int main()
{
long seed = TKsetSeed();
double AA,BB;
double stokes[4];
double Ex2,Sx2,Sy2,Ey2,Nx2,ExEys,EyExs,Ny2;
double ax,c,ay,d;
double ax_r,ax_i,ax2,c2,ay_r,ay_i,ay2,d2;
double c_r,c_i,d_r,d_i;
double noise_axex;
double noise_axsx;
double noise_cey;
double noise_csy;
double noise_nx;
double noise_ct1;
double noise_ct2;
double noise_ct3;
double noise_ct4;
double noise_ct5;
double noise_ct6;
double noise_ct7;
double noise_ct8;
double noise_ct9;
double noise_ct10;
double ndof;
int nbin;
int i;
double c_bw = 256.0e6/1024.0;
double t_sub = 60;
double rho2;
nbin = 256;
Nx2 = 0.1; // Noise term for LNA 1
Ny2 = 0.1; // Noise term for LNA 2
Sx2 = 0.1; // Sky noise
Sy2 = 0.1; // Sky noise
ax_r = 0.01;
ax_i = 0.04;
c_r = 0.02;
c_i = 0.005;
ay_r = 0.02;
ay_i = 0.05;
d_r = 0.02;
d_i = 0.005;
ax2 = ax_r*ax_r+ax_i*ax_i;
c2 = c_r*c_r+c_i*c_i;
ax =sqrt(ax2);
c = sqrt(c2);
ay2 = ay_r*ay_r+ay_i*ay_i;
d2 = d_r*d_r+d_i*d_i;
ay =sqrt(ay2);
d = sqrt(d2);
for (i=0;i<nbin;i++)
{
if (i > 50 && i < 200) // Cal ON
{
Ex2 = 1;
Ey2 = 1;
stokes[0] = 1;
stokes[1] = 0;
stokes[2] = 1;
stokes[3] = 0;
}
else // Cal OFF
{
Ex2 = 0;
Ey2 = 0;
stokes[0] = 1;
stokes[1] = 0;
stokes[2] = 0;
stokes[3] = 0;
}
// Calculate mean value of AA
AA = ax2*(Ex2+Sx2) + c2*(Ey2 + Sy2) + Nx2 + stokes[2]*(ax_r*c_r + ax_i*c_i)
+ stokes[3]*(ax_i*c_r-ax_r*c_i);
// Calculate auto noise terms
ndof = c_bw*t_sub/(double)nbin;
noise_axex = ax2*Ex2/sqrt(ndof);
noise_axsx = ax2*Sx2/sqrt(ndof);
noise_cey = c2*Ey2/sqrt(ndof);
noise_csy = c2*Sy2/sqrt(ndof);
noise_nx = Nx2/sqrt(ndof);
AA += TKgaussDev(&seed)*noise_axex;
AA += TKgaussDev(&seed)*noise_axsx;
AA += TKgaussDev(&seed)*noise_cey;
AA += TKgaussDev(&seed)*noise_csy;
AA += TKgaussDev(&seed)*noise_nx;
// Calculate cross noise terms
rho2 = pow(stokes[2]/2.0,2)+pow(stokes[3]/2.0,2);
if (Ex2 > 0 && Ey2 > 0)
noise_ct1 = 2*ax*c*sqrt(Ex2)*sqrt(Ey2)/sqrt(ndof)*sqrt(0.5*(1+rho2/Ex2/Ey2));
else noise_ct1 = 0;
noise_ct2 = 2*ax*c*sqrt(Sx2)*sqrt(Sy2)/sqrt(ndof);
noise_ct3 = 2*ax*c*sqrt(Ex2)*sqrt(Sy2)/sqrt(ndof);
noise_ct4 = 2*ax*c*sqrt(Sx2)*sqrt(Ey2)/sqrt(ndof);
noise_ct5 = 2*c*c*sqrt(Ey2)*sqrt(Sy2)/sqrt(ndof);
noise_ct6 = 2*ax*ax*sqrt(Ex2)*sqrt(Sx2)/sqrt(ndof);
noise_ct7 = 2*ax*sqrt(Ex2)*sqrt(Nx2)/sqrt(ndof);
noise_ct8 = 2*ax*sqrt(Sx2)*sqrt(Nx2)/sqrt(ndof);
noise_ct9 = 2*c*sqrt(Ey2)*sqrt(Nx2)/sqrt(ndof);
noise_ct10 = 2*c*sqrt(Sy2)*sqrt(Nx2)/sqrt(ndof);
AA += TKgaussDev(&seed)*noise_ct1;
AA += TKgaussDev(&seed)*noise_ct2;
AA += TKgaussDev(&seed)*noise_ct3;
AA += TKgaussDev(&seed)*noise_ct4;
AA += TKgaussDev(&seed)*noise_ct5;
AA += TKgaussDev(&seed)*noise_ct6;
AA += TKgaussDev(&seed)*noise_ct7;
AA += TKgaussDev(&seed)*noise_ct8;
// NOW CALCULATE BB
// Calculate mean value of BB
BB = ay2*(Ey2+Sy2) + d2*(Ex2 + Sx2) + Ny2 + stokes[2]*(ay_r*d_r + ay_i*d_i)
+ stokes[3]*(ay_i*d_r-ay_r*d_i);
// Calculate auto noise terms
noise_axex = ay2*Ey2/sqrt(ndof); // This naming scheme is misleading - just copied from AA
noise_axsx = ay2*Sy2/sqrt(ndof);
noise_cey = d2*Ex2/sqrt(ndof);
noise_csy = d2*Sx2/sqrt(ndof);
noise_nx = Ny2/sqrt(ndof);
BB += TKgaussDev(&seed)*noise_axex;
BB += TKgaussDev(&seed)*noise_axsx;
BB += TKgaussDev(&seed)*noise_cey;
BB += TKgaussDev(&seed)*noise_csy;
BB += TKgaussDev(&seed)*noise_nx;
// Calculate cross noise terms
rho2 = pow(stokes[2]/2.0,2)+pow(stokes[3]/2.0,2);
if (Ey2 > 0 && Ex2 > 0)
noise_ct1 = 2*ay*d*sqrt(Ey2)*sqrt(Ex2)/sqrt(ndof)*sqrt(0.5*(1+rho2/Ex2/Ey2));
else noise_ct1 = 0;
noise_ct2 = 2*ay*d*sqrt(Sy2)*sqrt(Sx2)/sqrt(ndof);
noise_ct3 = 2*ay*d*sqrt(Ey2)*sqrt(Sx2)/sqrt(ndof);
noise_ct4 = 2*ay*d*sqrt(Sy2)*sqrt(Ex2)/sqrt(ndof);
noise_ct5 = 2*d*d*sqrt(Ex2)*sqrt(Sx2)/sqrt(ndof);
noise_ct6 = 2*ay*ay*sqrt(Ey2)*sqrt(Sy2)/sqrt(ndof);
noise_ct7 = 2*ay*sqrt(Ey2)*sqrt(Ny2)/sqrt(ndof);
noise_ct8 = 2*ay*sqrt(Sy2)*sqrt(Ny2)/sqrt(ndof);
noise_ct9 = 2*d*sqrt(Ex2)*sqrt(Ny2)/sqrt(ndof);
noise_ct10 = 2*d*sqrt(Sx2)*sqrt(Ny2)/sqrt(ndof);
BB += TKgaussDev(&seed)*noise_ct1;
BB += TKgaussDev(&seed)*noise_ct2;
BB += TKgaussDev(&seed)*noise_ct3;
BB += TKgaussDev(&seed)*noise_ct4;
BB += TKgaussDev(&seed)*noise_ct5;
BB += TKgaussDev(&seed)*noise_ct6;
BB += TKgaussDev(&seed)*noise_ct7;
BB += TKgaussDev(&seed)*noise_ct8;
printf("%d %g %g\n",i,AA,BB);
// double noise_axex;
// double noise_axsx;
// double noise_cey;
// double noise_csy;
// double noise_nx;
}
}
void populateRedNoiseModel(rednoisemodel_t* model,long seed){
int t_npts;
int i;
double freq,A,index;
double t_samp,f_bin,t_span;
float *data;
fftwf_plan plan;
fftwf_complex *spectrum;
double secperyear=365*86400.0;
t_samp=(model->end - model->start)/(float)model->npt;
model->start-=t_samp;
model->end+=t_samp*2.0;
if (seed == 0){
seed=TKsetSeed();
}else if (seed > 0){
seed=-seed;
}
t_npts=model->npt*model->nreal;
spectrum = (fftwf_complex*) fftwf_malloc((t_npts/2+1)*sizeof(fftwf_complex));
data = (float*) fftwf_malloc(t_npts*sizeof(float));
t_span=(model->end - model->start)/365.25; // years
t_samp=t_span/(float)model->npt;
model->tres=t_samp*365.25;
f_bin=1.0/(t_span*model->nreal); // frequency in yr^-1
// To convert PSD to FFT power, need to multiply by N^2/T.
// BUT FFTW does not divide by N^2 on inverse transform
// so we need to divide by N^2.
// The factor of 4, converts one-sided P to 2-sided P as
// we input one-sided, and FFTW expected 2-sided.
//
// I am now 99% sure this is correct. George looked at it too!
// M. Keith 2013.
A=model->pwr_1yr /(4*t_span*model->nreal);
// we are forming "amplitudes" not powers
// so square root.
index=model->index/2.0;
A = sqrt(A);
// form a complex spectrum, then do a c2r transform.
spectrum[0]=0;
for (i=1; i < t_npts/2+1; i++){
freq=(double)i*f_bin;
double scale=0;
if(model->mode==MODE_T2CHOL){
// same definition as the Cholesky code (except index is negative)
scale=A*pow(1.0+pow(fabs(freq)/model->flatten,2),index/2.0);
}
if(model->mode==MODE_SIMPLE){
if (freq < model->flatten)
freq=model->flatten;
scale = A*pow(freq,index);
if (freq < model->cutoff)scale=0;
}
// complex spectrum
spectrum[i]=(scale*TKgaussDev(&seed) + I*scale*TKgaussDev(&seed));
}
plan=fftwf_plan_dft_c2r_1d(t_npts,spectrum,data,FFTW_ESTIMATE);
fftwf_execute(plan);
fftwf_destroy_plan(plan);
fftwf_free(spectrum);
model->data=data;
}
extern "C" int graphicalInterface(int argc,char *argv[],pulsar *psr,int *npsr)
{
char parFile[MAX_PSR][MAX_FILELEN];
char timFile[MAX_PSR][MAX_FILELEN];
int i,nit,j,p;
char fname[MAX_FILELEN];
double globalParameter;
long double result;
long seed = TKsetSeed();
//
// For the output file
//
toasim_header_t* header;
toasim_header_t* read_header;
FILE* file;
double offsets[MAX_OBSN]; // Will change to doubles - should use malloc
// Create a set of corrections.
toasim_corrections_t* corr = (toasim_corrections_t*)malloc(sizeof(toasim_corrections_t));
corr->offsets=offsets;
corr->params=""; // Normally leave as NULL. Can store this along with each realisation.
// Same length string in every iteration - defined in r_param_length see below
corr->a0=0; // constant
corr->a1=0; // a1*x
corr->a2=0; // a2*x*X
*npsr = 0;
nit = 1;
printf("Graphical Interface: addGaussian\n");
printf("Author: G. Hobbs, M. Keith\n");
printf("Version: 1.0\n");
/* Obtain all parameters from the command line */
for (i=2;i<argc;i++)
{
if (strcmp(argv[i],"-nreal")==0){
nit=atoi(argv[++i]);
}
if (strcmp(argv[i],"-f")==0)
{
strcpy(parFile[*npsr],argv[++i]);
strcpy(timFile[*npsr],argv[++i]);
(*npsr)++;
}
if (strcmp(argv[i],"-seed")==0){
sscanf(argv[++i],"%d",&seed);
}
}
if (seed > 0)seed=-seed;
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
// Now read in all the .tim files
readTimfile(psr,timFile,*npsr); /* Load the arrival times */
preProcess(psr,*npsr,argc,argv);
for (p=0;p<*npsr;p++)
{
printf("NTOA = %d\n",psr[p].nobs);
header = toasim_init_header();
strcpy(header->short_desc,"addGaussian");
strcpy(header->invocation,argv[0]);
strcpy(header->timfile_name,timFile[p]);
strcpy(header->parfile_name,"Unknown");
header->idealised_toas="NotSet"; // What should this be
header->orig_parfile="NA";
header->gparam_desc=""; // Global parameters
header->gparam_vals="";
header->rparam_desc=""; // Desciprtion of the parameters
header->rparam_len=0; // Size of the string
header->seed = seed;
header->ntoa = psr[p].nobs;
header->nrealisations = nit;
// First we write the header...
sprintf(fname,"%s.addGauss",timFile[p]);
file = toasim_write_header(header,fname);
for (i=0;i<nit;i++)
{
if(i%10 == 0){
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("Iteration %d/%d",i+1,nit);
fflush(stdout);
}
for (j=0;j<psr[p].nobs;j++){
offsets[j] = (double)(psr[p].obsn[j].toaErr*1.0e-6*TKgaussDev(&seed));
}
toasim_write_corrections(corr,header,file);
}
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b");
printf("Iteration %d/%d\n",i,nit);
printf("Close file\n");
fclose(file);
}
return 0;
}
extern "C" int graphicalInterface(int argc,char *argv[],pulsar *psr,int *npsr)
{
longdouble imjd=-1.0,fmjd=-1.0,ra,grms=0.0;
longdouble toa,ha0,almst,amjd,hnobs,mjd,trmjd,tstep=0.0;
longdouble times[MAX_OBSN];
longdouble out[MAX_OBSN];
longdouble lowFreq,highFreq,alpha=-3.0,ampPL=1.0e-16;
int setref=0;
int nshots,npts;
int j,count=0,i,k,ii,jj,kk;
longdouble solsid = 1.002737909;
longdouble obslong = 149.0; /* Longitude of Parkes */
longdouble freq = 1440.0;
long iseed;
int site = 7,p;
int endit=0;
long idum = 0;
int nday = -1;
float ngap=-1.0;
char parFile[MAX_PSR][MAX_FILELEN];
char timFile[MAX_PSR][MAX_FILELEN];
char str[MAX_FILELEN],str2[MAX_FILELEN];
double hamax =-1.0;
char random[100];
char read_f=0;
FILE *fout,*fin;
char addCubic[100]="n",temp[100];
char formstr[50]="tempo2";
char smooth[100]="n";
int psrNum,giveRMS=-1,setrand=-1,setred=-1,Npsr=0;
int timesFile=0;
char fake_fname[100];
char have_outfile=0;
char outfile[100];
char timesfname[100];
char telID[128]="7"; // Hardcode to Parkes
int bunching=0; // flag on whether or not observations occur in groups
// size of gap between observing runs, and length of observing runs.
// These defaults give 7 observations every 28 days.
long double gapsize=21,hillsize=7,gapstartmjd;
// Flag whether or not to ask for red noise variables.
*npsr = 1;
strcpy(fake_fname,"fake.rf");
for (i=0;i<argc;i++){
if(strcmp(argv[i],"-ndobs")==0){
sscanf(argv[i+1],"%f",&ngap);
printf("Have >>%f<< days between observations\n",ngap);
}
if(strcmp(argv[i],"-nobsd")==0){
sscanf(argv[i+1],"%d",&nday);
printf("Have >>%d<< observations per day\n",nday);
}
if (strcmp(argv[i],"-idum")==0){
sscanf(argv[i+1],"%d",&idum);
printf("Have idum >>%d<<\n",idum);
}
if(strcmp(argv[i],"-ha")==0){
sscanf(argv[i+1],"%lf",&hamax);
printf("Have maximum absolute HA >>%lf<<\n",hamax);
}
if(strcmp(argv[i],"-randha")==0){
strcpy(&random[0],argv[i+1]);
printf("Have random >>%s<<\n",random);
setrand=1;
}
if(strcmp(argv[i],"-start")==0){
sscanf(argv[i+1],"%Lf",&imjd);
printf("Have initial MJD >>%lf<<\n",(double)imjd);
}
if(strcmp(argv[i],"-tel")==0){
sscanf(argv[i+1],"%s",telID);
}
if(strcmp(argv[i],"-end")==0){
sscanf(argv[i+1],"%Lf",&fmjd);
printf("Have final MJD >>%lf<<\n",(double)fmjd);
}
if(strcmp(argv[i],"-rms")==0){
sscanf(argv[i+1],"%Lf",&grms);
giveRMS=1;
printf("Have Gaussian noise rms >>%lf<<\n",(double)grms);
}
if(strcmp(argv[i],"-format")==0){
sscanf(argv[i+1],"%s",&formstr);
printf("Have output format >>%s<<\n",formstr);
}
if (strcmp(argv[i],"-times")==0){
timesFile=1;
sscanf(argv[i+1],"%s",×fname);
printf("Timesfile = %s\n",timesfname);
}
if (strcmp(argv[i],"-setref")==0)
setref=1;
if (strcmp(argv[i],"-o")==0){
have_outfile=1;
sscanf(argv[i+1],"%s",&outfile);
printf("outfile = %s\n",outfile);
}
if (strcmp(argv[i],"-readtim")==0){
read_f=1;
printf("Read name,freq,mjd\n");
}
if(strcmp(argv[i],"-group")==0){
bunching = 1;
sscanf(argv[i+1],"%Lf",&hillsize);
sscanf(argv[i+2],"%Lf",&gapsize);
printf("Will simulate runs of %lg observing days long and leave a gap of %lg days between runs.\n",
(double)hillsize,(double)gapsize);
}
if(strcmp(argv[i],"-h")==0){
printf("==========================================================================================\n");
printf(" fake Tempo2 plugin - usage instructions.\n");
printf(" tempo2 -gr fake -f file.par: The program will prompt you for parameters.\n");
printf("\n Command-line arguments:\n");
printf(" \t -f J0437-4715.par J1909-3744.par J1713+0747.par: specify a number of parfiles.\n");
printf(" \t -ndobs xxx: specify number of days between observations.\n");
printf(" \t -nobsd xxx: specify number of observations per day.\n");
printf(" \t -ha xxx: specify maximal absolute Hour Angle.\n");
printf(" \t -randha y: specify whether to use random HA coverage or not (y/n).\n");
printf(" \t -start xxxxx: specify start MJD.\n");
printf(" \t -end xxxxx: specify final MJD.\n");
printf(" \t -rms xxx: specify Gaussian noise rms (in ms).\n");
printf(" \t -times xxx: read observation times from specified file\n");
printf(" \t suppresses questions for red noise characteristics.\n");
printf(" \t -format parkes : sets the tim-file format to tempo. (Default: tempo2).\n");
printf(" \t -group 7 21 : simulate observations in groups of 7 days, with 21 days between groups.\n");
printf(" \t There will be nobsd observations every ndobs days during these 7 days.\n");
printf("\n\n \t -idum xxx: specify random number seed (default = set from clock)\n");
printf("\n The program will prompt you for the parameters not defined in the command line.\n");
printf("\n\n Have a nice day!\n\n");
printf("==========================================================================================\n");
exit(0);
}
if(strcmp(argv[i],"-f")==0){
Npsr=0;
while(argv[i+Npsr+1][0]!='-'){
strcpy(parFile[Npsr],argv[i+Npsr+1]);
printf("Have parfile %d: >>%s<<.\n",Npsr+1,parFile[Npsr]);
Npsr++;
if(i+Npsr+1>=argc) break;
}
printf("Have %d parameter files.\n",Npsr);
}
}
if (timesFile==1)
{
nday = 1;
ngap = 1;
hamax = 8;
setrand = 1;
imjd = 1;
fmjd = 1;
}
printf("Simulate arrival times for parameter file %s\n",argv[3]);
printf("----------------------------------------------------\n\n");
if(ngap<0){ printf("Enter number of days between observations . "); scanf("%f",&ngap);}
if(nday<0) { printf("Enter number of observations/day .......... "); scanf("%d",&nday);}
if(hamax<0 && nday!=1) {
printf("Enter max absolute HA...................... "); scanf("%lf", &hamax);}
if(setrand!=1){ printf("Random HA coverage? (y/n) ................. "); scanf("%s",&random);}
if(imjd<0) { printf("Enter initial MJD ......................... "); scanf("%Lf",&imjd);}
if(fmjd<0) { printf("Enter final MJD ........................... "); scanf("%Lf",&fmjd);}
if(giveRMS<0){
printf("Enter Gaussian noise rms (ms/auto)........ "); scanf("%s",temp);
giveRMS = sscanf(temp,"%Lf",&grms);
}
printf("GIVE RMS = %d\n",giveRMS);
if (idum==0)
{
printf("Setting random number seed from the clock\n");
idum = TKsetSeed();
}
iseed = idum;
psrNum = Npsr;
if (timesFile==1)
fin = fopen(timesfname,"r");
hnobs = nday/2.0;
for(ii=0;ii<Npsr;ii++){
count = 0;
strcpy(parFile[0],parFile[ii]);
printf("SET: %d\n",psr[0].param[param_pb].val[0]);
psr[0].nJumps=0;
psr[0].fitMode=0;
psr[0].eclCoord=0;
psr[0].nits=1;
psr[0].clockFromOverride[0] = '\0';
psr[0].nCompanion = 0;
psr[0].bootStrap = 0;
psr[0].units = SI_UNITS;
psr[0].ne_sw = NE_SW_DEFAULT;
psr[0].nWhite = 0; /* No whitening by default */
psr[0].timeEphemeris = IF99_TIMEEPH;
psr[0].dilateFreq = 1;
psr[0].planetShapiro = 1;
psr[0].correctTroposphere = 1;
psr[0].t2cMethod = T2C_IAU2000B;
psr[0].fixedFormat=0;
psr[0].nStorePrecision=0;
strcpy(psr[0].deleteFileName,"NONE");
strcpy(psr[0].tzrsite,"NULL");
psr[0].calcShapiro=1;
psr[0].ipm = 1;
psr[0].swm = 0;
psr[0].nPhaseJump=0;
for (i=0;i<MAX_PARAMS;i++)
{
for (j=0;j<psr[0].param[i].aSize;j++)
{
psr[0].param[i].fitFlag[j] = 0;
psr[0].param[i].paramSet[j] = 0;
psr[0].param[i].err[j] = 0;
psr[0].param[i].val[j] = 0;
}
}
// initialise(psr,0); /* Initialise the structures */
// printf("SET AFTER 1: %d\n",psr[0].param[param_pb].val[0]);
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
// printf("SET AFTER 2: %d %s\n",psr[0].param[param_pb].val[0],psr[0].name);
ra = (double)psr[0].param[param_raj].val[0]/2.0/M_PI;
/* Code based on fake1.f to calculate the TOA at transit for each of these observations */
trmjd = imjd;
/* 47892.0 = 1990??? */
almst = fortran_mod((trmjd-47892.0)*solsid+0.276105324+obslong/360.0,(longdouble)1.0);
/* Hour angle at 00h UT */
ha0 = almst - ra;
/* Approximate transit time */
if (ha0 < 0.0) ha0+=1.0;
trmjd += 1.0-ha0;
if (nday > 1)tstep = hamax/12.0/nday; /* Was 0.4/nday */
amjd = trmjd;
gapstartmjd = imjd+(hillsize)/solsid;
do {
for (j=0;j<nday;j++)
{
if (timesFile==1)
{
if (read_f){
if (fscanf(fin,"%s %Lf %Lf\n",fake_fname,&freq,&mjd)==3)
{
printf("Read %g %f\n",(double)mjd, (double)freq);
endit=0;
}
else
endit=1;
} else{
if (fscanf(fin,"%Lf",&mjd)==1)
{
printf("Read %g\n",(double)mjd);
endit=0;
}
else
endit=1;
}
}
else
{
if (random[0]=='y'||random[0]=='Y')
amjd=trmjd + (rand()/(longdouble)RAND_MAX - 0.5)*hamax/12.0;
else if (nday==1)
amjd=trmjd;
else
amjd=trmjd + ((j+1)-hnobs)*tstep;
mjd=amjd;
}
if (endit==0)
{
if (count==0 && setref==1)
{
psr[0].obsn[count].sat = psr[0].param[param_tzrmjd].val[0];
strcpy(psr[0].obsn[count].fname,"reference");
psr[0].obsn[count].freq = psr[0].param[param_tzrfrq].val[0];
if (giveRMS!=1) grms = psr[0].param[param_tres].val[0]/1e3;
// else grms=0.0;
psr[0].obsn[count].toaErr = grms*1000.0;
psr[0].obsn[count].origErr = grms*1000.0;
psr[0].obsn[count].phaseOffset = 0.0;
strcpy(psr[0].obsn[count].telID, psr[0].tzrsite);
psr[0].obsn[count].deleted = 0;
psr[0].obsn[count].clockCorr=1;
psr[0].obsn[count].delayCorr=1;
psr[0].obsn[count].efac=1;
count++;
}
psr[0].obsn[count].sat = mjd;
strcpy(psr[0].obsn[count].fname,fake_fname);
psr[0].obsn[count].freq = freq;
if (giveRMS!=1) grms = psr[0].param[param_tres].val[0]/1e3;
// else grms=0.0;
psr[0].obsn[count].toaErr = grms*1000.0;
psr[0].obsn[count].origErr = grms*1000.0;
psr[0].obsn[count].phaseOffset = 0.0;
strcpy(psr[0].obsn[count].telID, telID);
psr[0].obsn[count].deleted = 0;
psr[0].obsn[count].clockCorr=1;
psr[0].obsn[count].delayCorr=1;
psr[0].obsn[count].efac=1;
count++;
if (count>MAX_OBSN)
{
printf("Number of TOAs > MAX_OBSN.\n");
count--;
}
}
}
if((bunching == 1) && (trmjd >= (gapstartmjd-1))){
trmjd += gapsize/solsid;
gapstartmjd += (gapsize+hillsize)/solsid;
}
else{
trmjd+=ngap/solsid;
}
}while ((timesFile == 0 && amjd<fmjd) || (timesFile == 1 && endit==0));
if (timesFile==1)
fclose(fin);
psr[0].nobs=count;
if (have_outfile){
strcpy(str,outfile);
strcpy(timFile[0],outfile);
}else{
strcpy(str,parFile[0]);
str[strlen(str)-4]='\0';
strcat(str,".simulate");
strcpy(timFile[0],str);
}
/* Now run the tempo2 code */
preProcess(psr,*npsr,argc,argv);
callFit(psr,*npsr); /* Do all the fitting routines */
for (j=0;j<9;j++)
{
/* Now update the site arrival times depending upon the residuals */
for (i=0;i<psr[0].nobs;i++)
{
psr[0].obsn[i].sat -= psr[0].obsn[i].prefitResidual/SECDAY;
psr->obsn[i].nFlags = 0;
}
writeTim(str,psr,"tempo2");
// initialise(&psr[ii],0);
// Reset the jumps
psr[ii].nJumps = 0;
for(kk=0;kk<MAX_JUMPS;kk++){
psr[ii].jumpVal[kk] = 0.0;
psr[ii].jumpValErr[kk] = 0.0;
}
for(jj=0;jj<MAX_PARAMS;jj++){
psr[ii].param[jj].nLinkTo = 0;
psr[ii].param[jj].nLinkFrom = 0;
}
readParfile(psr,parFile,timFile,*npsr); /* Load the parameters */
readTimfile(psr,timFile,*npsr);
preProcess(psr,1,argc,argv);
/* Now run the superTEMPO code again */
callFit(psr,*npsr); /* Do all the fitting routines */
}
printf("Complete 10 iterations\n");
for (i=0;i<psr[0].nobs;i++)
{
psr[0].obsn[i].sat -= psr[0].obsn[i].prefitResidual/SECDAY;
psr->obsn[i].nFlags = 0;
}
for (i=0;i<psr[0].nobs;i++)
{
times[i] = (psr[0].obsn[i].sat-psr[0].param[param_posepoch].val[0]);
}
npts = psr[0].nobs;
/* Add Gaussian noise */
if (giveRMS!=1) grms = psr[0].param[param_tres].val[0]/1e3;
if (grms>0.0)
{
printf("Adding Gaussian noise with rms = %f\n",(float)grms);
for (i=0;i<psr[0].nobs;i++)
psr[0].obsn[i].sat += TKgaussDev(&idum)*grms/1000.0/SECDAY;
}
printf("Output TOA file written to %s\n",str);
writeTim(str,psr,formstr);
}
}