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 | 48 +++---------------------------------------------
1 files changed, 3 insertions(+), 45 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 462959d..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,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;
@@ -62,12 +62,6 @@
}
/* 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]);
oenergy=vtx->energy;
@@ -80,29 +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() */
-/* 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+=
@@ -110,21 +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 */
@@ -168,14 +134,6 @@
//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 */
--
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