Plane confinement plugin almost done :)

Samo Penic

2019-03-08 85898e259e6e2075a7f755583690024a63e9bb2b

Plane confinement plugin almost done :)

 src/general.h

@@ -312,7 +312,7 @@
    void (*vm_energy_before_prepare)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_before_execute)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_after_prepare)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_after_execute)(void *vesicle, ts_vertex *vtx);
    ts_double (*vm_energy_after_execute)(void *vesicle, ts_vertex *vtx, ts_vertex *backup_vertices);
    ts_double (*vm_before_montecarlo_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
    ts_double (*vm_new_state_accepted)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);
    ts_double (*vm_new_state_rejected)(void *vesicle, ts_vertex *vtx, ts_vertex *old_vtx);

 src/plugins/plane_confinement.c

@@ -2,6 +2,7 @@
#include "general.h"
#include "vertex.h"
#include "cell.h"
#include <math.h>
char plugin_name[] = "Plane confimenent";
char plugin_description[]= "Confines vesicle between two planes d/2 above z=0 and d/2 below z=0. The plates squeeze vesicle with some predefined force.";
char plugin_author[] = "SAMO PENIC";
@@ -9,6 +10,7 @@
ts_plugin_details *init (){
    ts_plugin_details *details=(ts_plugin_details *)calloc(1,sizeof(ts_plugin_details));
    details->name = plugin_name;
//    details->data = (void *)calloc(1,sizeof(ts_double));
    return details;    
}

@@ -20,7 +22,26 @@
        return TS_FAIL;
        }
    }

    return TS_SUCCESS;
}


ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *backupvtx){
// plane confinement energy due to compressing force
    ts_double delta_energy=0;
    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);
            }
        }
    }
    return delta_energy;

}

 src/plugins/pressure.c

@@ -22,7 +22,7 @@
    }
}

ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx){
ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *backup_vertices){
    ts_double delta_energy=0;
    if(vesicle->pswitch == 1){
        ts_double *dvol=(ts_double *)vesicle->plist->pointer->plugin->details->data;

 src/vertexmove.c

@@ -85,7 +85,7 @@

    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;
    }

@@ -110,21 +110,6 @@
            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 */