| | |
| | | /* vim: set ts=4 sts=4 sw=4 noet : */ |
| | | #include<stdlib.h> |
| | | #include<stdio.h> |
| | | #include<math.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,k; |
| | | ts_double r0,kc1,kc2,kc3,kc4; |
| | | ts_double l1,l2,l3,volume=0.0,area=0.0,vmsr,bfsr, vmsrt, bfsrt; |
| | | 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; |
| | | FILE *fd1; |
| | | // char filename[255]; |
| | | FILE *fd=fopen("statistics.csv","w"); |
| | | 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); |
| | | } |
| | | 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(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++){ |
| | | 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); |
| | | 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); |
| | | write_master_xml_file("test.pvd"); |
| | | 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); |
| | | vesicle_volume(vesicle); //calculates just volume. Area is not added to ts_vesicle yet! |
| | | get_area_volume(vesicle, &area,&volume); //that's why I must recalculate area (and volume for no particular reason). |
| | | r0=getR0(vesicle); |
| | | if(vesicle->sphHarmonics!=NULL){ |
| | | //r0=getR0(vesicle); |
| | | /* if(vesicle->sphHarmonics!=NULL){ |
| | | preparationSh(vesicle,r0); |
| | | //calculateYlmi(vesicle); |
| | | calculateUlmComplex(vesicle); |
| | |
| | | kc2=calculateKc(vesicle, 6,9); |
| | | kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l); |
| | | kc4=calculateKc(vesicle, 3,6); |
| | | |
| | | fd1=fopen("state.dat","w"); |
| | | |
| | | 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", |
| | |
| | | ); |
| | | } |
| | | 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,volume, area,l1,l2,l3,kc1, kc2, kc3,kc4); |
| | | |
| | | } |
| | | */ |
| | | |
| | | 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_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; |
| | |
| | | //find a bond and return a pointer to a bond... |
| | | //call single_bondflip_timestep... |
| | | retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec); |
| | | // b++; retval=TS_FAIL; |
| | | if(retval==TS_SUCCESS) bfsrcnt++; |
| | | } |
| | | |
| | |
| | | // 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; |
| | | } |
| | | |