void simulation(float mu, float koff){
/*set up variables for RNG, generate seed that's time-dependent,
* seed RNG with that value - guarantees that MPI instances will
* actually be different from each other*/
const gsl_rng_type * T;
gsl_rng_env_setup();
T = gsl_rng_default;
gsl_rng *r;
r = gsl_rng_alloc (T);
unsigned long int seed;
seed=gen_seed();
gsl_rng_set(r,seed);
/*old legacy stuff
//memset(lanes,0,NLANES*L*sizeof(int));
//lanes[8][48]=22;
//FILE *fp;*/
/*define total time of simulation (in units of polymerizing events)*/
int totaltime=500;
/*define number of ends in the system, necessary for depol
* calculation and rates. Also, define a toggle for the first pol
* event to reset*/
int ends=0;
int newends=0;
int first=1;
/*just declare a bunch of stuff that we will use*/
float domega,kon;
int accepted=0;
int filaments,noconsts;
int int_i;
int j,k,size,currfils,currlen,gap,l,m;
float i,p,coverage;
int type=0;
/*declare two matrices for the filaments per lane, one for the
* "permanent" stuff and one for temporary testing in the
* Metropolis scheme*/
int lanes[NLANES][L]={{0}};
int newlanes[NLANES][L]={{0}};
/*two floats to store the time of the next polymerization and depol
* events, that will be initialized later*/
float nexton=0;
float nextoff=VERYBIG;
/*declare three GMP arbitrary precision values: one for storing the
* current number of microstates, one for the new number when testing
* in the Metropolis scheme and one to store the difference*/
mpz_t states;
mpz_t newstates;
mpz_t deltastates;
mpz_init(states);
mpz_init(newstates);
mpz_init(deltastates);
/*sets up: the value of the chemical potential of a monomer, the
* on-rate (we're always taking it to be one), the off-rate
* (defined in relation to the on-rate) and the average size of
* a new polymer*/
kon=1;
//float kon=1.0;
//float koff=0.1; //try based on ends
//printf("%f %f\n",kon,koff);
int avg_size=3;
p=1.0/avg_size;
float inv_sites=1.0/(NLANES*(L-1));
clock_t t1 = clock();
/*sets up the I/O to a file - filename is dependent on MPI
* instance number to avoid conflicts*/
char* filename[40];
//int my_rank=0;
int my_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&my_rank);
sprintf(filename,"outputs_%1.1f_%1.1f/run%d.txt",mu,koff,my_rank);
FILE *fp = fopen(filename, "w");
//strcat(filename,threadnum);
//strcat(filename,".txt");
/*sets up the time for the first on event (first off only calculated
* after we have filaments!)*/
nexton=gsl_ran_exponential(r,1.0/kon);
//nextoff=gsl_ran_exponential(r,1.0/koff);
//printf("nexton=%f nexoff=%f, avg on=%f avg off=%f thread=%d\n",nexton,nextoff,1.0/kon,1.0/koff,omp_get_thread_num());
/*start of the main loop*/
for (i=0;i<totaltime;i=i+0.01){
clock_t t2 = clock();
//printf("thread=%d i=%f\n",omp_get_thread_num(),i);
/*before anything else, make a copy of the current lanes into
* the matrix newlanes*/
memcpy(newlanes,lanes,sizeof(lanes));
newends=ends;
/*calculate the current coverage (sites occupied divided by the
* total number of sites) and output to file the current "time"
* and coverage*/
coverage=0;
for (k=0;k<NLANES;k++){
for (j=1;j<lanes[k][0]+1;j++){
coverage=coverage+lanes[k][j];
}
}
//printf("total length=%f\n",coverage);
coverage=coverage*inv_sites;
//printf("coverage=%f\n",coverage);
fprintf(fp, "%f %f %f\n", i,coverage,ends,(double)(t2-t1)/CLOCKS_PER_SEC);
//printf("%f %f\n",i,coverage);
//printf("i=%f nexton=%f nextoff=%f type=%d\n",i,nexton,nextoff,type);
/*tests for events, with priority for polymerizing - if both
* are due, it will polymerize first and only depol in the next
* timestep*/
if (i>=nextoff){
type=2;}
if (i>=nexton){
type=1;
}
/*we will now calculate the number of filaments and constraints
* in the system, going over each lane - relatively
* straightforward!*/
filaments=0;
noconsts=0;
for (k=0;k<NLANES;k++){
//printf("according to main, %d filaments in lane %d\n",newlanes[k][0],k);
filaments=filaments+newlanes[k][0];
noconsts=noconsts+2*newlanes[k][0];
if (newlanes[k][0]>1){
noconsts=noconsts+newlanes[k][0];
}
}
/*polymerization event!*/
if (type==1){
/*big legacy stuff - leave it alone!*/
//printf("lanes at beginning: filaments=%d noconsts=%d\n",filaments,noconsts);
//for (k=0;k<NLANES;k++){
//printf("lane %d: ",k);
//for (j=1;j<lanes[k][0]+1;j++){
//printf("%d ",lanes[k][j]);
//}
//printf("\n");
//}
//if (i>0) count(states,argc, argv, lanes, filaments, noconsts);
//gmp_printf("%Zd\n",states);
/*sample exponential to get the size of the filament to be
* added (integer exponential is geometric!)*/
size=gsl_ran_geometric(r,p);
/*pick a lane at random to add the new filament*/
/*parentheses: in the system without stickers, as long as
* this step of random sampling doesn't change, we're fine -
* order inside lane doesn't really matter!*/
j=gsl_rng_uniform_int(r,NLANES);
/*calculate the current number of filaments and occupied
* length in the chosen lane*/
currfils=lanes[j][0];
currlen=0;
for (k=1;k<currfils+1;k++){
currlen=currlen+lanes[j][k];
}
//printf("currlen %d currfils %d\n",currlen,currfils);
/*test if there's enough space to insert the new filament*/
if (currlen+currfils+size+2>L)
continue;
/*if there is, pick a "gap" to insert the filament in
* (i.e. the place in the order of filaments of that lane)*/
else{
gap=1+gsl_rng_uniform_int(r,currfils+1);
/*if it's not at the end of the order, need to move the other
* ones in the lanes matrix to open space for the new one*/
if (gap!=currfils+1){
for (k=currfils;k>gap-1;k--){
newlanes[j][k+1]=newlanes[j][k];
}
}
/*insert new filament...*/
newlanes[j][gap]=size;
/*...and update the number of filaments in the lane*/
newlanes[j][0]++;
}
/*calculate number of filaments and constraints for the
* newlanes matrix - seems like a waste of a for loop, eh?*/
filaments=0;
noconsts=0;
for (k=0;k<NLANES;k++){
//printf("according to lanes, %d filaments in lane %d\n",newlanes[k][0],k);
filaments=filaments+newlanes[k][0];
noconsts=noconsts+2*newlanes[k][0];
if (newlanes[k][0]>1){
noconsts=noconsts+newlanes[k][0];
}
}
//printf("lanes after adding: filaments=%d noconsts=%d\n",filaments,noconsts);
//printf("proposed change:\n");
//for (k=0;k<NLANES;k++){
//printf("lane %d: ",k);
//for (j=1;j<newlanes[k][0]+1;j++){
//printf("%d ",newlanes[k][j]);
//}
//printf("\n");
//}
/*count microstates after addition!*/
count_new(&newstates, newlanes, filaments, noconsts);
//fprintf(fp,"count=");
//value_print(fp, P_VALUE_FMT, newstates);
//fprintf(fp,"\n");
//gmp_printf("states=%Zd\n",states);
//gmp_printf("newstates=%Zd\n",newstates);
/*calculate delta omega for the addition - chemical potential
* plus entropy difference - this should always work since we
* set states to 0 in the very first iteration*/
domega=-mu*size-mpzln(newstates)+mpzln(states);
//printf("delta omega: %f log10newstates=%f log10states=%f\n",domega, mpzln(newstates),mpzln(states));
/*metropolis test - if delta omega is negative, we accept
* the addition*/
if (domega<0){
memcpy(lanes,newlanes,sizeof(lanes));
mpz_set(states,newstates);
if (size==1){
ends=ends+1;
}else if (size>1){
ends=ends+2;
}
if (first==1){
first=0;
nextoff=gsl_ran_exponential(r,1.0/(koff*ends));
}else{
nextoff=i+gsl_ran_exponential(r,1.0/(koff*ends));
}
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
memcpy(lanes,newlanes,sizeof(lanes));
mpz_set(states,newstates);
if (size==1){
ends=ends+1;
}else if (size>1){
ends=ends+2;
}
if (first==1){
first=0;
nextoff=gsl_ran_exponential(r,1.0/(koff*ends));
}else{
nextoff=i+gsl_ran_exponential(r,1.0/(koff*ends));
}
//printf("accepted anyway!\n");
}
}
//printf("final result:\n");
//for (k=0;k<NLANES;k++){
//printf("lane %d: ",k);
//for (j=1;j<lanes[k][0]+1;j++){
//printf("%d ",lanes[k][j]);
//}
//printf("\n");
//}
/*calculate time of next polymerization event and reset type*/
nexton=nexton+gsl_ran_exponential(r,1.0/kon);
//printf("nexton: %f\n",nexton);
type=0;
}
/*Depol event! We need to check for number of filaments here
* (note that "filaments" here is the one calculated at the
* beginning of the for loop) because if there are no filaments
* we just need to recalculate nextoff and keep going*/
if (type==2 && filaments>0){
//printf("entered depol\n");
//printf("filaments: %d\n",filaments);
/*this is one of those conditions that shouldn't be necessary,
* but I needed to add this at some point and now I'm afraid
* to take it out and break the whole thing, so there you go*/
if (i>0 && filaments>0 ) {
//count(states,argc, argv, lanes, filaments, noconsts);
//gmp_printf("%Zd\n",states);
/*pick a filament to decrease size - this will be changed
* soon!*/
//j=gsl_rng_uniform_int(r,filaments)+1;
//printf("j=%d\n",j);
j=gsl_rng_uniform_int(r,ends)+1;
//fprintf(fp,"j=%d out of %d\n",j,ends);
/*need to replicate the routine below, but with more
* intelligence to track ends - maybe create small
* test program to try it in isolation?*/
/*go through lanes until you find the filament to be
* decreased in size. Then, decrease size by one, check
* whether the filament disappeared (in which case following
* filaments need to be shifted left and number of filaments
* in lane decreased). Finally, break from the for loop*/
int end_counter=0;
int doneit=0;
for (k=0;k<NLANES;k++){
//fprintf(fp,"k=%d nd_counter=%d, lane has %d filaments\n",k,end_counter,lanes[k][0]);
for (l=1;l<lanes[k][0]+1;l++){
if (lanes[k][l]==1){
end_counter=end_counter+1;
}else{
end_counter=end_counter+2;
}
if (j<=end_counter){
//fprintf(fp,"filaments=%d k=%d end_counter=%d thing to change=%d\n",filaments,k,end_counter,newlanes[k][l]);
newlanes[k][l]=newlanes[k][l]-1;
if (newlanes[k][l]==1){
newends=newends-1;
}
if (newlanes[k][l]==0){
for (m=l;m<newlanes[k][0];m++){
newlanes[k][m]=newlanes[k][m+1];
}
newlanes[k][0]--;
newends=newends-1;
}
doneit=1;
break;
}
}
if (doneit==1){
break;
}
}
}
//printf("nextoff=%f\n",nextoff);
type=0;
filaments=0;
noconsts=0;
for (k=0;k<NLANES;k++){
//printf("according to lanes, %d filaments in lane %d\n",newlanes[k][0],k);
filaments=filaments+newlanes[k][0];
noconsts=noconsts+2*newlanes[k][0];
if (newlanes[k][0]>1){
noconsts=noconsts+newlanes[k][0];
}
}
//printf("rank %d is dumping previous lanes:\n",my_rank);
//dump_lanes(lanes);
//printf("rank %d is dumping its %d filaments and noconsts %d\n",my_rank,filaments,noconsts);
//dump_lanes(newlanes);
/*metropolis test should go in here*/
count_new(&newstates, newlanes, filaments, noconsts); //<-segfault is here!
//fprintf(fp,"count=");
//value_print(fp, P_VALUE_FMT, newstates);
//fprintf(fp,"\n");
//gmp_printf("states=%Zd\n",states);
//gmp_printf("newstates=%Zd\n",newstates);
/*calculate delta omega for the addition - chemical potential
* plus entropy difference - this should always work since we
* set states to 0 in the very first iteration*/
domega=mu-mpzln(newstates)+mpzln(states);
//fprintf(fp,"depol domega=%f, diff in mpzln=%f\n",domega,domega-1);
if (domega<0){
memcpy(lanes,newlanes,sizeof(lanes));
mpz_set(states,newstates);
ends=newends;
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
memcpy(lanes,newlanes,sizeof(lanes));
mpz_set(states,newstates);
}
}
if (ends>0){
/*recalculate nextoff and reset type*/
nextoff=nextoff+gsl_ran_exponential(r,1.0/(koff*ends));
}else{
nextoff=VERYBIG;
//first=1;
}
/*recalculate the number of filaments and constraints (could
* be done more efficiently, but whatever)*/
filaments=0;
noconsts=0;
for (k=0;k<NLANES;k++){
//printf("according to lanes, %d filaments in lane %d\n",newlanes[k][0],k);
filaments=filaments+lanes[k][0];
noconsts=noconsts+2*lanes[k][0];
if (lanes[k][0]>1){
noconsts=noconsts+lanes[k][0];
}
//printf("before counting: filaments=%d noconsts=%d\n",filaments,noconsts);
}
/*recalculate total number of states - this will probably be
* part of the Metropolis test further up when this is done*/
count_new(&states, lanes, filaments, noconsts);
//fprintf(fp,"count=");
//value_print(fp, P_VALUE_FMT, states);
//fprintf(fp,"\n");
}
/*in case there's nothing to depolimerize, we set nextoff as a big
* float and reset the first flag*/
if (type==2 && filaments==0){
nextoff=VERYBIG;
//first=1;
type=0;
}
/*also, in any situation where there's no filament in the system,
* we set states to zero just to be on the safe side*/
if (filaments==0){
mpz_set_si(states,0);}
//else{
////printf("pass/ng to count: %d %d \n",filaments, noconsts);
//count_new(&states,lanes, filaments, noconsts);}
////for (k=0;k<NLANES;k++){
//////printf("lane %d: ",k);
////for (j=1;j<lanes[k][0]+1;j++){
//////printf("%d ",lanes[k][j]);
////}
////printf("\n");
//}
//printf("%d %d\n",size,j);
//printf("%d %f\n",omp_get_thread_num(),coverage);
}
/*clearing up - deallocating the arbitrary precision stuff, closing
* the I/O file and returning!*/
mpz_clear(states);
mpz_clear(newstates);
mpz_clear(deltastates);
gsl_rng_free (r);
fclose(fp);
return coverage;
}
void simulation_single(){
const int num_lanes=2;
int lane_size=100;
const gsl_rng_type * T;
gsl_rng_env_setup();
T = gsl_rng_default;
gsl_rng *r;
r = gsl_rng_alloc (T);
unsigned long int seed;
seed=gen_seed();
gsl_rng_set(r,seed);
int fil_length=150;
int stickers=1;
//glue-related!
//int stickers=0;
mpz_t states;
mpz_t newstates;
mpz_t deltastates;
mpz_init(states);
mpz_init(newstates);
mpz_init(deltastates);
const float timesteps=5000;
int my_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&my_rank);
char* filename[60];
sprintf(filename,"./output_single_filament_compact/run%d.txt",my_rank);
// sprintf(filename,"./output_single_filament_glue_%.2f/run%d.txt",kstick,my_rank);
printf("%s\n",filename);
FILE *fp = fopen(filename, "w");
if (fp == NULL) {
printf("Error");
return;
}
float mu=6.0;
float glue=1.0;
float koff=1.0;
float i;
int j,k;
float kstick=0.01;
float kunstick=0.01;
float stick_energy=3.0;
int type=0;
float nextoff=gsl_ran_exponential(r,1.0/koff);
float nextstick=gsl_ran_exponential(r,1.0/((fil_length-lane_size-stickers)*kstick));
float nextunstick=gsl_ran_exponential(r,1.0/(stickers*kunstick));
//glue-related!
// float nextstick=VERYBIG;
// float nextunstick=VERYBIG;
float peroverlap=kstick;
double domega;
float c0=1.0/lane_size;
int att_depol=0;
int acc_depol=0;
int att_stick=0;
int acc_stick=0;
int att_unstick=0;
int acc_unstick=0;
int att_contr=0;
int acc_contr=0;
int att_expan=0;
int acc_expan=0;
int att_special=0;
int acc_special=0;
float eta=0.2;
float fraction=0.0;
float delta=0.0;
clock_t t1 = clock();
//printf("before first count: %f fil_length: %d\n",kstick,fil_length);
count_isl_single(&states,fil_length,stickers,lane_size);
gmp_printf("states= %Zd\n",states);
int currpar=0;
for (i=0;i<timesteps;i=i+0.01){
fraction=fraction+0.01*delta;
//printf("%f %f %d\n",fraction,delta,currpar);
// if ((int)(fraction*20)%2!=currpar){
// fprintf(fp, "fraction=%f delta=%f\n",fraction,delta);
//
// }
// currpar=(int)(fraction*20)%2;
if (fabs(fraction)>1.0){
//fprintf(fp,"event occurring - i=%f delta=%f fraction=%f\n",i,delta,fraction);
if (fraction>0){
delta=check_contraction(fil_length,stickers,lane_size+1,c0,states,r,fp);
if (delta>VERYBIG/10){
delta=0;
fraction=0;
//fprintf(fp,"delta too big! delta is now %f\n",delta);
}else{
lane_size++;
}
}
else{
delta=check_contraction(fil_length,stickers,lane_size-1,c0,states,r,fp);
if (delta>VERYBIG/10){
delta=0;
fraction=0;
//fprintf(fp,"delta too big! delta is now %f\n",delta);
}else{
lane_size--;
}
}
fraction=0;
nextstick=i+gsl_ran_exponential(r,1.0/((fil_length-lane_size-stickers)*kstick));
}
if (stickers==0){
nextunstick=VERYBIG;
}
if (fil_length-lane_size-stickers<=0){
nextstick=VERYBIG;
}
//fprintf(fp, "fraction=%f delta=%f\n",fraction,delta);
//printf("%f %f %f %f %d %d %d %d %d %d %d %d %d %d %d %d %d\n", i,nextoff,nextstick,nextunstick,fil_length,stickers,lane_size,att_depol,acc_depol,att_stick,acc_stick,att_unstick,acc_unstick,att_contr,acc_contr,att_expan,acc_expan);
if (fil_length==0){
break;
}
if ((int)(i*100)%(int)timesteps==0){
clock_t t2 = clock();
printf("%d percent %f\n",(int)(i*100)/(int)timesteps,(double)(t2-t1)/CLOCKS_PER_SEC);
}
//fprintf(fp,"i=%f\n",i);
if ((int)(i*100)%50==0){
fprintf(fp, "%f %f %f %f %d %d %d %d %d %d %d %d %d %d %d %f %f %f %f\n", i,nextoff,nextstick,nextunstick,fil_length,stickers,lane_size,att_depol,acc_depol,att_stick,acc_stick,att_unstick,acc_unstick,att_special,acc_special,((fil_length-lane_size-stickers)*kstick),(stickers*kunstick),delta,fraction);
//gmp_fprintf(fp,"states= %Zd\n",states);
}
if (i>=nextoff){
type=1;}
if (i>=nextstick){
type=2;
}
if (i>=nextunstick){
type=3;
}
if (type==1){
int done=0;
att_depol=att_depol+1;
int newlength=fil_length-1;
// clock_t t3 = clock();
count_isl_single(&newstates,newlength,stickers,lane_size);
// clock_t t4 = clock();
// printf("depol time: %f\n",(double)(t4-t3)/CLOCKS_PER_SEC);
if (mpz_cmp_d(newstates,0.0)){
domega=-mu+glue-mpzln(newstates)+mpzln(states);
//glue-related!
// domega=-mu+glue+peroverlap-mpzln(newstates)+mpzln(states);
if (domega<0){
acc_depol++;
fil_length=newlength;
mpz_set(states,newstates);
done=1;
// fprintf(fp,"depol - domega=%f\n",domega);
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
fil_length=newlength;
acc_depol++;
mpz_set(states,newstates);
done=1;
// fprintf(fp,"depol - domega=%f\n",domega);
}else{
// fprintf(fp,"removal not accepted - domega=%f\n",domega);
}
}
}
if (done==0){
att_special++;
// clock_t t3 = clock();
count_isl_single(&newstates,newlength,stickers-1,lane_size);
// clock_t t4 = clock();
// printf("special depol time: %f\n",(double)(t4-t3)/CLOCKS_PER_SEC);
domega=stick_energy-mu+glue-mpzln(newstates)+mpzln(states);
if (domega<0){
fil_length=newlength;
stickers=stickers-1;
acc_depol++;
acc_special++;
mpz_set(states,newstates);
//fprintf(fp,"depol and removal - domega=%f\n",domega);
}
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
fil_length=newlength;
stickers=stickers-1;
acc_depol++;
acc_special++;
mpz_set(states,newstates);
//fprintf(fp,"depol and removal - domega=%f\n",domega);
}else{
// fprintf(fp,"depol w/unstick not accepted - domega=%f\n",domega);
}
}
}
att_contr++;
att_expan++;
delta=check_contraction(fil_length,stickers,lane_size,c0,states,r,fp);
delta=delta/eta;
// if (delta==-1){
// acc_contr++;
// }
// if (delta==+1){
// acc_expan++;
// }
// lane_size=lane_size+delta;
nextoff=i+gsl_ran_exponential(r,1.0/koff);
nextstick=i+gsl_ran_exponential(r,1.0/((fil_length-lane_size-stickers)*kstick));
type=0;
}
if (type==2){
att_stick++;
int newstickers=stickers+1;
// clock_t t3 = clock();
count_isl_single(&newstates,fil_length,newstickers,lane_size);
// clock_t t4 = clock();
// printf("new sticker time: %f\n",(double)(t4-t3)/CLOCKS_PER_SEC);
domega=-stick_energy-mpzln(newstates)+mpzln(states);
if (domega<0){
stickers=newstickers;
acc_stick++;
mpz_set(states,newstates);
// fprintf(fp,"added sticker - domega=%f\n",domega);
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
stickers=newstickers;
acc_stick++;
mpz_set(states,newstates);
// fprintf(fp,"added sticker - domega=%f\n",domega);
}else{
// fprintf(fp,"addition sticker rejected - domega=%f\n",domega);
}
}
att_contr++;
att_expan++;
delta=check_contraction(fil_length,stickers,lane_size,c0,states,r,fp);
delta=delta/eta;
// if (delta==-1){
// acc_contr++;
// }
// if (delta==+1){
// acc_expan++;
// }
// lane_size=lane_size+delta;
nextstick=i+gsl_ran_exponential(r,1.0/((fil_length-lane_size-stickers)*kstick));
nextunstick=i+gsl_ran_exponential(r,1.0/(stickers*kunstick));
type=0;
}
if (type==3){
att_unstick++;
int newstickers=stickers-1;
// clock_t t3 = clock();
count_isl_single(&newstates,fil_length,newstickers,lane_size);
// clock_t t4 = clock();
// printf("remove sticker time: %f\n",(double)(t4-t3)/CLOCKS_PER_SEC);
domega=stick_energy-mpzln(newstates)+mpzln(states);
if (domega<0){
acc_unstick++;
stickers=newstickers;
mpz_set(states,newstates);
//fprintf(fp,"removal - domega=%f\n",domega);
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
stickers=newstickers;
acc_unstick++;
mpz_set(states,newstates);
//fprintf(fp,"removal - domega=%f\n",domega);
}else{
// fprintf(fp,"removal of sticker not accepted - domega=%f\n",domega);
}
}
att_contr++;
att_expan++;
delta=check_contraction(fil_length,stickers,lane_size,c0,states,r,fp);
delta=delta/eta;
// if (delta==-1){
// acc_contr++;
// }
// if (delta==+1){
// acc_expan++;
// }
// lane_size=lane_size+delta;
nextunstick=i+gsl_ran_exponential(r,1.0/(stickers*kunstick));
nextstick=i+gsl_ran_exponential(r,1.0/((fil_length-lane_size-stickers)*kstick));
type=0;
}
}
mpz_clear(states);
mpz_clear(newstates);
mpz_clear(deltastates);
gsl_rng_free (r);
fclose(fp);
}
explicit randgen(boost::iterator_range<It> r, unsigned int seed = gen_seed())
: seed_(seed),
r_(r)
{}
void simulation_single(float kstick){
const int num_lanes=2;
int lane_size=1000;
const gsl_rng_type * T;
gsl_rng_env_setup();
T = gsl_rng_default;
gsl_rng *r;
r = gsl_rng_alloc (T);
unsigned long int seed;
seed=gen_seed();
gsl_rng_set(r,seed);
int fil_length=1500;
int stickers=1;
//glue-related!
//int stickers=0;
mpz_t states;
mpz_t newstates;
mpz_t deltastates;
mpz_init(states);
mpz_init(newstates);
mpz_init(deltastates);
float timesteps=50000;
int my_rank;
MPI_Comm_rank(MPI_COMM_WORLD,&my_rank);
char* filename[60];
sprintf(filename,"./output_single_filament_strong_%.2f/run%d.txt",kstick,my_rank);
// sprintf(filename,"./output_single_filament_glue_%.2f/run%d.txt",kstick,my_rank);
printf("%s\n",filename);
FILE *fp = fopen(filename, "w");
if (fp == NULL) {
printf("Error");
return;
}
float mu=6.0;
float glue=1.0;
float koff=1.0;
float i;
int j,k;
//float kstick=0.05;
float kunstick=kstick;
float stick_energy=8.0;
int type=0;
int delta=0;
float nextoff=gsl_ran_exponential(r,1.0/koff);
float nextstick=gsl_ran_exponential(r,1.0/kstick);
float nextunstick=gsl_ran_exponential(r,1.0/kunstick);
//glue-related!
// float nextstick=VERYBIG;
// float nextunstick=VERYBIG;
float peroverlap=kstick;
double domega;
float c0=1.0/lane_size;
int att_depol=0;
int acc_depol=0;
int att_stick=0;
int acc_stick=0;
int att_unstick=0;
int acc_unstick=0;
int att_contr=0;
int acc_contr=0;
int att_expan=0;
int acc_expan=0;
count_isl_single(&states,fil_length,stickers,lane_size);
for (i=0;i<timesteps;i=i+0.01){
if (fil_length==0){
break;
}
if ((int)(i*100)%(int)timesteps==0){
printf("%d\%\n",(int)(i*100)/timesteps);
}
if ((int)(i*100)%50==0){
fprintf(fp, "%f %f %f %f %d %d %d %d %d %d %d %d %d %d %d %d %d\n", i,nextoff,nextstick,nextunstick,fil_length,stickers,lane_size,att_depol,acc_depol,att_stick,acc_stick,att_unstick,acc_unstick,att_contr,acc_contr,att_expan,acc_expan);
}
if (i>=nextoff){
type=1;}
if (i>=nextstick){
type=2;
}
if (i>=nextunstick){
type=3;
}
if (type==1){
att_depol=att_depol+1;
int newlength=fil_length-1;
count_isl_single(&newstates,newlength,stickers,lane_size);
if (!mpz_cmp_d(newstates,0.0)){
count_isl_single(&newstates,newlength,stickers-1,lane_size);
domega=stick_energy-mu+glue-mpzln(newstates)+mpzln(states);
if (domega<0){
fil_length=newlength;
stickers=stickers-1;
acc_depol++;
mpz_set(states,newstates);
//fprintf(fp,"depol and removal - domega=%f\n",domega);
}
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
fil_length=newlength;
stickers=stickers-1;
acc_depol++;
mpz_set(states,newstates);
//fprintf(fp,"depol and removal - domega=%f\n",domega);
}else{
//fprintf(fp,"depol w/unstick not accepted - domega=%f\n",domega);
}
}
}else{
domega=-mu+glue-mpzln(newstates)+mpzln(states);
//glue-related!
// domega=-mu+glue+peroverlap-mpzln(newstates)+mpzln(states);
if (domega<0){
acc_depol++;
fil_length=newlength;
mpz_set(states,newstates);
//fprintf(fp,"depol - domega=%f\n",domega);
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
fil_length=newlength;
acc_depol++;
mpz_set(states,newstates);
//fprintf(fp,"depol - domega=%f\n",domega);
}else{
//fprintf(fp,"removal not accepted - domega=%f\n",domega);
}
}
}
att_contr++;
att_expan++;
delta=check_contraction(fil_length,stickers,lane_size,c0,states,r,fp);
if (delta==-1){
acc_contr++;
}
if (delta==+1){
acc_expan++;
}
lane_size=lane_size+delta;
nextoff=i+gsl_ran_exponential(r,1.0/koff);
type=0;
}
if (type==2){
att_stick++;
int newstickers=stickers+1;
count_isl_single(&newstates,fil_length,newstickers,lane_size);
domega=-stick_energy-mpzln(newstates)+mpzln(states);
if (domega<0){
stickers=newstickers;
acc_stick++;
mpz_set(states,newstates);
//fprintf(fp,"added sticker - domega=%f\n",domega);
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
stickers=newstickers;
acc_stick++;
mpz_set(states,newstates);
//fprintf(fp,"added sticker - domega=%f\n",domega);
}else{
//fprintf(fp,"addition sticker rejected - domega=%f\n",domega);
}
}
delta=check_contraction(fil_length,stickers,lane_size,c0,states,r,fp);
if (delta==-1){
acc_contr++;
}
if (delta==+1){
acc_expan++;
}
lane_size=lane_size+delta;
nextstick=i+gsl_ran_exponential(r,1.0/kstick);
type=0;
}
if (type==3){
att_unstick++;
int newstickers=stickers-1;
count_isl_single(&newstates,fil_length,newstickers,lane_size);
domega=stick_energy-mpzln(newstates)+mpzln(states);
if (domega<0){
acc_unstick++;
stickers=newstickers;
mpz_set(states,newstates);
//fprintf(fp,"removal - domega=%f\n",domega);
}
/*if it's positive, we calculate the probability of acceptance
* and test for it*/
else{
double prob=exp(-1.0*domega);
double fromthehat=gsl_rng_uniform(r);
//printf("metropolising: rng=%f, prob=%f\n",fromthehat,prob);
if (fromthehat<prob){
stickers=newstickers;
acc_unstick++;
mpz_set(states,newstates);
//fprintf(fp,"removal - domega=%f\n",domega);
}else{
//fprintf(fp,"removal of sticker not accepted - domega=%f\n",domega);
}
}
delta=check_contraction(fil_length,stickers,lane_size,c0,states,r,fp);
if (delta==-1){
acc_contr++;
}
if (delta==+1){
acc_expan++;
}
lane_size=lane_size+delta;
nextunstick=i+gsl_ran_exponential(r,1.0/kunstick);
type=0;
}
}
