/* vim: set ts=4 sts=4 sw=4 noet : */
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#include<stdlib.h>
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#include<math.h>
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#include "general.h"
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#include "vertex.h"
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#include "bond.h"
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#include "triangle.h"
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#include "vesicle.h"
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#include "energy.h"
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#include "timestep.h"
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#include "cell.h"
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//#include "io.h"
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#include "io.h"
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#include<stdio.h>
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#include "vertexmove.h"
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#include <string.h>
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#include "constvol.h"
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ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn){
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ts_uint i;
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ts_double dist;
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ts_bool retval;
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ts_uint cellidx;
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ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
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ts_double costheta,sintheta,phi,r;
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//This will hold all the information of vtx and its neighbours
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ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
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memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
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//Some stupid tests for debugging cell occupation!
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/* cellidx=vertex_self_avoidance(vesicle, vtx);
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if(vesicle->clist->cell[cellidx]==vtx->cell){
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fprintf(stderr,"Idx match!\n");
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} else {
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fprintf(stderr,"***** Idx don't match!\n");
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fatal("ENding.",1);
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}
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*/
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//temporarly moving the vertex
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// vtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
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// vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
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// vtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
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//random move in a sphere with radius stepsize:
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r=vesicle->stepsize*rn[0];
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phi=rn[1]*2*M_PI;
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costheta=2*rn[2]-1;
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sintheta=sqrt(1-pow(costheta,2));
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vtx->x=vtx->x+r*sintheta*cos(phi);
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vtx->y=vtx->y+r*sintheta*sin(phi);
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vtx->z=vtx->z+r*costheta;
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//distance with neighbours check
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for(i=0;i<vtx->neigh_no;i++){
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dist=vtx_distance_sq(vtx,vtx->neigh[i]);
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if(dist<1.0 || dist>vesicle->dmax) {
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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return TS_FAIL;
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}
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}
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// Distance with grafted poly-vertex check:
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if(vtx->grafted_poly!=NULL){
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dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
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if(dist<1.0 || dist>vesicle->dmax) {
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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return TS_FAIL;
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}
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}
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// TODO: Maybe faster if checks only nucleus-neighboring cells
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// Nucleus penetration check:
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//#define SQ(x) x*x
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if(vesicle->R_nucleus>0.0){
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if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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return TS_FAIL;
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}
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} else if(vesicle->R_nucleusX>0.0){
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// fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
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// if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
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if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
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// if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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return TS_FAIL;
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}
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}
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//#undef SQ
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//self avoidance check with distant vertices
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cellidx=vertex_self_avoidance(vesicle, vtx);
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//check occupation number
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retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
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if(retval==TS_FAIL){
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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return TS_FAIL;
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}
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//if all the tests are successful, then energy for vtx and neighbours is calculated
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for(i=0;i<vtx->neigh_no;i++){
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memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
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}
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if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
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for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
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}
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if(vesicle->tape->constareaswitch==2){
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for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
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}
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delta_energy=0;
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// vesicle_volume(vesicle);
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// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
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//update the normals of triangles that share bead i.
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for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
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oenergy=vtx->energy;
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energy_vertex(vtx);
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delta_energy=vtx->xk*(vtx->energy - oenergy);
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//the same is done for neighbouring vertices
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for(i=0;i<vtx->neigh_no;i++){
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oenergy=vtx->neigh[i]->energy;
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energy_vertex(vtx->neigh[i]);
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delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
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}
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if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch >0){
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for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
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if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
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};
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if(vesicle->tape->constareaswitch==2){
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/* check whether the darea is gt epsarea */
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for(i=0;i<vtx->tristar_no;i++) darea+=vtx->tristar[i]->area;
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if(fabs(vesicle->area+darea-A0)>epsarea){
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//restore old state.
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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for(i=0;i<vtx->neigh_no;i++){
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vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
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}
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for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
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//fprintf(stderr,"fajlam!\n");
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return TS_FAIL;
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}
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}
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if(vesicle->tape->constvolswitch==2){
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/*check whether the dvol is gt than epsvol */
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//fprintf(stderr,"DVOL=%1.16e\n",dvol);
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if(fabs(vesicle->volume+dvol-V0)>epsvol){
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//restore old state.
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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for(i=0;i<vtx->neigh_no;i++){
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vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
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}
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for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
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//fprintf(stderr,"fajlam!\n");
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return TS_FAIL;
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}
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} else
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// vesicle_volume(vesicle);
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// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
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if(vesicle->tape->constvolswitch == 1){
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retval=constvolume(vesicle, vtx, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
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if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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for(i=0;i<vtx->neigh_no;i++){
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vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
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}
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for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
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// fprintf(stderr,"fajlam!\n");
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return TS_FAIL;
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}
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// vesicle_volume(vesicle);
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// fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
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// fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
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// fprintf(stderr,"Denergy before=%e\n",delta_energy);
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delta_energy+=delta_energy_cv;
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// fprintf(stderr,"Denergy after=%e\n",delta_energy);
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}
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/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
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delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
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/* No poly-bond energy for now!
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if(vtx->grafted_poly!=NULL){
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delta_energy+=
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(pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
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pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
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}
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*/
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// fprintf(stderr, "DE=%f\n",delta_energy);
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//MONTE CARLOOOOOOOO
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// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
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if(delta_energy>=0){
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#ifdef TS_DOUBLE_DOUBLE
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if(exp(-delta_energy)< drand48())
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#endif
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#ifdef TS_DOUBLE_FLOAT
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if(expf(-delta_energy)< (ts_float)drand48())
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#endif
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#ifdef TS_DOUBLE_LONGDOUBLE
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if(expl(-delta_energy)< (ts_ldouble)drand48())
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#endif
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{
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//not accepted, reverting changes
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// fprintf(stderr,"MC failed\n");
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vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
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for(i=0;i<vtx->neigh_no;i++){
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vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
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}
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//update the normals of triangles that share bead i.
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for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
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// fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
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if(vesicle->tape->constvolswitch == 1){
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constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
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}
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// fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
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// vesicle_volume(vesicle);
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// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
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return TS_FAIL;
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}
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}
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//accepted
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// fprintf(stderr,"MC accepted\n");
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// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
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if(vtx->cell!=vesicle->clist->cell[cellidx]){
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retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
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// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
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if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
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}
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if(vesicle->tape->constvolswitch == 2){
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vesicle->volume+=dvol;
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} else
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if(vesicle->tape->constvolswitch == 1){
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constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
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}
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if(vesicle->tape->constareaswitch==2){
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vesicle->area+=darea;
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}
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// if(oldcellidx);
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//END MONTE CARLOOOOOOO
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// vesicle_volume(vesicle);
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// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
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return TS_SUCCESS;
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}
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ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
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ts_uint i;
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ts_bool retval;
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ts_uint cellidx;
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// ts_double delta_energy;
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ts_double costheta,sintheta,phi,r;
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ts_double dist;
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//This will hold all the information of vtx and its neighbours
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ts_vertex backupvtx;
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// ts_bond backupbond[2];
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memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
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//random move in a sphere with radius stepsize:
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r=vesicle->stepsize*rn[0];
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phi=rn[1]*2*M_PI;
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costheta=2*rn[2]-1;
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sintheta=sqrt(1-pow(costheta,2));
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vtx->x=vtx->x+r*sintheta*cos(phi);
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vtx->y=vtx->y+r*sintheta*sin(phi);
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vtx->z=vtx->z+r*costheta;
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//distance with neighbours check
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for(i=0;i<vtx->neigh_no;i++){
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dist=vtx_distance_sq(vtx,vtx->neigh[i]);
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if(dist<1.0 || dist>vesicle->dmax) {
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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return TS_FAIL;
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}
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}
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// Distance with grafted vesicle-vertex check:
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if(vtx==poly->vlist->vtx[0]){
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dist=vtx_distance_sq(vtx,poly->grafted_vtx);
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if(dist<1.0 || dist>vesicle->dmax) {
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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return TS_FAIL;
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}
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}
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//self avoidance check with distant vertices
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cellidx=vertex_self_avoidance(vesicle, vtx);
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//check occupation number
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retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
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if(retval==TS_FAIL){
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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return TS_FAIL;
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}
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//if all the tests are successful, then energy for vtx and neighbours is calculated
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/* Energy ignored for now!
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delta_energy=0;
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for(i=0;i<vtx->bond_no;i++){
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memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
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vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
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bond_energy(vtx->bond[i],poly);
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delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
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}
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if(vtx==poly->vlist->vtx[0]){
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delta_energy+=
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(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
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pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
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}
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if(delta_energy>=0){
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#ifdef TS_DOUBLE_DOUBLE
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if(exp(-delta_energy)< drand48() )
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#endif
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#ifdef TS_DOUBLE_FLOAT
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if(expf(-delta_energy)< (ts_float)drand48())
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#endif
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#ifdef TS_DOUBLE_LONGDOUBLE
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if(expl(-delta_energy)< (ts_ldouble)drand48())
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#endif
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{
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//not accepted, reverting changes
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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for(i=0;i<vtx->bond_no;i++){
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vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
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}
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return TS_FAIL;
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}
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}
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*/
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// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
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if(vtx->cell!=vesicle->clist->cell[cellidx]){
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retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
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// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
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if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
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}
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// if(oldcellidx);
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//END MONTE CARLOOOOOOO
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return TS_SUCCESS;
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}
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ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
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ts_uint i;
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ts_bool retval;
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ts_uint cellidx;
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ts_double delta_energy;
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ts_double costheta,sintheta,phi,r;
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ts_double dist[2];
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//This will hold all the information of vtx and its neighbours
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ts_vertex backupvtx,backupneigh[2];
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ts_bond backupbond[2];
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//backup vertex:
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memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
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//random move in a sphere with radius stepsize:
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r=vesicle->stepsize*rn[0];
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phi=rn[1]*2*M_PI;
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costheta=2*rn[2]-1;
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sintheta=sqrt(1-pow(costheta,2));
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vtx->x=vtx->x+r*sintheta*cos(phi);
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vtx->y=vtx->y+r*sintheta*sin(phi);
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vtx->z=vtx->z+r*costheta;
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//distance with neighbours check
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for(i=0;i<vtx->bond_no;i++){
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dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
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if(dist[i]<1.0 || dist[i]>vesicle->dmax) {
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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return TS_FAIL;
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}
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}
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// TODO: Maybe faster if checks only nucleus-neighboring cells
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// Nucleus penetration check:
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if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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return TS_FAIL;
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}
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//self avoidance check with distant vertices
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cellidx=vertex_self_avoidance(vesicle, vtx);
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//check occupation number
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retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
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if(retval==TS_FAIL){
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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return TS_FAIL;
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}
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//backup bonds
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for(i=0;i<vtx->bond_no;i++){
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memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
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vtx->bond[i]->bond_length=sqrt(dist[i]);
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bond_vector(vtx->bond[i]);
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}
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//backup neighboring vertices:
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for(i=0;i<vtx->neigh_no;i++){
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memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
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}
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//if all the tests are successful, then energy for vtx and neighbours is calculated
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delta_energy=0;
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if(vtx->bond_no == 2){
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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;
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delta_energy += vtx->energy - backupvtx.energy;
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}
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for(i=0;i<vtx->neigh_no;i++){
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if(vtx->neigh[i]->bond_no == 2){
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vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
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delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
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}
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}
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// poly->k is filament persistence length (in units l_min)
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delta_energy *= poly->k;
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if(delta_energy>=0){
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#ifdef TS_DOUBLE_DOUBLE
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if(exp(-delta_energy)< drand48() )
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#endif
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#ifdef TS_DOUBLE_FLOAT
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if(expf(-delta_energy)< (ts_float)drand48())
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#endif
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#ifdef TS_DOUBLE_LONGDOUBLE
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if(expl(-delta_energy)< (ts_ldouble)drand48())
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#endif
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{
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//not accepted, reverting changes
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vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
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for(i=0;i<vtx->neigh_no;i++){
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memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
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}
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for(i=0;i<vtx->bond_no;i++){
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vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
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}
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return TS_FAIL;
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}
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}
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// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
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if(vtx->cell!=vesicle->clist->cell[cellidx]){
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retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
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// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
|
if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);
|
}
|
// if(oldcellidx);
|
//END MONTE CARLOOOOOOO
|
return TS_SUCCESS;
|
}
|
