafted_vtx->y-posY)+znorm*(poly_list->poly[i]->grafted_vtx->z-posZ))>0.0 && j==0);
+ }
+ k++;
+ if(k>1000){
+ //undo changes to the cell
+ for(l=0;l<j;l++){
+ cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[l]);
+ cell_remove_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[l]);
+ }
+ return TS_FAIL;
+ }
+ }
+ prevPosX=posX;
+ prevPosY=posY;
+ prevPosZ=posZ;
+ }
+ printf("did it\n");
+ return TS_SUCCESS;
+
+}
+
+
+ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
- ts_uint i=0,j=0, idx;
+ ts_uint i=0,j=0; //idx;
ts_uint gvtxi;
- ts_double xnorm,ynorm,znorm,normlength;
-
- if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
-
- while(i<n_poly){
- gvtxi = rand() % vlist->n;
- if (vlist->vtx[gvtxi]->grafted_poly == NULL){
- poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
- i++;
+ ts_bool retval;
+ ts_double dphi,dh;
+ cell_occupation(vesicle); //needed for evading the membrane
+ // Grafting polymers:
+ int tries=0;
+ if (vlist!=NULL){
+ if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
+ while(i<n_poly){
+ gvtxi = rand() % vlist->n;
+ if (vlist->vtx[gvtxi]->grafted_poly == NULL){
+ poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
+ retval=poly_initial_distribution(poly_list, i, vesicle);
+ if(retval==TS_FAIL){
+ ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
+ poly_free(poly_list->poly[i]);
+ tries++;
+ }
+ else {
+ tries=0;
+ i++;
+ }
+ if(tries>5000){
+ fatal("Cannot find space for inner polymeres",1001);
+ }
+ }
}
}
-
+ else
+ {
+ for(i=0;i<n_poly;i++){
+ poly_list->poly[i] = init_poly(n_mono, NULL);
+ }
+ }
+
poly_list->n = n_poly;
-/* Make straight poylmers normal to membrane. Dist. between poly vertices put to 1*/
- for (i=0;i<poly_list->n;i++){
+ if (vlist!=NULL){
+ }
+ else
+ {
+ /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
+ ts_double a,R,H,tantheta,h,r,phi,A0=1.2;
- xnorm=0.0;
- ynorm=0.0;
- znorm=0.0;
- for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
- xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
- ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
- znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
- }
- normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
- xnorm=xnorm/normlength;
- ynorm=ynorm/normlength;
- znorm=znorm/normlength;
-
- for (j=0;j<poly_list->poly[i]->vlist->n;j++){
- poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
+ a = A0*(ts_double)vesicle->nshell;
+ R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0));
+ H = sqrt(a*a - R*R);
+ tantheta = sqrt(R*R - a*a/4.0)/H;
+
+ h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5;
+ r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
+ dphi = 2.0*asin(1.0/2.0/r)*1.001;
+ dh = dphi/2.0/M_PI*1.001;
+ phi=0.0;
+ for(i=0;i<poly_list->n;i++){
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ h = h + dh;
+ r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
+ dphi = 2.0*asin(1.0/2.0/r)*1.001;
+ dh = dphi/2.0/M_PI*1.001;
+ phi+=dphi;
+ //ji = j + i*poly_list->poly[i]->vlist->n;
+ poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi);
+ poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi);
+ poly_list->poly[i]->vlist->vtx[j]->z = h;// ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
+ }
}
}
//index correction for polymeres. Important, since each vtx has to have unique id
- idx=vlist->n;
+/* idx=vlist->n;
for(i=0;i<n_poly;i++){
for(j=0;j<n_mono;j++,idx++){
@@ -89,17 +234,17 @@
}
}
-
-
+*/
+
return poly_list;
}
ts_bool poly_free(ts_poly *poly){
- if (poly->grafted_vtx!=NULL){
- poly->grafted_vtx->grafted_poly=NULL;
- }
+// if (poly->grafted_vtx!=NULL){
+// poly->grafted_vtx->grafted_poly=NULL;
+// }
vtx_list_free(poly->vlist);
bond_list_free(poly->blist);
free(poly);
@@ -109,8 +254,9 @@
ts_bool poly_list_free(ts_poly_list *poly_list){
ts_uint i;
-
+ //fprintf(stderr,"no. of polys=%d\n", poly_list->n);
for(i=0;i<poly_list->n;i++){
+ // fprintf(stderr,"%d poly address in mem=%ld\n",i+1,(long)&(poly_list->poly[i]));
poly_free(poly_list->poly[i]);
}
free(poly_list->poly);
@@ -118,3 +264,42 @@
return TS_SUCCESS;
}
+
+
+ts_poly *remove_poly_with_index(ts_poly_list *poly_list, ts_uint idx){
+ ts_uint i;
+ ts_poly *removed_poly=poly_list->poly[idx];
+
+ poly_list->n--; //decrease the total number of polymeres
+ for(i=idx;i<poly_list->n;i++){ //move the rest of the polymeres up.
+ poly_list->poly[i]=poly_list->poly[i+1];
+// poly_list->poly[idx]->idx=idx;
+ }
+
+ return removed_poly;
+}
+
+
+ts_bool remove_random_polymeres(ts_poly_list *poly_list, ts_uint number){
+
+ ts_uint i, idx;
+ ts_poly *poly;
+
+ ts_poly **new_poly_array;
+ if(number>poly_list->n) fatal("The number of polymeres to be removed from the list is greater than the number of total polymeres in the list",999);
+ for(i=number;i>0;i--){
+ idx=rand() % poly_list->n;
+ poly=remove_poly_with_index(poly_list, idx);
+ poly_free(poly);
+ }
+ printf("Addr before %ld\n", (long)poly_list->poly);
+ new_poly_array=(ts_poly **)calloc(poly_list->n,sizeof(ts_poly *));
+ for(i=0;i<poly_list->n;i++){
+ new_poly_array[i]=poly_list->poly[i];
+ }
+ free(poly_list->poly);
+ poly_list->poly=new_poly_array;
+ printf("Addr after %ld\n", (long)poly_list->poly);
+ return TS_SUCCESS;
+}
+
--
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