Trisurf Monte Carlo simulator
Samo Penic
2016-06-21 e5858ff1dcf5cecfcfe81602f52d255de9d508f4
commit | author | age
7f6076 1 /* vim: set ts=4 sts=4 sw=4 noet : */
d7639a 2 #include<stdlib.h>
SP 3 #include<stdio.h>
aec47d 4 #include<math.h>
SP 5 //#include "io.h"
6 #include "general.h"
7 #include "timestep.h"
8 #include "vertexmove.h"
30ee9c 9 #include "bondflip.h"
d7a113 10 #include "frame.h"
SP 11 #include "io.h"
37d14a 12 #include "stats.h"
dc77e8 13 #include "sh.h"
459ff9 14 #include "shcomplex.h"
dc77e8 15 #include "vesicle.h"
5a3862 16 #include<gsl/gsl_complex.h>
M 17 #include<gsl/gsl_complex_math.h>
267db5 18 #include<string.h>
ac9826 19 #include <sys/stat.h>
SP 20
fedf2b 21
626811 22 ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations, ts_uint start_iteration){
5a3862 23     ts_uint i, j,k,l,m;
cfab63 24     ts_double r0,kc1=0,kc2=0,kc3=0,kc4=0;
c0ae90 25     ts_double l1,l2,l3,vmsr,bfsr, vmsrt, bfsrt;
37d14a 26     ts_ulong epochtime;
3d0247 27     FILE *fd1,*fd2=NULL,*fd3=NULL;
267db5 28      char filename[10000];
ac9826 29     //struct stat st;
SP 30     strcpy(filename,command_line_args.path);
31     strcat(filename,"statistics.csv");
32     //int result = stat(filename, &st);
33     FILE *fd;
34     if(start_iteration==0)
35         fd=fopen(filename,"w");
36     else
37         fd=fopen(filename,"a");
37d14a 38     if(fd==NULL){
SP 39         fatal("Cannot open statistics.csv file for writing",1);
40     }
ac9826 41     if(start_iteration==0)
SP 42         fprintf(fd, "Epoch OuterLoop VertexMoveSucessRate BondFlipSuccessRate Volume Area lamdba1 lambda2 lambda3 Kc(2-9) Kc(6-9) Kc(2-end) Kc(3-6)\n");
5a3862 43
M 44      if(vesicle->sphHarmonics!=NULL){
267db5 45         strcpy(filename,command_line_args.path);
SP 46         strcat(filename,"ulm2.csv"); 
ac9826 47 //    int result = stat(filename, &st);
SP 48     if(start_iteration==0)
267db5 49         fd2=fopen(filename,"w");
ac9826 50     else
SP 51         fd2=fopen(filename,"a");
5a3862 52         if(fd2==NULL){
M 53             fatal("Cannot open ulm2.csv file for writing",1);
54         }
ac9826 55         if(start_iteration==0) //file does not exist
SP 56             fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");    
5a3862 57
M 58     }
59
c60a49 60 /* RANDOM SEED SET BY CURRENT TIME */
M 61     epochtime=get_epoch();            
62     srand48(epochtime);
d7a113 63     centermass(vesicle);
SP 64     cell_occupation(vesicle);
fe5069 65     vesicle_volume(vesicle); //needed for constant volume at this moment
c0ae90 66     vesicle_area(vesicle); //needed for constant area at this moment
49981c 67     if(V0<0.000001) 
SP 68         V0=vesicle->volume; 
69     ts_fprintf(stdout,"Setting volume V0=%.17f\n",V0);
70     if(A0<0.000001)
71         A0=vesicle->area;
72         ts_fprintf(stdout,"Setting area A0=%.17f\n",A0);
a54977 73     epsvol=4.0*sqrt(2.0*M_PI)/pow(3.0,3.0/4.0)*V0/pow(vesicle->tlist->n,3.0/2.0);
c0ae90 74     epsarea=A0/(ts_double)vesicle->tlist->n;
a54977 75   //  fprintf(stderr, "DVol=%1.16f (%1.16f), V0=%1.16f\n", epsvol,0.003e-2*V0,V0);
626811 76     if(start_iteration<inititer) ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
SP 77     for(i=start_iteration;i<inititer+iterations;i++){
37d14a 78         vmsr=0.0;
SP 79         bfsr=0.0;
3de289 80 /*    vesicle_volume(vesicle);
SP 81     fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113 82         for(j=0;j<mcsweeps;j++){
37d14a 83             single_timestep(vesicle, &vmsrt, &bfsrt);
SP 84             vmsr+=vmsrt;
85             bfsr+=bfsrt;
d7a113 86         }
3de289 87 /*
SP 88     vesicle_volume(vesicle);
89     fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a 90         vmsr/=(ts_double)mcsweeps;
SP 91         bfsr/=(ts_double)mcsweeps;
d7a113 92         centermass(vesicle);
SP 93         cell_occupation(vesicle);
1ab449 94             dump_state(vesicle,i);
58230a 95         if(i>=inititer){
d7a113 96             write_vertex_xml_file(vesicle,i-inititer);
267db5 97             write_master_xml_file(command_line_args.output_fullfilename);
37d14a 98             epochtime=get_epoch();            
SP 99             gyration_eigen(vesicle, &l1, &l2, &l3);
c0ae90 100             vesicle_volume(vesicle); //calculates just volume. 
SP 101             vesicle_area(vesicle); //calculates area.
dc77e8 102             r0=getR0(vesicle);
632960 103             if(vesicle->sphHarmonics!=NULL){
SP 104                 preparationSh(vesicle,r0);
459ff9 105                 //calculateYlmi(vesicle);
SP 106                 calculateUlmComplex(vesicle);
107                 storeUlmComplex2(vesicle);
632960 108                 saveAvgUlm2(vesicle);
22cdfd 109                 kc1=calculateKc(vesicle, 2,9);
SP 110                 kc2=calculateKc(vesicle, 6,9);
111                 kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
1665aa 112                 kc4=calculateKc(vesicle, 3,6);
267db5 113                 strcpy(filename,command_line_args.path);
SP 114                 strcat(filename,"state.dat");  
115                 fd1=fopen(filename,"w");
5bb6bb 116                 fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M 117                 for(k=0;k<vesicle->vlist->n;k++){
118                     fprintf(fd1,"%e %e %e %e %e\n",
119                         vesicle->vlist->vtx[k]->x,
120                         vesicle->vlist->vtx[k]->y,
121                         vesicle->vlist->vtx[k]->z,
122                         vesicle->vlist->vtx[k]->solAngle,
123                         vesicle->vlist->vtx[k]->relR
124                     );
125                 }
126                 fclose(fd1);
5a3862 127         
M 128             fprintf(fd2,"%u ", i);
129             for(l=0;l<vesicle->sphHarmonics->l;l++){
130                 for(m=l;m<2*l+1;m++){
131                     fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
132                 }
133             }
134                 fprintf(fd2,"\n");
135     
136                 fflush(fd2);    
137
632960 138             }
dc77e8 139
c0ae90 140             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);
5a3862 141
632960 142             fflush(fd);    
144784 143         //    sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2 144         //    write_pov_file(vesicle,filename);
49981c 145         } //end if(inititer....)
SP 146         fd3=fopen(".status","w"); //write status file when everything is written to disk.
147         if(fd3==NULL){
148             fatal("Cannot open .status file for writing",1);
d7a113 149         }
49981c 150         fprintf(fd3,"%d",i);
SP 151         fclose(fd3);
152         ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
d7a113 153     }
37d14a 154     fclose(fd);
5a3862 155     if(fd2!=NULL) fclose(fd2);
d7a113 156     return TS_SUCCESS;
SP 157 }
d7639a 158
37d14a 159 ts_bool single_timestep(ts_vesicle *vesicle,ts_double *vmsr, ts_double *bfsr){
3de289 160 //    vesicle_volume(vesicle);
SP 161 //    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a 162     ts_bool retval;
SP 163     ts_double rnvec[3];
fe5069 164     ts_uint i,j, b;
37d14a 165     ts_uint vmsrcnt=0;
aec47d 166     for(i=0;i<vesicle->vlist->n;i++){
d7639a 167         rnvec[0]=drand48();
SP 168         rnvec[1]=drand48();
169         rnvec[2]=drand48();
aec47d 170         retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a 171     if(retval==TS_SUCCESS) vmsrcnt++;        
d7639a 172     }
SP 173
37d14a 174     ts_int bfsrcnt=0;
fedf2b 175     for(i=0;i<3*vesicle->vlist->n;i++){
fe5069 176     b=rand() % vesicle->blist->n;
d7639a 177         //find a bond and return a pointer to a bond...
SP 178         //call single_bondflip_timestep...
fe5069 179         retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289 180        //     b++; retval=TS_FAIL;
37d14a 181     if(retval==TS_SUCCESS) bfsrcnt++;        
fedf2b 182     }
M 183
184     for(i=0;i<vesicle->poly_list->n;i++){
58230a 185         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M 186             rnvec[0]=drand48();
187             rnvec[1]=drand48();
188             rnvec[2]=drand48();
189             retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);    
190         }
fedf2b 191     }
M 192
58230a 193
M 194     for(i=0;i<vesicle->filament_list->n;i++){
195         for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
196             rnvec[0]=drand48();
197             rnvec[1]=drand48();
198             rnvec[2]=drand48();
199             retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);    
200         }
fedf2b 201     }
M 202  
58230a 203
fedf2b 204 //    printf("Bondflip success rate in one sweep: %d/%d=%e\n", cnt,3*vesicle->blist->n,(double)cnt/(double)vesicle->blist->n/3.0);
37d14a 205     *vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP 206     *bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289 207 //    vesicle_volume(vesicle);
SP 208 //    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a 209     return TS_SUCCESS;
SP 210 }
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