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 | 288 ++++++++++++++++++++++++++++++++++++++++++---------------
1 files changed, 213 insertions(+), 75 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 7f6391f..362b895 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include "general.h"
@@ -8,87 +9,60 @@
#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,oenergy,dvol=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];
- 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);
- }
-*/
-
- //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;
+ //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;
+/* Entry point for plugin vm_hard_constraint() function */
+ 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;
}
- }
-
-// 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) {
- 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() */
- //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
+/* 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){
- for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
- };
+/* Entry point for plugin vm_energy_before_prepare() */
- delta_energy=0;
- //update the normals of triangles that share bead i.
+ 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() */
+
+//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);
@@ -100,10 +74,15 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- if(vesicle->pswitch == 1){
- for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
- delta_energy-=vesicle->pressure*dvol;
- };
+/* 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, backupvtx);
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
+ }
+/* End of vm_energy_after_execute() */
+
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
@@ -112,11 +91,33 @@
pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
}
*/
+
+
+/* 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(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
- if(exp(-delta_energy)< drand48() )
+ if(exp(-delta_energy)< drand48())
#endif
#ifdef TS_DOUBLE_FLOAT
if(expf(-delta_energy)< (ts_float)drand48())
@@ -125,30 +126,48 @@
if(expl(-delta_energy)< (ts_ldouble)drand48())
#endif
{
- //not accepted, reverting changes
+/*************************************************** 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]);
+ //update the normals of triangles that share bead i.
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+
+
+/* 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;
}
}
-
-// 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(oldcellidx);
- //END MONTE CARLOOOOOOO
+
+/* 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() */
+
return TS_SUCCESS;
}
+
+
+
ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
@@ -254,3 +273,122 @@
//END MONTE CARLOOOOOOO
return TS_SUCCESS;
}
+
+
+
+
+ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+ ts_uint i;
+ ts_bool retval;
+ ts_uint cellidx;
+ ts_double delta_energy;
+ ts_double costheta,sintheta,phi,r;
+ ts_double dist[2];
+ //This will hold all the information of vtx and its neighbours
+ ts_vertex backupvtx,backupneigh[2];
+ ts_bond backupbond[2];
+
+ //backup vertex:
+ memcpy((void *)&backupvtx,(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;
+
+
+ //distance with neighbours check
+ for(i=0;i<vtx->bond_no;i++){
+ dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
+ if(dist[i]<1.0 || dist[i]>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+ }
+
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+ if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+
+ //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,sizeof(ts_vertex));
+ return TS_FAIL;
+ }
+
+ //backup bonds
+ for(i=0;i<vtx->bond_no;i++){
+ memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
+ vtx->bond[i]->bond_length=sqrt(dist[i]);
+ bond_vector(vtx->bond[i]);
+ }
+
+ //backup neighboring vertices:
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
+ }
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+ delta_energy=0;
+
+ if(vtx->bond_no == 2){
+ vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+ delta_energy += vtx->energy - backupvtx.energy;
+ }
+
+ for(i=0;i<vtx->neigh_no;i++){
+ if(vtx->neigh[i]->bond_no == 2){
+ vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
+ delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
+ }
+ }
+
+ // poly->k is filament persistence length (in units l_min)
+ delta_energy *= poly->k;
+
+ if(delta_energy>=0){
+#ifdef TS_DOUBLE_DOUBLE
+ if(exp(-delta_energy)< drand48() )
+#endif
+#ifdef TS_DOUBLE_FLOAT
+ if(expf(-delta_energy)< (ts_float)drand48())
+#endif
+#ifdef TS_DOUBLE_LONGDOUBLE
+ if(expl(-delta_energy)< (ts_ldouble)drand48())
+#endif
+ {
+ //not accepted, reverting changes
+ vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+ for(i=0;i<vtx->neigh_no;i++){
+ memcpy(vtx->neigh[i],&backupneigh[i],sizeof(ts_vertex));
+ }
+ for(i=0;i<vtx->bond_no;i++){
+ vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+ }
+
+ return TS_FAIL;
+ }
+ }
+
+
+// oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+ 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.cell,vtx);
+ }
+// if(oldcellidx);
+ //END MONTE CARLOOOOOOO
+ return TS_SUCCESS;
+}
--
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