Storing previously debugged version

Samo Penic

2020-04-13 2a1e3d528265c3d366dab9ad4b0c4d3d65e1c4ed

 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>
@@ -8,51 +9,219 @@
#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>
#include <sys/stat.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;
   ts_uint i, j,k; //,l,m;
   ts_double kc1=0,kc2=0,kc3=0,kc4=0;
   ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
   ts_ulong epochtime;
   ts_double max_z,min_z;
   FILE *fd3=NULL;
    char filename[10000];
   //struct stat st;
   strcpy(filename,command_line_args.path);
   strcat(filename,"statistics.csv");
   //int result = stat(filename, &st);
   FILE *fd;
   if(start_iteration==0)
      fd=fopen(filename,"w");
   else
      fd=fopen(filename,"a");
   if(fd==NULL){
      fatal("Cannot open statistics.csv file for writing",1);
   }
   if(start_iteration==0)
      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"); 
//   int result = stat(filename, &st);
   if(start_iteration==0)
      fd2=fopen(filename,"w");
   else
      fd2=fopen(filename,"a");
   if(fd2==NULL){
      fatal("Cannot open ulm2.csv file for writing",1);
   } 

   if(start_iteration==0) //file does not exist
      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
   if(V0<0.000001) 
      V0=vesicle->volume; 
   ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
   if(A0<0.000001)
      A0=vesicle->area;
   ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
   epsvol=4.0*sqrt(2.0*M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
//   printf("epsvol=%e\n",epsvol);
   epsarea=A0/(ts_double)vesicle->tlist->n;

   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);
      vmsr=0.0;
      bfsr=0.0;

   //plane confinement
   if(vesicle->tape->plane_confinement_switch){
      min_z=1e10;
      max_z=-1e10;
      for(k=0;k<vesicle->vlist->n;k++){
         if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
         if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
      }
      vesicle->confinement_plane.force_switch=0;
      if(max_z>=vesicle->tape->plane_d/2.0){
         ts_fprintf(stdout, "Max vertex out of bounds (z>=%e). Plane set to max_z = %e.\n",vesicle->tape->plane_d/2.0,max_z);
         vesicle->confinement_plane.z_max = max_z;
         vesicle->confinement_plane.force_switch=1;
      } else {
         vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
      }
      if(min_z<=-vesicle->tape->plane_d/2.0){
         ts_fprintf(stdout, "Min vertex out of bounds (z<=%e). Plane set to min_z = %e.\n",-vesicle->tape->plane_d/2.0,min_z);
         vesicle->confinement_plane.z_min = min_z;
         vesicle->confinement_plane.force_switch=1;
      } else {
         vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
      }
      ts_fprintf(stdout,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
      if(vesicle->confinement_plane.force_switch) ts_fprintf(stdout,"Squeezing with force %e.\n",vesicle->tape->plane_F);
   }

   //end plane confinement

/*    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);
      if(i>=inititer){
         write_vertex_xml_file(vesicle,i-inititer);
/* BINARY DUMPS ARE OBSOLETE. SHOULD WORK AS OF MAR 2020, BUT NO LONGER MAINTAINED */
//               dump_state(vesicle,i);
         vesicle_volume(vesicle); //calculates just volume. 
                  vesicle_area(vesicle); //calculates area.
      if(vesicle->tape->constvolswitch==0){
         V0=vesicle->volume;
      }
      if(vesicle->tape->constareaswitch==0){
         A0=vesicle->area;
      }
      if(i>=inititer){
         write_vertex_xml_file(vesicle,i-inititer,NULL);
         write_master_xml_file(command_line_args.output_fullfilename);
         epochtime=get_epoch();			
         gyration_eigen(vesicle, &l1, &l2, &l3);
         //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);
      } //end if(inititer....)
      fd3=fopen(".status","w"); //write status file when everything is written to disk.
      if(fd3==NULL){
         fatal("Cannot open .status file for writing",1);
      }
      fprintf(fd3,"%d",i);
      fclose(fd3);
      ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
   }
   fclose(fd);
//   if(fd2!=NULL) fclose(fd2);
   return TS_SUCCESS;
}

ts_bool single_timestep(ts_vesicle *vesicle){
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,j,b;
    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++;        
    }

//   ts_int cnt=0;
   ts_int bfsrcnt=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[b],rnvec);
//   if(retval==TS_SUCCESS) cnt++;        
       //     b++; retval=TS_FAIL;
   if(retval==TS_SUCCESS) bfsrcnt++;        
    }

   for(i=0;i<vesicle->poly_list->n;i++){
@@ -76,7 +245,10 @@
 

//   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);
   *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;
}