From 2c4278db6ead5c27e30a3000097ed898c968534e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:45:22 +0000
Subject: [PATCH] Added direct force plugin and fixes in stretching energy
---
src/vertexmove.c | 125 +++++++----------------------------------
1 files changed, 23 insertions(+), 102 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 37508e9..362b895 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -20,7 +20,7 @@
ts_uint i;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, 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;
@@ -60,22 +60,9 @@
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);
@@ -87,47 +74,16 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
-
/* Entry point for plugin vm_energy_after_execute() */
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);
+ 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() */
-
- 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;
- }
-
-
- }
-
-/* 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+=
@@ -135,21 +91,6 @@
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);
- }
- }
- }
/* Entry point for plugin vm_before_montecarlo_constraint() function */
@@ -185,53 +126,34 @@
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;
- }
-
-
-
- if(vesicle->tape->constareaswitch==2){
- vesicle->area+=darea;
- }
-
/* Entry point for plugin vm_before_montecarlo_constraint() function */
vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_accepted;
@@ -241,14 +163,13 @@
}
/* End of vm_before_montecarlo_constraint() */
-
-
-
-
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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