Use nucleus displaced centre in vertex move

Samo Penic

2016-05-31 5c3143e7b7d0979d6eed07b6dfbe9f214159bdbb

 src/timestep.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<stdio.h>
#include<math.h>
@@ -5,28 +6,189 @@
#include "general.h"
#include "timestep.h"
#include "vertexmove.h"
#include "bondflip.h"
#include "frame.h"
#include "io.h"
#include "stats.h"
#include "sh.h"
#include "shcomplex.h"
#include "vesicle.h"
#include<gsl/gsl_complex.h>
#include<gsl/gsl_complex_math.h>
#include<string.h>

ts_bool single_timestep(ts_vesicle *vesicle){
ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
   ts_uint i, j,k,l,m;
   ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
   ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
   ts_ulong epochtime;
   FILE *fd1,*fd2=NULL,*fd3=NULL;
    char filename[10000];
    strcpy(filename,command_line_args.path);
    strcat(filename,"statistics.csv");
   FILE *fd=fopen(filename,"w");
   if(fd==NULL){
      fatal("Cannot open statistics.csv file for writing",1);
   }
   fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");

    if(vesicle->sphHarmonics!=NULL){
        strcpy(filename,command_line_args.path);
        strcat(filename,"ulm2.csv"); 
      fd2=fopen(filename,"w");
      if(fd2==NULL){
         fatal("Cannot open ulm2.csv file for writing",1);
      }
      fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");	

   }

/* RANDOM SEED SET BY CURRENT TIME */
   epochtime=get_epoch();			
   srand48(epochtime);

   centermass(vesicle);
   cell_occupation(vesicle);
   vesicle_volume(vesicle); //needed for constant volume at this moment
    vesicle_area(vesicle); //needed for constant area at this moment
   V0=vesicle->volume; 
    A0=vesicle->area;
   epsvol=4.0*sqrt(2.0*M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
    epsarea=A0/(ts_double)vesicle->tlist->n;
  //  fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
   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++){
      vmsr=0.0;
      bfsr=0.0;
/*    vesicle_volume(vesicle);
    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
      for(j=0;j<mcsweeps;j++){
         single_timestep(vesicle, &vmsrt, &bfsrt);
         vmsr+=vmsrt;
         bfsr+=bfsrt;
      }
/*
    vesicle_volume(vesicle);
    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
      vmsr/=(ts_double)mcsweeps;
      bfsr/=(ts_double)mcsweeps;
      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);
      fd3=fopen(".status","w");
      if(fd3==NULL){
         fatal("Cannot open .status file for writing",1);
      }
      fprintf(fd3,"%d",i);
      fclose(fd3);
      if(i>=inititer){
         write_vertex_xml_file(vesicle,i-inititer);
         write_master_xml_file(command_line_args.output_fullfilename);
         epochtime=get_epoch();			
         gyration_eigen(vesicle, &l1, &l2, &l3);
         vesicle_volume(vesicle); //calculates just volume. 
            vesicle_area(vesicle); //calculates area.
         r0=getR0(vesicle);
            if(vesicle->sphHarmonics!=NULL){
             preparationSh(vesicle,r0);
             //calculateYlmi(vesicle);
             calculateUlmComplex(vesicle);
             storeUlmComplex2(vesicle);
             saveAvgUlm2(vesicle);
                kc1=calculateKc(vesicle, 2,9);
                kc2=calculateKc(vesicle, 6,9);
                kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
                kc4=calculateKc(vesicle, 3,6);
                strcpy(filename,command_line_args.path);
                strcat(filename,"state.dat");  
            fd1=fopen(filename,"w");
            fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
            for(k=0;k<vesicle->vlist->n;k++){
               fprintf(fd1,"%e %e %e %e %e\n",
                  vesicle->vlist->vtx[k]->x,
                  vesicle->vlist->vtx[k]->y,
                  vesicle->vlist->vtx[k]->z,
                  vesicle->vlist->vtx[k]->solAngle,
                  vesicle->vlist->vtx[k]->relR
               );
            }
            fclose(fd1);
		
         fprintf(fd2,"%u ", i);
         for(l=0;l<vesicle->sphHarmonics->l;l++){
            for(m=l;m<2*l+1;m++){
               fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
            }
         }
            fprintf(fd2,"\n");
	
             fflush(fd2);	

            }

         fprintf(fd, "%lu %u %e %e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e %1.16e\n",epochtime,i,vmsr,bfsr,vesicle->volume, vesicle->area,l1,l2,l3,kc1, kc2, kc3,kc4);

          fflush(fd);	
      //   sprintf(filename,"timestep-%05d.pov",i-inititer);
      //   write_pov_file(vesicle,filename);
      }
   }
   fclose(fd);
   if(fd2!=NULL) fclose(fd2);
   return TS_SUCCESS;
}

ts_bool single_timestep(ts_vesicle *vesicle,ts_double *vmsr, ts_double *bfsr){
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
    ts_bool retval;
    ts_double rnvec[3];
    ts_uint i;
    ts_uint i,j, b;
    ts_uint vmsrcnt=0;
    for(i=0;i<vesicle->vlist->n;i++){
        rnvec[0]=drand48();
        rnvec[1]=drand48();
        rnvec[2]=drand48();
        retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
   if(retval==TS_SUCCESS) vmsrcnt++;        
    }

    for(i=0;i<vesicle->blist->n;i++){
        rnvec[0]=drand48();
        rnvec[1]=drand48();
        rnvec[2]=drand48();
   ts_int bfsrcnt=0;
    for(i=0;i<3*vesicle->vlist->n;i++){
   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);
        
    } 
   if(retval);
        retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
       //     b++; retval=TS_FAIL;
   if(retval==TS_SUCCESS) bfsrcnt++;        
    }

   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);	
      }
   }


   for(i=0;i<vesicle->filament_list->n;i++){
      for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
         rnvec[0]=drand48();
         rnvec[1]=drand48();
         rnvec[2]=drand48();
         retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_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);
   *vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
   *bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
//    vesicle_volume(vesicle);
//    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
    return TS_SUCCESS;
}