From 80887d68d0c59d5704815e31ff07ac81bb947a7d Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 18:44:41 +0000
Subject: [PATCH] small fix in reset-iteration-count
---
src/timestep.c | 504 +++++--------------------------------------------------
1 files changed, 53 insertions(+), 451 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index 5d4a447..92a4a25 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -1,472 +1,74 @@
#include<stdlib.h>
-#include<math.h>
-#include "general.h"
-#include "vertex.h"
-#include "bond.h"
-#include "triangle.h"
-#include "vesicle.h"
-#include "energy.h"
-#include "timestep.h"
-#include "cell.h"
-//#include "io.h"
#include<stdio.h>
+#include<math.h>
+//#include "io.h"
+#include "general.h"
+#include "timestep.h"
+#include "vertexmove.h"
+#include "bondflip.h"
+#include "frame.h"
+#include "io.h"
+
+ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
+ ts_uint i, j;
+
+ centermass(vesicle);
+ cell_occupation(vesicle);
+ if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
+ for(i=start_iteration;i<inititer+iterations;i++){
+ for(j=0;j<mcsweeps;j++){
+ single_timestep(vesicle);
+ }
+ centermass(vesicle);
+ cell_occupation(vesicle);
+ ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
+ dump_state(vesicle,i);
+ if(i>inititer){
+ write_vertex_xml_file(vesicle,i-inititer);
+ }
+ }
+ return TS_SUCCESS;
+}
ts_bool single_timestep(ts_vesicle *vesicle){
ts_bool retval;
ts_double rnvec[3];
- ts_uint i;
- for(i=0;i<vesicle->vlist.n;i++){
+ ts_uint i,j,b;
+ for(i=0;i<vesicle->vlist->n;i++){
rnvec[0]=drand48();
rnvec[1]=drand48();
rnvec[2]=drand48();
- retval=single_verticle_timestep(vesicle,&vesicle->vlist.vertex[i],rnvec);
+ retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
}
- for(i=0;i<vesicle->blist.n;i++){
- rnvec[0]=drand48();
+// ts_int cnt=0;
+ for(i=0;i<3*vesicle->vlist->n;i++){
+//why is rnvec needed in bondflip?
+/* rnvec[0]=drand48();
rnvec[1]=drand48();
rnvec[2]=drand48();
+*/
+ b=rand() % vesicle->blist->n;
//find a bond and return a pointer to a bond...
//call single_bondflip_timestep...
- retval=single_bondflip_timestep(vesicle,&vesicle->blist.bond[i],rnvec);
-
- }
+ retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
+// if(retval==TS_SUCCESS) cnt++;
+ }
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ rnvec[0]=drand48();
+ rnvec[1]=drand48();
+ rnvec[2]=drand48();
+ retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);
+ }
+
+ }
+
+// printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
+ if(retval);
return TS_SUCCESS;
}
-
-
-ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double
-*rn){
- ts_uint i;
- ts_double dist;
- ts_vertex tvtx;
- ts_bool retval;
- ts_uint cellidx;
- ts_double xold,yold,zold;
- ts_double delta_energy,oenergy;
- ts_vertex *ovtx;
-
- //randomly we move the temporary vertex
- tvtx.x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
- tvtx.y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
- tvtx.z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
- //check we if some length to neighbours are too much
-
- for(i=0;i<vtx->neigh_no;i++){
- dist=vertex_distance_sq(&tvtx,vtx->neigh[i]);
- if(dist<1.0 || dist>vesicle->dmax) return TS_FAIL;
- }
- //self avoidance check with distant vertices
- cellidx=vertex_self_avoidance(vesicle, &tvtx);
- //check occupation number
- retval=cell_occupation_number_and_internal_proximity(&vesicle->clist,cellidx,vtx,&tvtx);
- if(retval==TS_FAIL){
- return TS_FAIL;
- }
-
- //if all the tests are successful, then we update the vertex position
- xold=vtx->x;
- yold=vtx->y;
- zold=vtx->z;
- ovtx=malloc(sizeof(ts_vertex));
- vertex_full_copy(ovtx,vtx);
- vtx->x=tvtx.x;
- vtx->y=tvtx.y;
- vtx->z=tvtx.z;
-
- 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]);
- //energy and curvature
- energy_vertex(vtx);
- delta_energy=vtx->xk*(vtx->energy - ovtx->energy);
- //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);
- }
- // fprintf(stderr, "DE=%f\n",delta_energy);
- //MONTE CARLOOOOOOOO
- 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->x=xold;
- vtx->y=yold;
- vtx->z=zold;
- //update the normals of triangles that share bead i.
- for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
- //energy and curvature
- energy_vertex(vtx);
- //the same is done for neighbouring vertices
- for(i=0;i<vtx->neigh_no;i++) energy_vertex(vtx->neigh[i]);
- free(ovtx->bond_length);
- free(ovtx->bond_length_dual);
- free(ovtx);
- return TS_FAIL;
- }
-}
- //END MONTE CARLOOOOOOO
-
- //TODO: change cell occupation if necessary!
-
- free(ovtx->bond_length);
- free(ovtx->bond_length_dual);
- free(ovtx);
- return TS_SUCCESS;
-}
-
-ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn){
-/*c Vertex and triangle (lm and lp) indexing for bond flip:
-c +----- k-------+ +----- k ------+
-c |lm1 / | \ lp1 | |lm1 / \ lp1 |
-c | / | \ | | / \ |
-c |/ | \ | FLIP |/ lm \ |
-c km lm | lp kp ---> km ---------- kp
-c |\ | / | |\ lp / |
-c | \ | / | | \ / |
-c |lm2 \ | / lp2 | |lm2 \ / lp2 |
-c +------it------+ +----- it -----+
-c
-*/
- ts_vertex *it=bond->vtx1;
- ts_vertex *k=bond->vtx2;
- ts_uint nei,neip,neim;
- ts_uint i,j;
- ts_double oldenergy, delta_energy;
- // ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lp2=NULL, *lm1=NULL, *lm2=NULL;
-
- ts_vertex *kp,*km;
-
- if(it->neigh_no< 3) return TS_FAIL;
- if(k->neigh_no< 3) return TS_FAIL;
- if(k==NULL || it==NULL){
- fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
- }
-
-
- for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
- if(it->neigh[i]==k){
- nei=i;
- break;
- }
- }
- neip=nei+1; // I don't like it.. Smells like I must have it in correct order
- neim=nei-1;
- if(neip>=it->neigh_no) neip=0;
- if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
-there the neim is never <0 !!! */
- // fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
- km=it->neigh[neim]; // We located km and kp
- kp=it->neigh[neip];
-
- if(km==NULL || kp==NULL){
- fatal("In bondflip, cannot determine km and kp!",999);
- }
-
- // fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
-
-/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
- * km. If it is true, then don't flip! */
- for(i=0;i<km->neigh_no;i++){
- if(km->neigh[i] == kp) return TS_FAIL;
- }
- // fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
-/* if bond would be too long, return... */
- if(vertex_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
- // fprintf(stderr,"Bond will not be too long.. Continue.\n");
-
-/* we make a bond flip. this is different than in original fortran */
-// 0. step. Get memory prior the flip
- oldenergy=0;
- oldenergy+=k->xk* k->energy;
- oldenergy+=kp->xk* kp->energy;
- oldenergy+=km->xk* km->energy;
- oldenergy+=it->xk* it->energy;
-// for(i=0;i<k->neigh_no;i++) oldenergy+=k->neigh[i]->xk*k->neigh[i]->energy;
-// for(i=0;i<kp->neigh_no;i++) oldenergy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
-// for(i=0;i<km->neigh_no;i++) oldenergy+=km->neigh[i]->xk*km->neigh[i]->energy;
-// for(i=0;i<it->neigh_no;i++) oldenergy+=it->neigh[i]->xk*it->neigh[i]->energy;
-/*
-fprintf(stderr,"*** Naslov k=%d\n",k);
-fprintf(stderr,"*** Naslov it=%d\n",it);
-fprintf(stderr,"*** Naslov km=%d\n",km);
-fprintf(stderr,"*** Naslov kp=%d\n",kp);
-
-for(i=0;i<k->neigh_no;i++)
- fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
-for(i=0;i<it->neigh_no;i++)
- fprintf(stderr,"it sosed=%d\n",it->neigh[i]);
-
-for(i=0;i<km->neigh_no;i++)
- fprintf(stderr,"km sosed=%d\n",km->neigh[i]);
-for(i=0;i<kp->neigh_no;i++)
- fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]);
-
-
-*/
- // fprintf(stderr,"I WAS HERE! Before bondflip!\n");
- ts_flip_bond(k,it,km,kp, bond);
- // fprintf(stderr,"I WAS HERE! Bondflip successful!\n");
-
-/* Calculating the new energy */
- delta_energy=0;
- for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]);
- for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]);
- for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]);
- for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]);
- delta_energy+=k->xk* k->energy;
- delta_energy+=kp->xk* kp->energy;
- delta_energy+=km->xk* km->energy;
- delta_energy+=it->xk* it->energy;
-// for(i=0;i<k->neigh_no;i++) delta_energy+=k->neigh[i]->xk*k->neigh[i]->energy;
-// for(i=0;i<kp->neigh_no;i++) delta_energy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
-// for(i=0;i<km->neigh_no;i++) delta_energy+=km->neigh[i]->xk*km->neigh[i]->energy;
-// for(i=0;i<it->neigh_no;i++) delta_energy+=it->neigh[i]->xk*it->neigh[i]->energy;
- delta_energy-=oldenergy;
- // fprintf(stderr,"I WAS HERE! Got energy!\n");
-/* MONTE CARLO */
- 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
- // fprintf(stderr,"Failed to move, due to MC\n");
-
-// ts_flip_bond(km,kp,it,k, bond);
- ts_flip_bond(kp,km,k,it, bond);
-
-
-/*
-fprintf(stderr,"*** Naslov k=%d\n",k);
-fprintf(stderr,"*** Naslov it=%d\n",it);
-fprintf(stderr,"*** Naslov km=%d\n",km);
-fprintf(stderr,"*** Naslov kp=%d\n",kp);
-for(i=0;i<k->neigh_no;i++)
- fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
-for(i=0;i<it->neigh_no;i++)
- fprintf(stderr,"it sosed=%d\n",it->neigh[i]);
-
-
-for(i=0;i<km->neigh_no;i++)
- fprintf(stderr,"km sosed=%d\n",km->neigh[i]);
-for(i=0;i<kp->neigh_no;i++)
- fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]);
-*/
-
-
-
- // fprintf(stderr,"Reverted condition!\n");
- return TS_FAIL;
- }
- }
- // fprintf(stderr,"Success\n");
-
-
-/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
- return TS_SUCCESS;
-}
-
-
-ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp,
-ts_bond *bond){
-
- ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
- ts_uint i,j, lmidx, lpidx;
-if(k==NULL || it==NULL || km==NULL || kp==NULL){
- fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
-}
-// 1. step. We find lm and lp from k->tristar !
- for(i=0;i<it->tristar_no;i++){
- for(j=0;j<k->tristar_no;j++){
- if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
- if((it->tristar[i]->vertex[0] == km || it->tristar[i]->vertex[1]
-== km || it->tristar[i]->vertex[2]== km )){
- lm=it->tristar[i];
- // lmidx=i;
- }
- else
- {
- lp=it->tristar[i];
- // lpidx=i;
- }
-
- }
- }
- }
-if(lm==NULL || lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
-
-//we look for important triangles lp1 and lm2.
-
- for(i=0;i<k->tristar_no;i++){
- for(j=0;j<kp->tristar_no;j++){
- if((k->tristar[i] == kp->tristar[j]) && k->tristar[i]!=lp){ //ce gre za skupen trikotnik
- lp1=k->tristar[i];
- }
- }
-}
-
- for(i=0;i<it->tristar_no;i++){
- for(j=0;j<km->tristar_no;j++){
- if((it->tristar[i] == km->tristar[j]) && it->tristar[i]!=lm){ //ce gre za skupen trikotnik
- lm2=it->tristar[i];
- }
- }
- }
-/*
-// DEBUG TESTING!
-fprintf(stderr,"*** Naslov k=%d\n",k);
-fprintf(stderr,"*** Naslov it=%d\n",it);
-fprintf(stderr,"*** Naslov km=%d\n",km);
-fprintf(stderr,"*** Naslov kp=%d\n",kp);
-
-for(i=0;i<k->neigh_no;i++)
- fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
-for(i=0;i<it->neigh_no;i++)
- fprintf(stderr,"it sosed=%d\n",it->neigh[i]);
-
-
-// END DEBUG TESTING!
-*/
-if(lm2==NULL || lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
-
-
-//fprintf(stderr,"1. step: lm, lm2, lp1 and lp found!\n");
-
-/*
-//DEBUG TESTING
-fprintf(stderr,"--- Naslov lm=%d",lm);
-
-
-fprintf(stderr," vtxs(%d, %d, %d)\n",lm->vertex[0],lm->vertex[1], lm->vertex[2]);
-fprintf(stderr,"--- Naslov lp=%d",lp);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lp->vertex[0],lp->vertex[1], lp->vertex[2]);
-fprintf(stderr,"--- Naslov lm2=%d",lm2);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lm2->vertex[0],lm2->vertex[1], lm2->vertex[2]);
-fprintf(stderr,"--- Naslov lp1=%d",lp1);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lp1->vertex[0],lp1->vertex[1], lp1->vertex[2]);
-
-for(i=0;i<lm->neigh_no;i++)
- fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]);
-for(i=0;i<lp->neigh_no;i++)
- fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]);
-// END DEBUG TESTING
-*/
-/*
-// DEBUG TESTING!
-
-for(i=0;i<3;i++){
-
- if(lp1->neigh[i]==lp) fprintf(stderr,"Nasel sem par lp1->lp\n");
- if(lp->neigh[i]==lp1) fprintf(stderr,"Nasel sem par lp->lp1\n");
- if(lm2->neigh[i]==lm) fprintf(stderr,"Nasel sem par lm2->lm\n");
- if(lm->neigh[i]==lm2) fprintf(stderr,"Nasel sem par lm->lm2\n");
-}
-// END DEBUG TESTING!
-*/
-
-
-// 2. step. We change the triangle vertices... (actual bond flip)
- for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
- for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
-//fprintf(stderr,"2. step: actual bondflip made\n");
-// 2a. step. If any changes in triangle calculations must be done, do it here!
-// * normals are recalculated here
- triangle_normal_vector(lp);
- triangle_normal_vector(lm);
-// 3. step. Correct neighbours in vertex_list
-
-
- vertex_remove_neighbour(k,it);
- vertex_remove_neighbour(it,k);
- //Tukaj pa nastopi tezava... Kam dodati soseda?
- vertex_insert_neighbour(km,kp,k);
- vertex_insert_neighbour(kp,km,it);
-// vertex_add_neighbour(km,kp); //pazi na vrstni red.
-// vertex_add_neighbour(kp,km);
-//fprintf(stderr,"3. step: vertex neighbours corrected\n");
-
-// 3a. step. If any changes to ts_vertex, do it here!
-// bond_length calculatons not required for it is done in energy.c
-
-// 4. step. Correct bond_list (don't know why I still have it!)
- bond->vtx1=km;
- bond->vtx2=kp;
-//fprintf(stderr,"4. step: bondlist corrected\n");
-
-
-// 5. step. Correct neighbouring triangles
-
- triangle_remove_neighbour(lp,lp1);
- // fprintf(stderr,".\n");
- triangle_remove_neighbour(lp1,lp);
- // fprintf(stderr,".\n");
- triangle_remove_neighbour(lm,lm2);
- // fprintf(stderr,".\n");
- triangle_remove_neighbour(lm2,lm);
-
- triangle_add_neighbour(lm,lp1);
- triangle_add_neighbour(lp1,lm);
- triangle_add_neighbour(lp,lm2); //Vrstni red?!
- triangle_add_neighbour(lm2,lp);
-
-//fprintf(stderr,"5. step: triangle neigbours corrected\n");
-
-
-// 6. step. Correct tristar for vertices km, kp, k and it
- vertex_add_tristar(km,lp); // Preveri vrstni red!
- vertex_add_tristar(kp,lm);
- vertex_remove_tristar(it,lm);
- vertex_remove_tristar(k,lp);
-//fprintf(stderr,"6. step: tristar corrected\n");
-
-/*
-//DEBUG TESTING
-fprintf(stderr,"--- Naslov lm=%d",lm);
-
-
-fprintf(stderr," vtxs(%d, %d, %d)\n",lm->vertex[0],lm->vertex[1], lm->vertex[2]);
-fprintf(stderr,"--- Naslov lp=%d",lp);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lp->vertex[0],lp->vertex[1], lp->vertex[2]);
-fprintf(stderr,"--- Naslov lm2=%d",lm2);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lm2->vertex[0],lm2->vertex[1], lm2->vertex[2]);
-fprintf(stderr,"--- Naslov lp1=%d",lp1);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lp1->vertex[0],lp1->vertex[1], lp1->vertex[2]);
-
-for(i=0;i<lm->neigh_no;i++)
- fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]);
-for(i=0;i<lp->neigh_no;i++)
- fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]);
-// END DEBUG TESTING
-*/
- energy_vertex(k);
- energy_vertex(kp);
- energy_vertex(km);
- energy_vertex(it);
-
-
-// END modifications to data structure!
-
-
- return TS_SUCCESS;
-}
--
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