Trisurf Monte Carlo simulator
Samo Penic
2019-08-08 d43116b7d609fa9cabae4068d037c1af3a20dae8
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;
0dd5ba 27     ts_double max_z,min_z;
3d0247 28     FILE *fd1,*fd2=NULL,*fd3=NULL;
267db5 29      char filename[10000];
ac9826 30     //struct stat st;
SP 31     strcpy(filename,command_line_args.path);
32     strcat(filename,"statistics.csv");
33     //int result = stat(filename, &st);
34     FILE *fd;
35     if(start_iteration==0)
36         fd=fopen(filename,"w");
37     else
38         fd=fopen(filename,"a");
37d14a 39     if(fd==NULL){
SP 40         fatal("Cannot open statistics.csv file for writing",1);
41     }
ac9826 42     if(start_iteration==0)
SP 43         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 44
M 45      if(vesicle->sphHarmonics!=NULL){
267db5 46         strcpy(filename,command_line_args.path);
SP 47         strcat(filename,"ulm2.csv"); 
ac9826 48 //    int result = stat(filename, &st);
SP 49     if(start_iteration==0)
267db5 50         fd2=fopen(filename,"w");
ac9826 51     else
SP 52         fd2=fopen(filename,"a");
819a09 53     if(fd2==NULL){
S 54         fatal("Cannot open ulm2.csv file for writing",1);
55     }
56     if(start_iteration==0) //file does not exist
57         fprintf(fd2, "Timestep u_00^2 u_10^2 u_11^2 u_20^2 ...\n");    
5a3862 58     }
M 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
88bdd7 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;
819a09 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);
88bdd7 74     epsarea=A0/(ts_double)vesicle->tlist->n;
SP 75
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;
0dd5ba 80
SP 81     //plane confinement
82     if(vesicle->tape->plane_confinement_switch){
83         min_z=1e10;
84         max_z=-1e10;
85         for(k=0;k<vesicle->vlist->n;k++){
86             if(vesicle->vlist->vtx[k]->z > max_z) max_z=vesicle->vlist->vtx[k]->z;
87             if(vesicle->vlist->vtx[k]->z < min_z) min_z=vesicle->vlist->vtx[k]->z;
88         }
89         vesicle->confinement_plane.force_switch=0;
90         if(max_z>=vesicle->tape->plane_d/2.0){
91             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);
92             vesicle->confinement_plane.z_max = max_z;
93             vesicle->confinement_plane.force_switch=1;
94         } else {
95             vesicle->confinement_plane.z_max=vesicle->tape->plane_d/2.0;
96         }
97         if(min_z<=-vesicle->tape->plane_d/2.0){
98             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);
99             vesicle->confinement_plane.z_min = min_z;
100             vesicle->confinement_plane.force_switch=1;
101         } else {
102             vesicle->confinement_plane.z_min=-vesicle->tape->plane_d/2.0;
103         }
104         ts_fprintf(stdout,"Vesicle confinement by plane set to (zmin, zmax)=(%e,%e).\n",vesicle->confinement_plane.z_min,vesicle->confinement_plane.z_max);
105         if(vesicle->confinement_plane.force_switch) ts_fprintf(stdout,"Squeezing with force %e.\n",vesicle->tape->plane_F);
106     }
107
108     //end plane confinement
109
3de289 110 /*    vesicle_volume(vesicle);
SP 111     fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume); */
d7a113 112         for(j=0;j<mcsweeps;j++){
37d14a 113             single_timestep(vesicle, &vmsrt, &bfsrt);
SP 114             vmsr+=vmsrt;
115             bfsr+=bfsrt;
d7a113 116         }
3de289 117 /*
SP 118     vesicle_volume(vesicle);
119     fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume); */
37d14a 120         vmsr/=(ts_double)mcsweeps;
SP 121         bfsr/=(ts_double)mcsweeps;
d7a113 122         centermass(vesicle);
SP 123         cell_occupation(vesicle);
1ab449 124             dump_state(vesicle,i);
58230a 125         if(i>=inititer){
0a2c81 126             write_vertex_xml_file(vesicle,i-inititer,NULL);
267db5 127             write_master_xml_file(command_line_args.output_fullfilename);
37d14a 128             epochtime=get_epoch();            
SP 129             gyration_eigen(vesicle, &l1, &l2, &l3);
c0ae90 130             vesicle_volume(vesicle); //calculates just volume. 
SP 131             vesicle_area(vesicle); //calculates area.
dc77e8 132             r0=getR0(vesicle);
632960 133             if(vesicle->sphHarmonics!=NULL){
SP 134                 preparationSh(vesicle,r0);
459ff9 135                 //calculateYlmi(vesicle);
SP 136                 calculateUlmComplex(vesicle);
137                 storeUlmComplex2(vesicle);
632960 138                 saveAvgUlm2(vesicle);
22cdfd 139                 kc1=calculateKc(vesicle, 2,9);
SP 140                 kc2=calculateKc(vesicle, 6,9);
141                 kc3=calculateKc(vesicle, 2,vesicle->sphHarmonics->l);
1665aa 142                 kc4=calculateKc(vesicle, 3,6);
267db5 143                 strcpy(filename,command_line_args.path);
SP 144                 strcat(filename,"state.dat");  
145                 fd1=fopen(filename,"w");
5bb6bb 146                 fprintf(fd1,"%e %e\n",vesicle->volume, getR0(vesicle));
M 147                 for(k=0;k<vesicle->vlist->n;k++){
148                     fprintf(fd1,"%e %e %e %e %e\n",
149                         vesicle->vlist->vtx[k]->x,
150                         vesicle->vlist->vtx[k]->y,
151                         vesicle->vlist->vtx[k]->z,
152                         vesicle->vlist->vtx[k]->solAngle,
153                         vesicle->vlist->vtx[k]->relR
154                     );
155                 }
156                 fclose(fd1);
5a3862 157         
M 158             fprintf(fd2,"%u ", i);
159             for(l=0;l<vesicle->sphHarmonics->l;l++){
160                 for(m=l;m<2*l+1;m++){
161                     fprintf(fd2,"%e ", gsl_complex_abs2(vesicle->sphHarmonics->ulmComplex[l][m]) );
162                 }
163             }
164                 fprintf(fd2,"\n");
165     
166                 fflush(fd2);    
167
632960 168             }
dc77e8 169
c0ae90 170             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 171
632960 172             fflush(fd);    
144784 173         //    sprintf(filename,"timestep-%05d.pov",i-inititer);
fe24d2 174         //    write_pov_file(vesicle,filename);
49981c 175         } //end if(inititer....)
SP 176         fd3=fopen(".status","w"); //write status file when everything is written to disk.
177         if(fd3==NULL){
178             fatal("Cannot open .status file for writing",1);
d7a113 179         }
49981c 180         fprintf(fd3,"%d",i);
SP 181         fclose(fd3);
182         ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
d7a113 183     }
37d14a 184     fclose(fd);
5a3862 185     if(fd2!=NULL) fclose(fd2);
d7a113 186     return TS_SUCCESS;
SP 187 }
d7639a 188
37d14a 189 ts_bool single_timestep(ts_vesicle *vesicle,ts_double *vmsr, ts_double *bfsr){
3de289 190 //    vesicle_volume(vesicle);
SP 191 //    fprintf(stderr,"Volume before TS=%1.16e\n", vesicle->volume);
d7639a 192     ts_bool retval;
SP 193     ts_double rnvec[3];
fe5069 194     ts_uint i,j, b;
37d14a 195     ts_uint vmsrcnt=0;
aec47d 196     for(i=0;i<vesicle->vlist->n;i++){
d7639a 197         rnvec[0]=drand48();
SP 198         rnvec[1]=drand48();
199         rnvec[2]=drand48();
aec47d 200         retval=single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
37d14a 201     if(retval==TS_SUCCESS) vmsrcnt++;        
d7639a 202     }
SP 203
37d14a 204     ts_int bfsrcnt=0;
fedf2b 205     for(i=0;i<3*vesicle->vlist->n;i++){
fe5069 206     b=rand() % vesicle->blist->n;
d7639a 207         //find a bond and return a pointer to a bond...
SP 208         //call single_bondflip_timestep...
fe5069 209         retval=single_bondflip_timestep(vesicle,vesicle->blist->bond[b],rnvec);
3de289 210        //     b++; retval=TS_FAIL;
37d14a 211     if(retval==TS_SUCCESS) bfsrcnt++;        
fedf2b 212     }
M 213
214     for(i=0;i<vesicle->poly_list->n;i++){
58230a 215         for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
M 216             rnvec[0]=drand48();
217             rnvec[1]=drand48();
218             rnvec[2]=drand48();
219             retval=single_poly_vertex_move(vesicle,vesicle->poly_list->poly[i],vesicle->poly_list->poly[i]->vlist->vtx[j],rnvec);    
220         }
fedf2b 221     }
M 222
58230a 223
M 224     for(i=0;i<vesicle->filament_list->n;i++){
225         for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){
226             rnvec[0]=drand48();
227             rnvec[1]=drand48();
228             rnvec[2]=drand48();
229             retval=single_filament_vertex_move(vesicle,vesicle->filament_list->poly[i],vesicle->filament_list->poly[i]->vlist->vtx[j],rnvec);    
230         }
fedf2b 231     }
M 232  
58230a 233
fedf2b 234 //    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 235     *vmsr=(ts_double)vmsrcnt/(ts_double)vesicle->vlist->n;
SP 236     *bfsr=(ts_double)bfsrcnt/(ts_double)vesicle->vlist->n/3.0;
3de289 237 //    vesicle_volume(vesicle);
SP 238 //    fprintf(stderr,"Volume after TS=%1.16e\n", vesicle->volume);
d7639a 239     return TS_SUCCESS;
SP 240 }
241
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243