From b5cd8cc72380e9ca576ec942753391df85a2a436 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 28 Feb 2019 19:14:54 +0000
Subject: [PATCH] Many new plugins :D
---
src/vertexmove.c | 134 +++++++++++++++++++++-----------------------
1 files changed, 64 insertions(+), 70 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 2517f69..c512ccd 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -9,96 +9,52 @@
#include "energy.h"
#include "timestep.h"
#include "cell.h"
-//#include "io.h"
#include "io.h"
#include<stdio.h>
#include "vertexmove.h"
#include <string.h>
#include "constvol.h"
+#include "plugins.h"
ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn){
ts_uint i;
- ts_double dist;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
+ ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
ts_double costheta,sintheta,phi,r;
//This will hold all the information of vtx and its neighbours
- ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
- memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
+ ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
+ memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
- //Some stupid tests for debugging cell occupation!
-/* cellidx=vertex_self_avoidance(vesicle, vtx);
- if(vesicle->clist->cell[cellidx]==vtx->cell){
- fprintf(stderr,"Idx match!\n");
- } else {
- fprintf(stderr,"***** Idx don't match!\n");
- fatal("ENding.",1);
- }
-*/
+ //random move in a sphere with radius stepsize:
+ r=vesicle->stepsize*rn[0];
+ phi=rn[1]*2*M_PI;
+ costheta=2*rn[2]-1;
+ sintheta=sqrt(1-pow(costheta,2));
+ vtx->x=vtx->x+r*sintheta*cos(phi);
+ vtx->y=vtx->y+r*sintheta*sin(phi);
+ vtx->z=vtx->z+r*costheta;
- //temporarly moving the vertex
-// vtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
-// vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
-// vtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
-
-//random move in a sphere with radius stepsize:
- r=vesicle->stepsize*rn[0];
- phi=rn[1]*2*M_PI;
- costheta=2*rn[2]-1;
- sintheta=sqrt(1-pow(costheta,2));
- vtx->x=vtx->x+r*sintheta*cos(phi);
- vtx->y=vtx->y+r*sintheta*sin(phi);
- vtx->z=vtx->z+r*costheta;
-
-
-//distance with neighbours check
- for(i=0;i<vtx->neigh_no;i++){
- dist=vtx_distance_sq(vtx,vtx->neigh[i]);
- if(dist<1.0 || dist>vesicle->dmax) {
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- return TS_FAIL;
- }
- }
-
-// Distance with grafted poly-vertex check:
- if(vtx->grafted_poly!=NULL){
- dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
- if(dist<1.0 || dist>vesicle->dmax) {
+// plane confinement check whether the new position of vertex will be out of bounds
+ if(vesicle->tape->plane_confinement_switch){
+ if(vtx->z>vesicle->confinement_plane.z_max || vtx->z<vesicle->confinement_plane.z_min){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
}
-// TODO: Maybe faster if checks only nucleus-neighboring cells
-// Nucleus penetration check:
-//#define SQ(x) x*x
-if(vesicle->R_nucleus>0.0){
- 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){
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- return TS_FAIL;
- }
-} else if(vesicle->R_nucleusX>0.0){
-// fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
-// 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){
- 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){
-// if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- return TS_FAIL;
+/* Entry point for plugin vm_hard_constraint() function */
+ ts_plugin_chain *ptr=vesicle->plist->chain->vm_hard_constraint;
+ while(ptr!=NULL){
+ retval = ptr->plugin->function->vm_hard_constraint(vesicle,vtx, &backupvtx[0]);
+ if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ ptr=ptr->next;
}
-}
-//#undef SQ
-//self avoidance check with distant vertices
- cellidx=vertex_self_avoidance(vesicle, vtx);
- //check occupation number
- retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
- if(retval==TS_FAIL){
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- return TS_FAIL;
- }
-
//if all the tests are successful, then energy for vtx and neighbours is calculated
for(i=0;i<vtx->neigh_no;i++){
@@ -113,9 +69,13 @@
for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
}
-
+ //stretching energy 1 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
+ }
delta_energy=0;
-
+
+
// vesicle_volume(vesicle);
// fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
@@ -191,6 +151,17 @@
}
/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
+
+ //stretching energy 2 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle, vtx->tristar[i]);
+ dstretchenergy+=vtx->tristar[i]->energy;
+ }
+ }
+
+ delta_energy+=dstretchenergy;
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -198,6 +169,22 @@
pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
}
*/
+
+// plane confinement energy due to compressing force
+ if(vesicle->tape->plane_confinement_switch){
+ if(vesicle->confinement_plane.force_switch){
+ //substract old energy
+ if(abs(vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_max)>1e-10) {
+ delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-backupvtx[0].z,2);
+ delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_max-vtx->z,2);
+ }
+ if(abs(-vesicle->tape->plane_d/2.0-vesicle->confinement_plane.z_min)>1e-10) {
+ delta_energy-=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-backupvtx[0].z,2);
+ delta_energy+=vesicle->tape->plane_F / pow(vesicle->confinement_plane.z_min-vtx->z,2);
+ }
+ }
+ }
+
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
@@ -221,6 +208,12 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ //stretching energy 3 of 3
+ if(vesicle->tape->stretchswitch==1){
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle,vtx->tristar[i]);
+ }
+ }
// fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
if(vesicle->tape->constvolswitch == 1){
@@ -235,6 +228,7 @@
//accepted
// fprintf(stderr,"MC accepted\n");
// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ cellidx=vertex_self_avoidance(vesicle, vtx);
if(vtx->cell!=vesicle->clist->cell[cellidx]){
retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
// if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
--
Gitblit v1.9.3