From 9a1f16ae3affc4db83f2eb2623418ac5cff2af03 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 20:07:56 +0000
Subject: [PATCH] Code cleanup
---
src/vertexmove.c | 97 +++++++-----------------------------------------
1 files changed, 14 insertions(+), 83 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index ac29b18..a238bf5 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -20,10 +20,9 @@
ts_uint i;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, oenergy, 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;
+ ts_vertex backupvtx[20];
memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
//random move in a sphere with radius stepsize:
@@ -54,7 +53,6 @@
}
/* 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);
@@ -62,65 +60,27 @@
}
/* End of vm_energy_before_prepare() */
- //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;
-
-//update the normals of triangles that share bead i.
- for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(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]);
oenergy=vtx->energy;
- energy_vertex(vtx);
- delta_energy=vtx->xk*(vtx->energy - oenergy);
- //the same is done for neighbouring vertices
- for(i=0;i<vtx->neigh_no;i++){
- oenergy=vtx->neigh[i]->energy;
- energy_vertex(vtx->neigh[i]);
- delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
- }
-
+ energy_vertex(vtx);
+ delta_energy=vtx->xk*(vtx->energy - oenergy);
+ //the same is done for neighbouring vertices
+ for(i=0;i<vtx->neigh_no;i++){
+ oenergy=vtx->neigh[i]->energy;
+ energy_vertex(vtx->neigh[i]);
+ 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+=
@@ -128,21 +88,6 @@
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 */
@@ -187,14 +132,6 @@
//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]);
- }
- }
-
-
/* Entry point for plugin vm_before_montecarlo_constraint() function */
vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_rejected;
@@ -214,12 +151,6 @@
retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
}
-
-
- 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;
--
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