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/vertexmove.c | 252 +++++++++++++++-----------------------------------
1 files changed, 75 insertions(+), 177 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index e62967b..362b895 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -20,84 +20,49 @@
ts_uint i;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0, dstretchenergy=0.0;
+ ts_double delta_energy, oenergy;
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));
-//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;
+ //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;
-
-// 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;
- }
-
-}
-
- // 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;
- }
- }
-//#undef SQ
/* Entry point for plugin vm_hard_constraint() function */
- for(i=0; i<vesicle->plist->n;i++){
- retval = vesicle->plist->plugin[i]->function->vm_hard_constraint(vesicle,vtx,&backupvtx[0]);
+ vesicle->plist->pointer=vesicle->plist->chain->vm_hard_constraint;
+ while(vesicle->plist->pointer!=NULL){
+ retval = vesicle->plist->pointer->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;
}
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
}
+/* End of vm_hard_constraint() */
-
-//if all the tests are successful, then energy for vtx and neighbours is calculated
+/* Backuping the neighbours */
for(i=0;i<vtx->neigh_no;i++){
memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
}
- if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
- for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
+/* Entry point for plugin vm_energy_before_prepare() */
+
+ vesicle->plist->pointer=vesicle->plist->chain->vm_energy_before_prepare;
+ while(vesicle->plist->pointer!=NULL){
+ vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
}
+/* End of vm_energy_before_prepare() */
- if(vesicle->tape->constareaswitch==2){
- 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);
-
- //update the normals of triangles that share bead i.
+//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
oenergy=vtx->energy;
energy_vertex(vtx);
@@ -109,77 +74,16 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch >0){
- for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
- if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
- };
+/* Entry point for plugin vm_energy_after_execute() */
- if(vesicle->tape->constareaswitch==2){
- /* check whether the darea is gt epsarea */
- for(i=0;i<vtx->tristar_no;i++) darea+=vtx->tristar[i]->area;
- if(fabs(vesicle->area+darea-A0)>epsarea){
- //restore old state.
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- for(i=0;i<vtx->neigh_no;i++){
- vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
- }
- for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //fprintf(stderr,"fajlam!\n");
- return TS_FAIL;
- }
-
-
- }
-
- if(vesicle->tape->constvolswitch==2){
- /*check whether the dvol is gt than epsvol */
- //fprintf(stderr,"DVOL=%1.16e\n",dvol);
- if(fabs(vesicle->volume+dvol-V0)>epsvol){
- //restore old state.
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- for(i=0;i<vtx->neigh_no;i++){
- vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
- }
- for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //fprintf(stderr,"fajlam!\n");
- return TS_FAIL;
- }
-
- } else
-// vesicle_volume(vesicle);
-// fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
- if(vesicle->tape->constvolswitch == 1){
- retval=constvolume(vesicle, vtx, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
- if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- for(i=0;i<vtx->neigh_no;i++){
- vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
- }
- for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- // fprintf(stderr,"fajlam!\n");
- return TS_FAIL;
- }
-// vesicle_volume(vesicle);
-// fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
-// fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
-// fprintf(stderr,"Denergy before=%e\n",delta_energy);
-
- delta_energy+=delta_energy_cv;
-// fprintf(stderr,"Denergy after=%e\n",delta_energy);
- }
-/* 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;
- }
+ vesicle->plist->pointer=vesicle->plist->chain->vm_energy_after_execute;
+ while(vesicle->plist->pointer!=NULL){
+ delta_energy+=vesicle->plist->pointer->plugin->function->vm_energy_after_execute(vesicle, vtx, backupvtx);
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
}
+/* End of vm_energy_after_execute() */
- delta_energy+=dstretchenergy;
-
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -188,24 +92,29 @@
}
*/
-// 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);
- }
+
+/* Entry point for plugin vm_before_montecarlo_constraint() function */
+ vesicle->plist->pointer=vesicle->plist->chain->vm_before_montecarlo_constraint;
+ while(vesicle->plist->pointer!=NULL){
+ retval = vesicle->plist->pointer->plugin->function->vm_before_montecarlo_constraint(vesicle,vtx, &backupvtx[0]);
+ if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+ return TS_FAIL;
}
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
}
+/* End of vm_before_montecarlo_constraint() */
+
+
+
+
// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
-// if(vtx->c!=0.0) printf("DE=%f\n",delta_energy);
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
if(exp(-delta_energy)< drand48())
@@ -217,61 +126,50 @@
if(expl(-delta_energy)< (ts_ldouble)drand48())
#endif
{
- //not accepted, reverting changes
- // fprintf(stderr,"MC failed\n");
+/*************************************************** MC step rejected **************************************************************/
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
for(i=0;i<vtx->neigh_no;i++){
vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
}
- //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]);
- }
- }
+ //update the normals of triangles that share bead i.
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(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){
- constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
- }
-// fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
-// vesicle_volume(vesicle);
-// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
+
+/* Entry point for plugin vm_before_montecarlo_constraint() function */
+ vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_rejected;
+ while(vesicle->plist->pointer!=NULL){
+ vesicle->plist->pointer->plugin->function->vm_new_state_rejected(vesicle,vtx, &backupvtx[0]);
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
+ }
+/* End of vm_before_montecarlo_constraint() */
+
+
return TS_FAIL;
}
}
- //accepted
- // fprintf(stderr,"MC accepted\n");
-// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+/*************************************************** MC step accepted **************************************************************/
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);
- if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
-
+ if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
}
- if(vesicle->tape->constvolswitch == 2){
- vesicle->volume+=dvol;
- } else
- if(vesicle->tape->constvolswitch == 1){
- constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
- }
+/* Entry point for plugin vm_before_montecarlo_constraint() function */
+ vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_accepted;
+ while(vesicle->plist->pointer!=NULL){
+ vesicle->plist->pointer->plugin->function->vm_new_state_accepted(vesicle,vtx, &backupvtx[0]);
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
+ }
+/* End of vm_before_montecarlo_constraint() */
- if(vesicle->tape->constareaswitch==2){
- vesicle->area+=darea;
- }
-// if(oldcellidx);
- //END MONTE CARLOOOOOOO
-// vesicle_volume(vesicle);
-// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
return TS_SUCCESS;
}
+
+
+
ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
ts_uint i;
ts_bool retval;
--
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