void
count_test(void)
{
struct count *count = count_new();
struct timeval tv;
int i;
gettimeofday(&tv, NULL);
count_internal_increment(count, &tv, 3);
if (count_get_sum(&count->seconds) != 3)
errx(1, "second count should be 1");
tv.tv_sec += 61;
count_internal_increment(count, &tv, 2);
count_internal_increment(count, &tv, 0);
if (count_get_sum(&count->seconds) != 2)
errx(1, "second count should be 1");
if (count_get_sum(&count->minutes) != 3)
errx(1, "minute count should be 1");
tv.tv_sec += 3540;
count_internal_increment(count, &tv, 1);
if (count_get_sum(&count->seconds) != 1)
errx(1, "second count should be 1");
if (count_get_sum(&count->minutes) != 2)
errx(1, "minute count should be 1");
if (count_get_sum(&count->hours) != 3)
errx(1, "hour count should be 1");
count_internal_print(stderr, count, "test-count");
for (i = 0; i < 24; i++) {
tv.tv_sec += 3600;
count_internal_increment(count, &tv, 0);
}
count_internal_print(stderr, count, "test-count");
if (count_get_sum(&count->seconds) ||
count_get_sum(&count->minutes) ||
count_get_sum(&count->hours))
errx(1, "all counts should be zero");
fprintf(stderr, "\t%s: OK\n", __func__);
}
int main(int argc, char *argv[])
{
struct Map_info in, out, vis;
struct GModule *module; /* GRASS module for parsing arguments */
struct Option *input, *output; /* The input map */
struct Option *coor, *ovis;
char *mapset;
struct Point *points;
struct Line *lines;
int num_points, num_lines;
int n = 0;
/* initialize GIS environment */
G_gisinit(argv[0]); /* reads grass env, stores program name to G_program_name() */
/* initialize module */
module = G_define_module();
module->keywords = _("vector, path, visibility");
module->description = _("Visibility graph construction.");
/* define the arguments needed */
input = G_define_standard_option(G_OPT_V_INPUT);
output = G_define_standard_option(G_OPT_V_OUTPUT);
coor = G_define_option();
coor->key = "coordinate";
coor->key_desc = "x,y";
coor->type = TYPE_STRING;
coor->required = NO;
coor->multiple = YES;
coor->description = _("One or more coordinates");
ovis = G_define_option();
ovis->key = "vis";
ovis->type = TYPE_STRING;
ovis->required = NO;
ovis->description = _("Add points after computing the vis graph");
/* options and flags parser */
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
Vect_check_input_output_name(input->answer, output->answer,
GV_FATAL_EXIT);
Vect_set_open_level(2);
mapset = G_find_vector2(input->answer, NULL); /* finds the map */
if (mapset == NULL)
G_fatal_error("Vector map <%s> not found", input->answer);
if (Vect_open_old(&in, input->answer, mapset) < 1) /* opens the map */
G_fatal_error(_("Unable to open vector map <%s>"),
G_fully_qualified_name(input->answer, mapset));
if (Vect_open_new(&out, output->answer, WITHOUT_Z) < 0) {
Vect_close(&in);
G_fatal_error(_("Unable to create vector map <%s>"), output->answer);
}
if (ovis->answer != NULL) {
mapset = G_find_vector2(ovis->answer, NULL);
if (Vect_open_old(&vis, ovis->answer, mapset) < 1)
G_fatal_error(_("Unable to open vector map <%s>"),
G_fully_qualified_name(ovis->answer, mapset));
if (Vect_copy_map_lines(&vis, &out) > 0)
G_fatal_error(_("Unable to copy elements from vector map <%s>"),
G_fully_qualified_name(ovis->answer, mapset));
}
if (G_projection() == PROJECTION_LL)
G_warning(_("Lat-long projection"));
/* counting how many points and lines we have to allocate */
count(&in, &num_points, &num_lines);
/* modify the number if we have new points to add */
if (coor->answers != NULL)
num_points += count_new(coor->answers);
/* and allocate */
points = G_malloc(num_points * sizeof(struct Point));
lines = G_malloc(num_lines * sizeof(struct Line));
/* and finally set the lines */
load_lines(&in, &points, &num_points, &lines, &num_lines);
if (coor->answers != NULL)
add_points(coor->answers, &points, &num_points);
if (ovis->answer == NULL)
construct_visibility(points, num_points, lines, num_lines, &out);
else
visibility_points(points, num_points, lines, num_lines, &out, n);
G_free(points);
G_free(lines);
Vect_build(&out);
Vect_close(&out);
Vect_close(&in);
exit(EXIT_SUCCESS);
}
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;
}
int main(int argc, char *argv[])
{
struct Map_info in, out, vis;
struct GModule *module; /* GRASS module for parsing arguments */
struct Option *input, *output; /* The input map */
struct Option *coor, *ovis;
struct Point *points;
struct Line *lines;
int num_points, num_lines;
int n = 0;
/* initialize GIS environment */
G_gisinit(argv[0]); /* reads grass env, stores program name to G_program_name() */
/* initialize module */
module = G_define_module();
G_add_keyword(_("vector"));
G_add_keyword(_("network"));
G_add_keyword(_("shortest path"));
G_add_keyword(_("visibility"));
module->description = _("Performs visibility graph construction.");
/* define the arguments needed */
input = G_define_standard_option(G_OPT_V_INPUT);
output = G_define_standard_option(G_OPT_V_OUTPUT);
coor = G_define_standard_option(G_OPT_M_COORDS);
ovis = G_define_standard_option(G_OPT_V_MAP);
ovis->key = "visibility";
ovis->required = NO;
ovis->label = _("Name of input vector map containing visible points");
ovis->description = _("Add points after computing the visibility graph");
/* options and flags parser */
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
Vect_check_input_output_name(input->answer, output->answer,
G_FATAL_EXIT);
Vect_set_open_level(2);
if (Vect_open_old(&in, input->answer, "") < 1) /* opens the map */
G_fatal_error(_("Unable to open vector map <%s>"), input->answer);
if (Vect_open_new(&out, output->answer, WITHOUT_Z) < 0) {
Vect_close(&in);
G_fatal_error(_("Unable to create vector map <%s>"), output->answer);
}
if (ovis->answer != NULL) {
if (Vect_open_old(&vis, ovis->answer, "") < 1)
G_fatal_error(_("Unable to open vector map <%s>"), ovis->answer);
if (Vect_copy_map_lines(&vis, &out) > 0)
G_fatal_error(_("Unable to copy elements from vector map <%s>"),
ovis->answer);
}
if (G_projection() == PROJECTION_LL)
G_warning(_("Lat-long projection"));
/* counting how many points and lines we have to allocate */
count(&in, &num_points, &num_lines);
/* modify the number if we have new points to add */
if (coor->answers != NULL)
num_points += count_new(coor->answers);
/* and allocate */
points = G_malloc(num_points * sizeof(struct Point));
lines = G_malloc(num_lines * sizeof(struct Line));
/* and finally set the lines */
load_lines(&in, &points, &num_points, &lines, &num_lines);
if (coor->answers != NULL)
add_points(coor->answers, &points, &num_points);
if (ovis->answer == NULL)
construct_visibility(points, num_points, lines, num_lines, &out);
else
visibility_points(points, num_points, lines, num_lines, &out, n);
G_free(points);
G_free(lines);
Vect_copy_head_data(&in, &out);
Vect_hist_copy(&in, &out);
Vect_hist_command(&out);
Vect_build(&out);
Vect_close(&out);
Vect_close(&in);
exit(EXIT_SUCCESS);
}