TEMPO2 user manual - Jodrell Bank Centre for Astrophysics
Contents
1. For instance in order to display the site arrival time the barycentric arrival time and the Solar Shapiro delay for each observation for i 0 i lt psr 0 nobs i printf values Lf Lf fWn psr 0 obsn il sat psr 0 obsn il bat psr 0 obsn i shapiroDelaySun 14 1 2 A new graphical interface When a graphical interface is used TEMPO2 checks the command line arguments initialises the memory and then passes control to the graphical interface The reading of the parameter and observation files calculating barycentric arrival times obtaining residuals fitting and displaying the output must all be done within the graphical interface The following TEMPO2 functions are commonly called 32 readParfile Read the parameter file readTimfile Read the observation file preProcess Needs to be called after reading the parameter and observation files formBatsAll Forms the barycentric arrival times formResiduals Forms the timing residuals doFit Calls the fitting algorithms text utput The standard output display An example of a simple interface would be include lt stdio h gt include lt string h gt include lt stdlib h gt include lt math h gt include tempo2 h using namespace std The main function called from the TEMPO02 package is graphicalInterface Therefore this function is required in all plugins extern C int2. 24224 sss 14 1 2 A new graphical interface ee 14 2 The main sourcecode u wo ea ee ew BORE a SUR Bok wR ae Ge ek UR e 15 Tempo2 error and warning messages I5 I Error4nessageS iocur melo wide Ga ae a A ee a ee GP es rcp roe a a T 15 2 Warning messages qos enum a ee en a ed aR a AA IP Y 16 Common questions 17 In progress 18 Acknowledgements 31 31 31 32 34 34 34 34 35 35 35 List of Figures 1 a pre fit timing residuals for the test data set and b post fit timing residuals 8 2 An example of the basic graphical interface A P P diagram is produced with the pulsar being analysed highlighted eh 23 3 Example of the chisq plug in for determining the most likely values of the orbital period PB and longitude of periastron OM es 24 4 The solar system Shapiro delay for PSR J1810 2005 shown using the DELAYS graphical interface plugin i 25 eS Sea ee det Pow doh Gk ae PUR Aur dub UP EAE hid A 25 5 Simulating pulsar timing residuals for a pulsar with a proper motion in right ascension of 200 mas yr using the FAKE plugin 27 6 An example of the plk graphical interface in use The post fit residuals for PSR J0437 4715 are plotted with 20 observations shown in green and 10 cm observations in red The white circles and black lines indicate arrival times between orbital phases 0 4 and 0 6 28 7 Example of the SPLK graphical interface plug in for showing
3. EDOT or ECCDOT Rate of change of eccentricity OMDOT Periastron advance degrees yr PBDOT 1st time derivative of binary period PBX X th time derivative of binary period GAMMA post Keplerian gamma term s DR Relativistic deformation of the orbit DTH Relativistic deformation of the orbit AO Aberration parameter AO BO Aberration parameter BO BP Tensor multi scalar parameter beta prime BPP Tensor multi scalar parameter beta prime prime DTHETA Relativistic deformation of the orbit XOMDOT Rate of periastron advance minus GR prediction deg yr AFAC A1DOT or XDOT TASC Epoch of ascending node MJD EPSIDOT EPS2DOT KOM KIN SHAPMAX MTOT BPJEP_X BPJPH X BPJA1 X BPJEC X BPJOM_X BPJPB_X Total system mass solar masses tempo2 gr plk myfile tempo where the first line in the file contains flags with 1 to indicate that the parameter should be fit and 0 for not fitting Column Parameter 1 Phase 2 PO 3 P1 4 P2 5 RAJ 6 DECJ T PMRA 8 PMDEC 9 A1 10 ECC 11 TO 12 PB 13 OM 14 OMDOT 15 GAMMA 16 DM 13 17 PX 18 PBDOT 19 M1 not implemented 20 SINI 21 MTOT 22 M2 23 DTHETA 24 BP not implemented 25 BPP not implemented 2T Binary model O none 1 BT 2 EH 3 DD 4 DDGR 5 H88 6 BT 7 DDT 8 DD 9 2 BT orbits The actual parameter values are given on three extra lines The second line in the file gives Columns Parameter 1 12 Pulsar name 21 40 RAJ
4. T gt S E 1 MJD 51175 5 MJD 51175 5 Figure 1 a pre fit timing residuals for the test data set and b post fit timing residuals tempo2 gr plk f psri_2 par psri tim which should produce a plot of the pre fit residuals as shown in Figure la Pressing 2 on the plot will show the post fit residuals Figure 1b 4 Required files TEMPO2 requires certain files in order to run correctly These files are provided with the download and are discussed in the following sections 4 1 Clock correction files Times of arrival provided to TEMPO2 are recorded against local observatory clocks These times differ from those recorded against a uniform clock firstly because observatory clocks are typically maintained in approximate synchrony with Coordinated Universal Time UTC which itself is not uniform and secondly because they deviate from ideal UTC owing to deviations in uniformity in the underlying frequency standard usually a hydrogen maser The ultimate aim of the clock correction process is to tra
5. V define the user parameter ctrl V for pre fit plotting decompose the timing model fits W toggle fitting using weights x redo fit using post fit parameters ctrl X place periodic marks on the x scale y Rescale y axis only z Zoom using mouse add positive phase jump add negative phase jump add period to add residuals above cursor in zoom mode include previous observation in zoom mode include next observation plot pre fit residuals vs date plot post fit residuals vs date plot pre fit residuals vs orbital phase plot post fit residuals vs orbital phase plot pre fit residuals serially plot post fit residuals serially plot pre fit residuals vs day of year plot post fit residuals vs day of year plot pre fit residuals vs frequency plot post fit residuals vs frequency o c H H l i POONA OARWNRKFVA 28 J0457 4715 J0437 4715 F ENS e JE E EGG DO E SE 3 TT ot 1 or PL gi Pay 0 ar 1 7 m m Y ni oor o Q 10 N 3 Sor i E io o i i BO i Li b 2 3 tE 2 o 1 i c o cL 4 ul J 1 TO YAA PM E F 4 xr 3 loy als 1elircrclssst Lol lo 4 4 dla il y 41 3050 3100 3150 3200 3250 3050 3100 3150 3200 3250 MJD 50019 0 MJD 50019 0 1909 3744 1909 3744 T T T T 3 oL M J L l 3 li E i l QO H 4l 3 j F 3 1 Es x a V i 7 FON 4 5 L 2 Sg i o E a s X L i PE i 7 i LO a 1 1 1 1
6. instead Clock warnings e Warning CLK1 MJD later than last entry in time dat Imprecise clock corrections will be applied 34 16 Common questions Our web page provides a feedback form that allows the user to alert the software developers of any problems in the software 1 How do I cite tempo2 in my publication For basic TEMPO2 usage please give a reference to Hobbs Edwards amp Manchester 2006 submitted to MNRAS For details of the timing model please refer to Edwards Hobbs amp Manchester 2006 in preparation 2 How do I increase the number of observations that can be loaded in tempo2 Use NOBS X on the command line where X is the number of observations required the current default is 10000 observations 17 In progress TEMPO2 is continually being developed We are currently developing the following e A set of plug ins to simulate the effects of gravitational wave sources on pulsar timing residuals and to place limits on the existence of any such gravitational wave sources in real pulsar timing data 18 Acknowledgements The TEMPO2 package is based on the original TEMPO Fortran code This software was developed over many years by multiple authors including J Taylor R Manchester D Nice W Peters J Weisberg A Irwin and N Wex We thank the Australian pulsar community J Weisberg D Lorimer and M Kramer for suggestions and comments on TEMPO2 35
7. 0 98000 7 i WBC 20 archives w040207_115804 cFTp 1431 21700000 53042 50986685147659827 0 98000 7 i WBC 20 archives w040207_142934 cFTp 1431 43500000 53042 60951958276880092 0 99000 7 i WBC 20 archives w040208_081840 cFTp 1563 91900000 53043 34710640092290035 0 82000 7 i WBC 20 archives w040208 083501 cFTp 1432 49900000 53043 36886551809849877 0 78000 7 i WBC 20 archives n2004 06 27 04 13 58 FTp 685 24900000 53183 18848980008860039 0 06000 7 i nCPSR2 50 2site arrival times can be obtained from pulse profiles and a standard template using software packages such as pat 3note the pulse arrival time is measured by the summation of many thousands of individual pulses from the pulsar 15 Table 4 Flags in arrival time files Flag Parameter Type dm DM cm pc float p Phase offset float t Telescope identifier string archives n2004 07 15 18 33 23 FTp 685 24900000 53201 79496983790510001 0 08000 7 i nCPSR2 50 archives n2004 07 15 19 39 47 FTp 685 24900000 53201 81959222764389850 0 22000 7 i nCPSR2 50 archives n2004 07 15 19 42 31 FTp 685 24800000 53201 84208218378509869 0 19000 7 i nCPSR2 50 The PAT software in the PSRCHIVE package has been updated to output arrival time files using this or earlier formats A list of available commands that can be included in an arrival time file are provided in table 5 Note that when writing out a new arrival time file from TEMPO2 using a plugin such
8. 1 l 1 1 1 1 1 600 800 1000 600 800 1000 MJD 50019 0 MJD 50019 0 Figure 7 Example of the SPLK graphical interface plug in for showing the pre and post fit timing residuals for multiple pulsar simultaneously plot pre fit residuals vs TOA error plot post fit residuals vs TOA error plot pre fit residuals vs user values plot post fit residuals vs user values y plot pre fit residuals vs year plot post fit residuals vs year 13 11 polytest To be written 13 12 splk A simple graphical interface that displays pre fit and post fit timing residuals for multiple pulsars Fig ure 7 Key strokes enable the user to plot all the pulsars using the same x and y axes or to scale each axis separately and the timing residuals can be output in an ASCII format to a file tempo2 gr splk f mypari par mytimi tim f mypar2 par mytim2 tim f mypar3 par mytim3 tim 13 13 stridefit The STRIDEFIT plugin is used to fit for a pulsar parameter commonly DM using small sections of data and plotting the variation in that parameter versus time Example usage is tempo2 gr stridefit f psr par psr tim The plugin will subsequently ask for the parameter for study e g DM PMRA PMDEC The STRIDEFIT works by running a window with a width entered from a start time to an end time with a given time step These can all be entered on the command line tempo2 gr stridefit f psr par psr tim param DM start 50000 end 52
9. 3 64 3 64 0 0 N OMDOT deg yr 0 0159999997519168 0 0159999997519168 0 0 N M2 0 236 0 236 0 0 N START MJD 50640 9281162413 49350 5129309451 0 1290 4 N FINISH MJD 52088 8971386924 53000 5197060478 0 911 62 N TRACK MJD 0 0 0 0 N TZRMJD 51204 6438924841 51204 6438924841 0 0 N TZRFRQ MHz 1413 39997808495 1413 39997808495 0 0 N Binary model DD Mass function Minimum companion mass Median companion mass Maximum companion mass MTOT derived from sin i and m2 Inclination angle deg 0 001243113190 0 1403 solar masses 0 1637 solar masses 0 3493 solar masses 1 818606841374 42 74994182955 0 0 The residuals can be inspected using 0 000000047151 solar masses ir WDEC mro mr m mp WIPMRA MPMDEC WFX ERAU MDECJ mro mr mr mp MPMEA MPMDEC WFX meo ma mo mece mon MOMDOT meo mal Wo mecc mon WIOMDOT RE FIT New par Mew tim REA BNew par Mew tim J0437 4715 rms 6 895 us pre fit J0437 4715 rms 0 096 us post fit 5 TE s Ac N 2x1 idual t A i No Postfit Residual se zi E zx gt E
10. TOAs Tracks phase wrap arounds if time step is less than x days 6 1 Setting dispersion measures In some situations the dispersion measure is measured accurately for every observation This information can be provided to tempo2 by adding dm DMval on the end of each arrival time line in the TIM file If this is not present then the dispersion measure in the PAR file is used instead 6 2 Jodrell Bank Observatory binary format It is also possible to provide pulse arrival times in the Jodrell Bank format binary file that containing barycentric arrival times For instance a typical usage would be tempo2 f psrav eph psrav bat jbo delete psrav del 7 Atmospheric propagation delays to be written 8 Command line arguments TEMPO2 has a number of options that can be controlled from the command line Options include e debug provides output useful for identifying problems with the software e delete fname delete the observations listed in the file fname by their site arrival times or obser vations name e clock x define the clock in conversion to TT as X e epoch x set the epoch of the parameter file to be MJD x 17 8 1 f x par y tim specifies the parameter par and arrival time tim files to use for subsequent processing If only a tim file is present without f option then the parameter file will be assumed to be y par filter x filters the set of observations see below fit x turn on fitting
11. by 1 randomly selecting observations to produce a new dataset of the same length as the original the observations are selected with replacement ie in the new dataset some of the original observations will be omitted while others will be replicated 2 recalculating the parameter and 3 repeating as many times as possible 10 Predictive mode For on line and off line folding of pulsar data TEMPO2 can produce a set of polynomial coefficients to predict the pulse phase at any given time After a standard TEMPO 2 fit has been carried out the parameters will include the following e tzrmjd a reference TOA calculated as the first site arrival time with an MJD greater than PE POCH The residual after fitting is subsequently removed from tzrmjd to produce a site arrival time that produces zero residual e tzrfrq The frequency of the arrival time corresponding to tzrmjd e tzrsite The telescope site code corresponding to tzrmjd TEMPO2 can be used to produce predictions in a new format or in a new format 10 1 Tempo2 format To be written 10 2 Tempol format Example usage tempo2 f 0437 4715 par polyco 53000 53001 300 12 8 pks 1400 0 tempoi will request that TEMPO2 makes a prediction for J0437 4715 from MJDs 53000 to 53001 with each divided into segments each of nspan 300 minutes The number of coefficients for use in the fitting ncoeff 12 The maximum hour angle range for the prediction maxha 8 The observatory site for
12. in the form hhmmss ss 41 60 DECJ in the form ddmmss ss 61 70 PMRA 71 80 PMDEC The third line gives Columns Parameter 2 20 PO 21 40 P1 41 60 PEPOCH as Julian date 61 70 P2 71 80 PX The fourth line gives Columns Parameter 9 20 DM Further lines provide the binary parameters not implemented yet 5 0 1 tpo file format Both the parameters and the arrival times may be provided in a single file The first line of this file must be HEAD followed by the parameters in the same format as above These are followed by TOAS and a list of arrival times 5 0 2 Changing the model epoch It is possible to convert the period epoch from that given in the parameter file using the epoch command on the command line For instance epoch 52000 will update the period epoch rotational frequency and its first derivative to the new epoch using the inputted values of F0 F1 and F2 Can use epoch centre or epoch center to set to the centre of the data span epoch left will set the epoch to the first observation 14 5 1 Jumps It is often necessary to fit for a constant offset between two sets of arrival times For instance the templates used to determine arrival times at different frequencies may not be perfectly aligned or an offset may exist between the arrival times provided by different observatories The command JUMP in the parameter file is used to define jumps JUMP MJD vi v2 will provide a jump between all TOAs with MJD
13. of the old Parkes or Jodrell style TEMPO files or may use a new formatting structure The current TEMPO2 format is identified with FORMAT 1 at the start of the observation file Each observation line can be entered in a free format manner there is no limit on the number of decimal places or characters supplied for each parameter The file has the following form file freq sat satErr siteID lt flags gt where the flags are listed in Table 4 It is important for the TOAs to be given to high precision TEMPO2 reads all parameters with long double precision Other undefined flags may be used in the arrival time files These flags can provide any information and could be used for example in determining colours used for plotting with a personal graphical interface An example observation file is given below FORMAT 1 C archives w040205_062810 cFTp 3072 52800000 53040 27037033597299853 10 07000 7 i WBC 10 archives w040206 070831 cFTp 3092 99900000 53041 31851839551620031 1 16000 7 i WBC_10 C archives w040206_084839 cFTp 3068 03800000 53041 38807867413299846 9 97000 7 i WBC 10 archives w040206 111139 cFTp 3105 49900000 53041 47201962440929890 1 15000 7 i WBC 10 archives w040207 070619 cFTp 3092 99900000 53042 30720476755460169 1 21000 7 i WBC 10 archives w040207 081328 cFTp 1367 99900000 53042 35109949197099866 1 09000 7 i WBC 20 archives w040207 084227 cFTp 1415 14600000 53042 36843163794929978
14. printf Pulsar spin frequency Lg n psr 0 param param_f val 0 for i 0 i lt psr 0 nobs it printf Residual 14f n double psr 0 obsn i residual This plug in displays the pulsar s name obtained from the parameter file its post fit spin frequency and the post fit timing residuals on the screen The software is built around a STRUCTURE called PULSAR which is defined in TEMPO2 H The most important definitions in this structure are char name The pulsar name char binaryModel The binary model e g T2 BT ELL1 double ne sw The electron density at 1AU due to the solar wind int fitMode 1 if fitting with errors 0 not fitting with errors int nobs Number of observations int nits Number of iterations used for the fit int ipm 1 if the interplanetary DM correction is used O otherwise An array of pulsars is defined and therefore in order to display the name of the first three pulsars analysed printf pulsar 1 printf pulsar 2 printf pulsar 3 s n psr 0 name s n psr 1 name s n psr 2 name The structure also includes an array of parameters PARAM which are defined as param_raj param_decj param_f param_pepoch param_posepoch param_dmepoch param_dm param_pmra param_pmdec param_px param sini param pb param tO param ai param om param pmrv param ecc param edot param xpbdot param pbdot param aidot 31 param omdot
15. the prediction is site code pks at an observing frequency of freq 1400 0 Therefore the format used in definining the prediction is polyco mjdi mjd2 nspan ncoeff maxha site code freq 19 note the use of the quote marks around the parameters POLYCO_NEW DAT that takes the form of TEMPO1 For instance TEMPO2 should produce a file 0437 4715 27 Dec 03 123000 00 53000 52083333330 2 646966 0 269 7 575 27109839749 228820 173 687948999098 atca 960 12 600 000 0 5593 0 1742 5 42287549188530393e 08 1 29656588048219029e 01 8 73567925939434345e 05 3 77430102018454689e 08 3 61675384452316159e 11 5 30580886494090104e 16 2 11398949708346726e 17 7 50678735870179551e 22 7 17204723641224429e 24 2 20834139169245321e 28 1 38834331804078410e 30 6 03780300115982370e 35 TEMPO2 also produces a file NEWPOLYCO DAT which has the same parameters but listed to more decimal places Each parameter is listed on an individual line note the tempol software switches off clock corrections in predictive mode To emulate this the CLK flag in the parameter file should be set to CLK UNCORR 11 Global parameters To be written 12 Output formats The default output format provides the pre and post fit rms residuals the number of points in the fit and if a weighted fit has been carried out the reduced x value of the fit For each parameter the values of the pre and post fit parameters are listed alongside the uncertainty in the post fi
16. 0 version of this integral stored at TEMP02 ephemeris TDB 1950 2050 by specifying TIMEEPH FB90 in the pulsar parameter file 4 4 Planetary ephemeris In order to correct the arrival time to the solar system s barycentre TEMPO2 requires a solar system ephemeris By default the JPL ephemeris DE200 is chosen Different JPL ephemerides may be selected using the EPHEM FILE command in the parameter file For example EPHEM FILE pulsar psr runtime tempo tempo_ephem DE405 1950 2050 would select the DE405 JPL ephemeris If the full path is defined from TEMP02 ephemeris then the DE405 ephemeris could be selected from EPHEM DE405 4 5 Observatory definitions It is necessary for TEMPO2 to know the coordinates of the observatory In the original TEMPO a file OBSYS DAT was used that contained the coordinates of each observatory and a single character identifying code This code was used in the arrival time file Unfortunately different users used different codes for the same observatory and therefore the arrival time files were not transferable between different installations of TEMPO To avoid this TEMPO2 provides a read only database of observatories each identified by a short non cryptic mnemonic This resides in TEMPO observatory observatories dat In addition for backwards compatability or for experimental use further defintitions can be placed in extra files TEMPO2 parses every file in TEMPO observatory Each line should con
17. 000 width 300 dt 100 29 m 3 pc c DM 42 2 T j l 6 4 2 0 2 4 6 Year Figure 8 Example of the STRIDEFIT graphical interface plug in which calculates the pulsar s dispersion measure as a function fo time The STRIDEFIT plugin will produce a graph of the parameter versus time Clicking on any point will list the points that were used in deriving the parameter If there is reason to believe that any particular point is in error for instance trying to obtain a DM value with only one observing frequency then the point can be deleted using the right mouse button An example STRIDEFIT output is shown in Figure 8 After plotting the following key strokes may be used provides help zero x value for first point centre points toggle plotting day year rescale the axes quit fit a straight line to a region selected by the mouse fit and remove a straight line redo the stridefit re enter the MJD of the end point re enter the MJD of the start point change the font size for plotting enter the minimum number of observations required for a point set the graphical device re enter the width of the fit region re enter the time step or left mouse identify closest point or right mouse delete closest point zoom using the mouse list all the values list all the values and ouput to file PPRPN gt r gt qd30 wpDou0nV o RM uyNe PP 13 14 transform Transforms a TEMPO1 parameter file into a TEMPO2 compatable fi
18. 2 5056134 285 KNOCKIN m 3923069 135 146804 404 5009320 570 DEFFORD n 0 0 1 0 0 0 COE coe 3822473 365 153692 318 5085851 303 JB_MKII jbmk2 3822294 825 153862 275 5085987 071 JB_42ft jb42 1719555 576 5327021 651 4 3051967 932 LA PALMA p 1 20 1 5 000e 02 0 016 1 000e 02 50640 928 52088 897 UTC NIST DE200 3 64E 12 2 000e 13 51204 64376750220085 1413 400 7 1 5 5 000e 01 7 19 1 400e 01 0 6788 1 200e 03 0 236 1 700e 02 In more detail for a pulsar which a spin period of PO 1 23456 s with no fitting required PO 1 23456 To fit to this parameter use PO 1 23456 1 or with an uncertainty which is ignored by TEMPO2 PO 1 23456 1 0 00003 Other commands may be given in parameter files that control the algorithms used by TEMPO2 TEMPO2 only requires the following parameters PSRJ DM F0 PEPOCH RAJ and DECJ If no period epoch is provided then the position epoch is assumed to be the same as the period epoch It is also possible to provide the pulsar parameters in the old style tempo format where the arrival times and the parameters are given in the same file In this mode TEMPO2 is called only using one file e g 11 Table 2 Pulsar parameters that can be entered in a parameter file Label Description Units PSRJ PSRB or PSR Pulsar name FX e g F0 F1 F2 The X th time derivative of the rotational frequency s AD PO or P Spin period of pulsar sec P1 or Pdot Spin down rate of pu
19. 9162220122 0 0 N OM deg 1 2 1 2 0 0 N ECC 1 9186e 05 1 9186e 05 0 0 N PBDOT 10 12 3 64 3 64 0 0 N OMDOT deg yr 0 0159999997519168 0 0159999997519168 0 0 N M2 0 236 0 236 0 0 N START MJD 50640 9281162413 49350 5129309451 0 1290 4 N FINISH MJD 52088 8971386924 53000 5197060478 0 911 62 N TRACK MJD 0 0 0 0 N TZRMJD 51204 6438924841 51204 6438924841 0 0 N 20 TZRFRQ MHz 1413 39997808495 1413 39997808495 Binary model DD Mass function Minimum companion mass Median companion mass Maximum companion mass MTOT derived from sin i and m2 Inclination angle deg 0 001243113190 0 1403 solar masses 0 1637 solar masses 0 3493 solar masses 1 818606841374 0 000000047151 solar masses 42 74994182955 40 0 Other output formats have been developed and can be used as plug ins e g tempo2 output NAME fuv where NAME is the name of the output format The plug ins provided with TEMPO2 are listed below 12 1 general The GENERAL output format allows the user to detemine in a general manner the presentation of the fitted parameters For instance tempo2 output general s NORAD ALL _f TAB 20 amp ALL _p TAB 50 n f psr par psr tim will produce output in a IXTEXformat RAJ rad DECJ rad FO s 1 F1 s 2 PEPOCH MJD POSEPOCH MJD DMEPOCH MJD DM cm 3 pc PB d A1 1t s TASC MJD EPS1 EPS2 START MJD FINISH MJD TRACK MJD TZRMJD TZRFRQ MH
20. A 5 F 5 x 4 L x E Li 2 5 E o a s NE et hu Pod To E So ial v 3 7 ol EE 2 cs 4 NI t i LI E Ur lo D coe p je Mode oou peo te q gout oer po xc d 4l we l 1500 1000 500 0 500 1000 MJD 51500 0 Figure 5 Simulating pulsar timing residuals for a pulsar with a proper motion in right ascension of 200 mas yr using the FAKE plugin 13 10 plk PLK provides the user with a graphical interface that plots pre fit and post fit timing residuals versus parameters such as day TOA number binary phase or observing frequency It is based on the plk standalone package written for the original TEMPO but has been significantly enhanced The profiles corresponding to TOAs may be viewed and the TOAs deleted or identified using mouse clicks Phase jumps can easily be added and the data refit in order to improve the timing model A simple menu system allows the user to change the fitted parameters and to produce new arrival time and parameter files This graphical interface only works in single pulsar mode An example of the output is shown in Figure 6 usage tempo2 gr plk f mypar par mytim tim Options available are b Bin TOAs within certain time bin c Change fitting parameters C run unix command with filenames for highlighted observations ctrl c Toggle between period epoch and centre for the reference epoch d or right mouse delete point D or middle mouse view profile ctrl D delete highlighted
21. QUITY 84381 412 Filtering If is often useful to be able to filter the observation file before processing For instance an observer may use multiple back end systems or observatories These can be defined using flags archives n2003 01 10 17 07 45 FTp 1340 749 52649 7257990374280 0 67 7 i nCPSR2 20 archives w040206_150608 cFTp 3067 999 53041 6404217220093 34 43 7 i WBC 10 archives w040206 160503 cFTp 3067 999 53041 6813940348552 42 73 7 i WBC 10 archives w040207 133403 cFTp 1421 439 53042 5667819871316 6 92 7 i WBC 20 archives w040207_134155 cFTp 1417 998 53042 5819726383262 4 59 7 i WBC 20 If all the WBC_10 and nCPSR2 20 observations should be ignored then use tempo2 f mypar par mytim tim filter i nCPSR2 20 i WBC 10 18 8 3 Aliases Occasionally the user must repeatedly run the same tempo2 command which contains multiple arguments This can be simplified using aliases Aliases are placed in a file called TEMPO 2 alias dat as follows jodrell f psrav eph psrav bat jbo del psrav del quick newpar gr plk The user can then type tempo2 jodrell gr plk instead of tempo2 f psrav eph psrav bat jbo del psrav del gr plk 9 The bootstrap fitting algorithm Bootstrapping fitting methods can produce more realistic parameter values and uncertainties when signif icant correlations between parameters are present The bootstrapping method implemented in TEMPO2 estimates the uncertainty on a parameter
22. TEMPO user manual George Hobbs Russell Edwards Australia Telescope National Facility CSIRO PO Box 76 Epping NSW 1710 Australia documentation V2 0 Contents 1 INTRODUCTION 6 2 Obtaining and installing tempo2 6 3 A simple example of using tempo2 6 4 Required files 8 41 Clock correction fil s ia eR Roe REDIERE ce eus 8 4 1 1 Updating clock corrections e 9 4 2 Earth Orientation Parameters 4 2 ll ere 9 43 Mime ephemeriS sw A ee hee ae a ata ee 9 4 4 Planetary ephemeris i o pese e asco ee a kA ee ee Pe ed Ee ee d 10 4 5 Observatory definitions 4 ee ee 10 5 Parameter files 10 5 0 1 Aportile format Ys Gi s bee oe eR Oe ee Se dare hex 14 5 0 2 Changing the model epoch 0 00 0000 000000008 14 Sel JUMPS e cue Sots euro etes ihe che a Nd Bok Re med eerte eee A Ak heh gl 15 5 2 Removing Timing Noise 4 2 42 da a ee eers 15 5 9 Detaultwalues ea E EIE AA A ete HE RE RE 15 6 Observation files 15 6 1 Setting dispersion measures llle en 17 6 2 Jodrell Bank Observatory binary format 2 een 17 7 Atmospheric propagation delays 17 8 Command line arguments 17 8 1 The TEMPO emulation Mode 18 8 2 iJ iltenhg 2 6d uausguxe s 4 doce dri Pd BAR heb be dd LV REV d 18 A DP 19 9 The bootstrap fitting algorithm 19 10 Predictive mode 19 101 EMP O2 format aei Wh Anke em COR Ege ted Re ea a eR OS e d 19 10 2 TEMPOT format 55 vy ERREUR a SB oe Gee kb UY ae ee A Y d 19 11 Global para
23. acter ITOA Format columns item 1 2 ignored but must not be blank 10 28 TOA decimal point must be in column 15 29 34 TOA uncertainty 35 45 Observing frequency MHz 46 55 DM correction NOT IMPLEMENTED IN TEMP02 58 59 Observatory 2 characters 16 Table 5 Commands that may be included in an arrival time file Command Meaning EFAC x T2EFAC backend dfb x GLOBAL EFAC x FMIN x INCLUDE x INFO x MODE NOSKIP PHASE x SIGMA x SKIP TIME x TRACK x Multiply uncertainties by x Multiply TOA uncertainties with flag backend dfb by x Multiply all TOA uncertainties by x If for some or all of the TOAs an EFAC y is present as well then those TOAs will be multiplied by x x y Ignore TOAs with uncertainties greater than x pus Ignore TOAs with uncertainties less than x jus Put uncertainties of less than x us to x us Ignore all remaining lines in the arrival time file Additional uncertainty in us added in quadrature Ignore TOAs at frequencies greater than x Ignore TOAs at frequencies less than x Include the arrival times in file x Identify all following points with a given highlighting code MODE 0 default implies that the TOA error is not taken into account during the fitting procedure MODE 1 uses the uncer tainties see section on fitting End of SKIP statement Add phase jump Set uncertainties of following TOAs to x ps Skip all lines until NOSKIP is read Add x seconds to following
24. aking is arbitrary This path is then appended to the global list of pre defined paths Since TEMPO2 always checks this list before attempting automatic path construction subsequent transformations will always use this path if it is applicable even if the MJDs of some TOAs would have allowed for a better path Caution is therefore advised in using the automatic path construction feature when multiple paths exist 4 1 1 Updating clock corrections The distribution of TEMPO2 includes several useful files containing corrections based on the BIPM s Circular T offsets between U TC and its various realisations as well as the GPS clock and the IERS Bulletin C announcing leap seconds A suite of ancillary software is available on the TEMPO2 website which provides among other things a means for parsing Circular T to update the relevant clock correction files update clkcorr This program can also parse clock monitoring data from the Parkes Observatory Interested parties are invited to contribute code for the parsing of clock data from other sources 4 2 Earth Orientation Parameters To compute the Roemer delay the position of the observatory must be known This depends not only on the Earth s orbit but on the Earth s orientation and rotation The necessary parameters are obtained by interpolation of the C05 series of Earth Orientation Parameters EOPs from the IERS The file TEMPO02 earth README specifies the web address for downloading
25. as plk for example see Sec tion 13 10 most of these commands will not be replicated but are instead directly executed EFLOOR EMIN EMAX and EQUAD for example will be absorbed in the TOA uncertainties The exception to this is EFAC which is written to the tim file without affecting the uncertainties GLOBAL EFAC T2EFAC and EFAC are combined into a single EFAC value though The old Parkes style structure contains a label indicating the observation such as a file name containing the folded profile the observing frequency MHz the site arrival time MJD a phase offset us the uncertainty on the TOA us and an identification flag for the telescope used These identification flags are defined by the user and differ between users For example f981016 092219 FT 0 0 1374 000 51102 3925603118473 0 00 138 00 7 TEMPO can read arrival times in the Parkes Princeton and ITOA formats All these formats are fixed format and are defined as Princeton Format columns item 1 1 Observatory code 1 character 2 2 Must be blank 16 24 Observing frequency MHz 25 44 TOA decimal point must be in column 30 or 31 45 53 TOA uncertainty 69 78 DM correction NOT IMPLEMENTED IN TEMP02 Parkes Format columns item 1 1 Must be blank 26 34 Observing frequency MHz 35 55 TOA decimal point must be in column 42 56 63 Phase offset fraction of PO added to TOA 64 71 TOA uncertainty 80 80 Observatory 1 char
26. for parameter x this command line option can be repeated for multiple parameters gr x use the x graphical interface h displays help information jbo expect input in the Jodrell Bank psrav bat format list lists information about the residuals time delays etc that have been used by TEMPO2 machine x define the processor being used model name x define the pulsar name to be x ignoring what is in the parameter file newpar produces a new par file from the fitted parameters nobs re defines the maximum number of observations to be stored simultaneously in memory nofit switch off the fitting algorithms noWarnings switch off displaying warnings npsr re defines the maximum number of pulsars to be stored simultaneously in memory output name uses the name plugin instead of displaying the standard TEMPO2 output polyco runs TEMPO2 in predictive mode pre only calculates the pre fit residuals residuals outputs the residuals to a file called residuals dat set X a set the parameter X to the value a ignoring the value in the parameter file tempoi enables tempol compatibility mode The tempol emulation mode In the TEMPO1 compatibility mode the following parameters are automatically set these can also be set manually in the parameter file 8 2 UNITS TDB TIMEEPH FB90 TIMEEPH DILATEFREQ N PLANET SHAPIRO N T2CMETHOD TEMPO CORRECT_TROPOSHPHERE N NE SW 9 961 ECLIPTIC OBLI
27. graphicalInterface int argc char argv pulsar psr int npsr 1 char parFile MAX_PSR MAX_FILELEN char timFile MAX PSR MAX_FILELEN int i double globalParameter npsr 1 For a graphical interface that only shows results for one pulsar printf Graphical Interface name n printf Author author n printf Version version number n Obtain the par and the tim file from the command line if argc 4 Only provided tim name 1 strcpy timFile 0 argv 3 strcpy parFile 0 argv 3 parFile 0 strlen parFile 0 3 0 strcat parFile 0 par y btain all parameters from the command line for i 2 i lt argce it 1 if stremp argv i f 0 strcpy parFile 0 argv i 1 strcpy timFile 0 argv i 2 a readParfile psr parFile timFile npsr Load the parameters readTimfile psr timFile npsr Load the arrival times preProcess psr npsr argc argv for i 0 1 lt 2 i Do two iterations for pre and post fit residuals 1 formBatsAll psr npsr Form the barycentric arrival times formResiduals psr npsr 0 0 Form the residuals if i 0 doFit psr npsr amp globalParameter 0 0 Do the fitting else text utput psr npsr globalParameter 0 0 0 Display the output Now you have the parameters and residuals which can be displayed or plotted return 0 33 14 2 The main source code The TEMPO2 softwa
28. ion The pulsar structure also contains the set of observations and corresponding parameters The observa tion structure contains other less common parameters are defined in the TEMPO2 H file longdouble sat Site arrival time longdouble bat Barycentric arrival time int deleted 1 if observation has been deleted longdouble prefitResidual Pre fit residual longdouble residual residual double freq Frequency of observation in MHz double freqSSB Frequency of observation in barycentric frame in Hz double toaErr Error on TOA in us char fname MAX_FILELEN Name of data file giving TOA char tellID 100 Telescope ID longdouble correctionTT_TB Correction to TDB TCB double einsteinRate Derivative of correctionTT_TB longdouble correctionTT_Teph Correction to Teph longdouble correctionUT1 Correction from site TOA to UT1 double shapiroDelaySun Shapiro Delay due to the Sun double shapiroDelayJupiter Shapiro Delay due to Jupiter double shapiroDelaySaturn Shapiro Delay due to Saturn double shapiroDelayUranus Shapiro Delay due to Uranus double shapiroDelayNeptune Shapiro Delay due to Neptune double troposphericDelay Delay due to neutral refraction in atmosphere double tdis1 Interstellar dispersion measure delay double tdis2 Dispersion measure delay due to solar system longdouble roemer Roemer delay
29. istic age see Figure 2 for an example tempo2 gr basic f my The plugin also provides information such as the pulsar s spin period its derivative and the characteristic age 7 P 2P It is possible to display only pulsars within a certain declination range and to list all the pulsars currently being displayed This allows the user to obtain a list of pulsars that have similar rotational characteristics to the pulsar currently being analysed by TEMPO2 13 2 calcDM To be written 13 3 This graphical interface is used to create analyse the X value of the fit or the post fit rms residual for a one or two dimensional grid of parameter values The interface repeatedly carries out the fitting routines for specific values of one or two parameters and displays the results as a graph contour or gray scale plot chisq 23 Residuals 0 02 0 025 0 59495683483769 0 015 0 01 AOM OM 5x1075 9 9 9 0 2x10 4x107 6x107 APB PB 5 7410423416053 chisa v 1 0 G Hobbs Figure 3 Example of the chisq plug in for determining the most likely values of the orbital period PB and longitude of periastron OM This plugin is based on the parmap program developed by Swinburne University 13 4 compare Graphical interface used to compare the residuals obtained using two different parameter par files For instance different solar system ephemeris could be defined in the parameter files and the results compared
30. le tempo2 gr transform tempoi par tempo2 par back 30 where the back command is used to convert from TEMPO2 to TEMPO 14 Developing the software The plug in features of TEMPO2 implies that users can add to the functionality of TEMPO2 by producing their own plug in In this section we first discuss how such plug ins can be produced We also provide a few notes for users who are interested in developing the actual main source code and become part of the TEMPO2 development team 14 1 Creating a plug in Plug ins are relatively easy to create in C or C These plug ins may use other libraries such as PGPLOT TCL TK or QT As described above plug ins can be created to change the output format or as a graphical interface 14 1 1 A new output format When an output format plug in is used the TEMPO2 software reads in the specified parameter and observation files carries out the standard techniques to obtain pre and post fit timing residuals and their corresponding parameter values and then passes control to the output format software to display the results An example output format in C is as follows include lt stdio h gt include lt stdlib h gt include lt string h gt include lt math h gt ttinclude tempo2 h Essential for a tempo2 plugin extern C int tempoQOutput pulsar psr int npsr char timFile MAX_FILELEN char parFile MAX FILELEN 1 int i printf Pulsar name s n psr 0 name
31. lsar x10715 PEPOCH Epoch of period determination MJD RAJ or RA J2000 right ascension hh mm ss sss DECJ or DEC J2000 declination dd mm ss sss ELONG or LAMBDA Ecliptic longitude deg ELAT or BETA Ecliptic latitude deg POSEPOCH Epoch of position measurement If not present a warning is MJD given and PEPOCH is used instead PMLAMBDA or PMELONG Proper motion in ecliptic longitude mas yr PMBETA or PMELAT Proper motion in ecliptic latitude mas yr PMRA proper motion in right ascension mas yr PMDEC proper motion in declination mas yr DMEPOCH Epoch of DM measurement MJD DM Dispersion measure cm73pc DMX X th time derivative of the dispersion measure cm pcs X FDD Frequency dependent delay PX Parallax mas PMRV Radial velocity GLEP_X Glitch epoch MJD GLPH X Glitch phase increment GLFO_X Glitch permanent pulse frequency increment Hz GLF1 X Glitch permanent frequency deriv increment s 2 GLFOD X Glitch pulse frequency increment Hz GLTD X Glitch Decay time constant Hz WAVE OM Frequency of fundamental sinusoid for whitening WAVEX Amplitude of sine and cosine for the X th harmonic for whiten ing TEMPO1 Run in tempo emulation mode e g TDB units UNITS Set units to SI or TDB MODE Fitting with errors MODE 1 or without MODE 0 JUMP Add a constant offset between specified TOAs CLK Definition of clock to use TRES Rms timing residual us NOTRACK Switch off tracking mode NO SS SHAPIRO Switch off the calculation of the Solar system Shapiro delay IPM 0 to swi
32. meters 20 12 Output formats 20 I2 l geueral c4 ES RS RG A EMS ER AT RESET We ag GS 21 DA alas se a wag ene Gh Bodo BAT OM teh Bake Ge Rant Ee ie wither i bay ay Bae Boa an n 21 T23 St A a t t a a a RE S An aa a a a ae e e a a a 22 TOA n de aa a at at c dolly toe SA A A BR Sok a ee A de aaa Be a 22 13 Graphical interfaces 23 IS DASG is cette too kegs ee Pek ts A dd a itu A aq aes BE a ls 23 13 2s6aleDM a n nous ne RB ea dee ee eee ae D AI UR IS It 23 13 37 CMS c od ese uere ad dee Ae bk ur m Gok ue det es Ai ela Wk Ge dente ke et Patas Ye 23 13 4 Compare c sy yu eee EN SEE bre RT oeste HE de MC ete vo ev rod Ar e 24 13 5 compareReS oen EU euni E pu Ue He A he eo ROME S SE EUR 24 13 6 delays 5 mis RIS eue a testes b bee Wb Pose eet lt a 24 1326 GtrOrTS i4 thes els nem Ae Eom hk X mue cu om RU ol dk Bee a Re dk RM gels ep BLU ce 25 IC EC E DL ved ak de ey eh hed A A ce 25 13 9 Soria 20525 eurer do A ee dU ae aR GP TRE e d de M oe Gees 26 T9 L0plke s ue dad ear eut dae A Ne nat ted Pre gr opt de ge mate Ty 27 1311 polytest 2x94 Gok Ok ee ee oe EUR Gad eR A IR ede uper SR Y Te 2S ples ak IS shi ete Bah BCU ahah para AE Le fay pede tiens vao des Sod Cav sty Jae tO 13 TOStRIGeGHG ser ose dai RI eur eret dedit Na epee oh ee da YE Gye SAP SN ied LITA CEATISIOETIE ote eco DS en oe Gus a x i ud dh atc enn di age e teo dob wee e 14 Developing the software 14 1 Creating a plugin 4i 53 ace EA Red Se ESE GEO 14 1 1 A new output format
33. nsform all site arrival times to a chosen realisation of TT Terrestrial Time which in an ideal realisation is a uniform clock ticking SI seconds on the geoid By default this is TT TAI which since 1971 differs from UTC by a constant offset plus an integer number of leap seconds Alternative realisations of TT can be specified using the the CLOCK keyword in the parameter file The clock correction process proceeds entirely on the basis of linear interpolation of user supplied tab ulations of the difference between named pairs of clocks as a function of Modified Julian Day MJD These files reside in the directory TEMPO2 clock Lines beginning with the hash character are treated as comments The first line must be a comment specifying the name of the clock to convert from the name of the clock to convert to and an optional badness value which defaults to 1 For example the following specifies that the values in the file can be added to times measured against the Parkes clock UTC PKS to transform them to the frame of the Global Positioning System GPS clock UTC GPS UTC PKS UTC GPS 10 Non comment lines consist of a sequence of pairs of MJDs and offsets in seconds specifying the difference between the second and first clocks as a function of date For example 50844 72917 7 49068e 07 50845 77083 7 47637e 07 50846 81250 7 46650e 07 lThe frame in which the MJD is measured is not specified it is a
34. oad option to download the software to your local machine This software requires compilation before it will run Up to date installation instructions are available in a README file with the download Note TEMPO2 makes heavy use of long double precision in its calculations Most compiler architecture combinations support long doubles of 80 or 128 bits in size which is sufficient TEMPO2 has been successfully tested under Linux gcc x86 Solaris SPARC and Mac OS 10 4 gcc PowerPC Unfortunately some systems only provide 64 bit long doubles i e identical to a standard double these include Mac OS 10 3 9 and earlier and many Windows compilers While parts of the source code make reference to a software quad precision library this feature is no longer functional 3 A simple example of using tempo2 The TEMPO2 website http www atnf csiro au research pulsar tempo2 provides a set of example files for use to test the software PSR1 PAR contains the catalogued parameters for PSR J0437 4715 in standard TEMPO2 format see 5 PSR1 TIM contains a set of simulated observations of this pulsar over a 10 yr period with an rms residual of 100 ns See 86 for details of the contents of this file Running tempo2 f psri par psri tim should provide some information about clock correction files and also Results for PSR J0437 4715 RMS pre fit residual 0 096 us RMS post fit residual 0 096 us Number of points in fit 367 PARAMETER P
35. om Earth to barycentre fearth ssb3 magnitude of z component from Earth to barycentre sun_earthi magnitude of x component from Sun to Earth sun_earth2 magnitude of y component from Sun to Earth sun_earth3 magnitude of z component from Sun to Earth ism interstellar medium dispersion delay elev Source elevation npulse pulse number clock complete clock corrections to TT ipm interplanetary medium dispersion delay freq observing frequency pre prefit timing residual in seconds pre_phase prefit timing residual in phase post postfit timing residual in seconds post_phase postfit timing residual in phase err TOA error binphase binary phase For example to display the barycentric arrival times the Shapiro delay due to Jupiter and the post fit residual use tempo2 output general2 f par par tim tim s bat shapiroJ post n 12 3 list The LIST output lists the basic parameters that are being used in the TEMPO2 calculations For example tempo2 output list f mspi par msp1 tim will list the site arrival times pre and post fit residuals clock correction to UTC barycentric arrival time other clock corrections the solar system Shapiro delay the dispersion measure time delays due to the interstellar and planetary medium the Roemer delay SOE ODS SIO um vise Ne Es ephemeris values for the position of the Sun with respect to the solar system barycentre E ephemeris values fo
36. param tasc param epsi param eps2 param m2 param gamma param mtot param glep param glph param glfO param glfi param glfOd param gltd param start param finish param track param bp param bpp param tzrmjd param tzrfrq param fdd param dr param dtheta param tspan param bpjep param bpjph param bpjai param bpjec param bpjom param bpjpb param wave om param kom param kin param shapmax param dth param a0 param bO param xomdot param afac param epsidot param eps2dot param tres For each parameter the user can obtain char label Label about this parameter char shortlabel Label about this parameter without units longdouble val Value of parameter longdouble err Uncertainty on parameter value int fitFlag 1 if fitting required int paramSet 1 if parameter has been set longdouble prefit Pre fit value of the parameter longdouble prefitErr Pre fit value of the uncertainty int aSize Number of elements in the array for this parameter Each parameter is stored as an array with each element of the array typically storing time derivatives of the parameter For instance to obtain the value of the spin frequency and its first two derivatives printf values Lg Lg LgWn psr 0 param param_f va1 0 psr 0 param param_f val 1 psr 0 param param_f va1 2 Note C requires the symbol LG or LF to display values in long double precis
37. points e multiply all TOA errors by given amount f finish of zoom section F run FITWAVES ctrl F remove FITWAVES curve from residuals g change graphics device G change gridding on graphics device h this help file H highlight points with specific flag in tim file i or left mouse identify point j draw line between each points 1 list all data points in zoomed region L add label to plot ctrl 1 add line to plot m measure distance between two points M toggle removing mean from the residuals 27 0437 4715 2x10 9 Residual sec 0 T A Pa oes HB E RA Lu eB wa M rote 2x10 l 5050 5100 5150 3200 5250 MJD 50019 0 Figure 6 An example of the plk graphical interface in use The post fit residuals for PSR J0437 4715 are plotted with 20 observations shown in green and 10cm observations in red The white circles and black lines indicate arrival times between orbital phases 0 4 and 0 6 ctrl m toggle menu bar o obtain highlight all points currently in plot P Change model parameter values P write new par file ctrl P Toggle fitting versus pulse phase q quit f Reset reload par and tim file s start of zoom section S save a new tim file ctrl S Overplot Shapiro delay u unzoom U unhighlight selected points v view profiles for highlighted points
38. r masses MTOT derived from sin i and m2 1 8186068413766 Inclination angle deg 42 74994182955 0 0 PSR1_2 PAR is similar to PSR1 PAR except that the parameter values have been changed slightly from their true values As above running tempo2 f psri_2 par psri tim should produce Results for PSR J0437 4715 RMS pre fit residual 6 895 us RMS post fit residual 0 096 us Number of points in fit 367 PARAMETER Pre fit Post fit Uncertainty Difference Fit RAJ rad 1 2097885336826 1 20978853474746 2 1206e 11 1 0649e 09 Y RAJ hms 04 37 15 7865 04 37 15 7865146 2 916e 07 1 4643e 05 DECJ rad 0 824709094076948 0 824709094473468 1 5157e 11 3 9652e 10 Y DECJ dms 47 15 08 4615 47 15 08 46158 3 1264e 06 8 1788e 05 FO s 1 173 68794630603 173 687946306032 9 5579e 15 2 3306e 12 Y F1 s 2 1 728e 15 1 72831367406148e 15 2 3325e 22 3 1367e 19 Y PEPOCH MJD 51194 0001248168 51194 0001248168 0 0 N POSEPOCH MJD 51194 0001248168 51194 0001248168 0 0 N DMEPOCH MJD 51194 51194 0 0 N DM cm 3 pc 2 64690012312213 2 64690012312213 0 0 N PMRA mas yr 121 43799811708 121 43799811708 0 0 N PMDEC mas yr 71 4379988923397 71 4379988923397 0 0 N PX mas 7 19 7 19 0 0 N SINI 0 6788 0 6788 0 0 N PB d 5 741046089 5 74104608900813 1 0437e 11 8 1286e 12 Y TO MJD 51194 6240248265 51194 6240248265 0 0 N A1 1t s 3 36669162220122 3 36669162220122 0 0 N OM deg 1 2 1 2 0 0 N ECC 1 9186e 05 1 9186e 05 0 0 N PBDOT 10 12
39. r the earth moon barycentre with respect to the solar system barycentre me LT ephemeris values for the moon with respect to the Earth E N the position of the observatory with respect to the centre of the Earth E ae a 3 vector pointing at the pulsar from the observatory 12 4 stats Provides information on the residuals and observations such as the median TOA uncertainty for different observing frequencies For example tempo2 output stats f gh par gh tim will give Number of TOAs in fit 227 Residual 0 000985 us Earliest arrival time at MJD 53041 318518 Most recent arrival time at MJD 53248 801042 Span 207 5 days Observing frequencies 1429 29 3099 00 22 O o TN 10186 F olig E 0 o L Er o o 2 o E oc 3 1O tof eels o ja o L Es 016 o oO L O O E o O 4 o o 9 Beg 106 go i Ls 890 o 9999 eo o P tows 8 9 9 d o O 8 O Z al 101 L O a m roils La raad LU TYial 3 10 0 01 0 1 1 10 Period s Figure 2 An example of the basic graphical interface A P P diagram is produced with the pulsar being analysed highlighted Freq N Minimum Maximum Mean Median RMS MHz Uncertainty us Uncertainty us Uncertainty us Uncertainty us us All 226 0 17 2 70 1 23 0 30 9 8452e 12 1429 29 95 0 97 2 70 2 54 2 57 3099 00 131 0 17 1 27 0 29 0 28 13 Graphical interfaces 13 1 basic Plots a P P diagram and calculates the pulsar s character
40. re can be obtained from the ATNF CVS repository SOFT_ATNF TEMPO2 please contact members of the ATNF pulsar group for more information To install type gt make install The plug ins provided with the source code are stored in SOFT_ATNF TEMPO2 PLUGIN and the docu mentation in SOFT_ATNF TEMPO2 DOCUMENTATION 15 Tempo2 error and warning messages Errors result from serious problems with the pulsar analysis which may not be able to complete at all Warnings indicate possible problems in the analysis Generally the analysis will keep going 15 1 Error messages File handling errors e ERROR FILE1 No tim file given on command line e ERROR FILE2 No par file given on command line e ERROR FILE3 Unable to open parfile X for pulsar Y e ERROR FILE4 Unable to open timefile X e ERROR FILE5 Unable to open file OBSERVATORY_CLOCK_2_UTC_NIST e ERROR FILE6 Unable to open the leap second file e ERROR FILE7 Unable to open OBSYS DAT Parameter file errors e ERROR PAR1 Have not set a period epoch in X Clock errors e ERROR Too many lines in uti file increase array size in tai2tdb e ERROR CLK2 Must increase MAX_CLKCORR e ERROR CLK3 must increase size of MAX_LEAPSEC e ERROR CLK4 Date X out of range of TDB TDT table Ephemeris errors e ERROR EPHEM1 Ephemeris file X not loaded 15 2 Warning messages Parameter file warnings e WARNING PAR2 Have not set a position epoch in X The period epoch will be used
41. re fit Post fit Uncertainty Difference Fit RAJ rad 1 20978853473707 1 20978853473707 0 0 N RAJ hms 04 37 15 7865145 04 37 15 7865145 0 0 DECJ rad 0 824709094464799 0 824709094464799 0 0 N DECJ dms 47 15 08 46158 47 15 08 46158 0 0 FO s 1 173 687946306032 173 687946306032 0 0 N F1 s 2 1 7283139464043e 15 1 7283139464043e 15 0 0 N PEPOCH MJD 51194 0001248168 51194 0001248168 0 0 N POSEPOCH MJD 51194 0001248168 51194 0001248168 0 0 N DMEPOCH MJD 51194 51194 0 0 N DM cm 3 pc 2 64690012312213 2 64690012312213 0 0 N PMRA mas yr 121 43799811708 121 43799811708 0 0 N PMDEC mas yr 71 4379988923397 71 4379988923397 0 0 N PX mas 7 19 7 19 0 0 N SINI 0 6788 0 6788 0 0 N PB d 5 74104608901605 5 74104608901605 0 0 N TO MJD 51194 6240248265 51194 6240248265 0 0 N A1 1t s 3 36669162220122 3 36669162220122 0 0 N OM deg 1 2 1 2 0 0 N ECC 1 9186e 05 1 9186e 05 0 0 N PBDOT 107 12 3 64 3 64 0 0 N OMDOT deg yr 0 0159999997519168 0 0159999997519168 0 0 N M2 0 236 0 236 0 0 N START MJD 50640 9281162413 49350 5129309451 0 1290 4 N FINISH MJD 52088 8971386924 53000 5197060478 0 911 62 N TRACK MJD 0 0 0 0 N TZRMJD 51204 6438924841 51204 6438924841 0 0 N TZRFRQ MHz 1413 39997808495 1413 39997808495 0 0 N Binary model DD Mass function 0 001243113190 0 000000000000 solar masses Minimum companion mass 0 1403 solar masses Median companion mass 0 1637 solar masses Maximum companion mass 0 3493 sola
42. s between v1 and v2 compared to all the other TOAs JUMP FREQ vi v2 will section all TOAs with observing frequencies between v1 and v2 MHz JUMP TEL id will section all TOAs observed with telescope id JUMP NAME str will section all TOAs with observation IDs that contain the string str JUMP flag val will select all TOAs with specified flag e g o and value val 5 2 Removing Timing Noise Even with accurate spin and positional parameters the residuals for some particularly the young pul sars contain remnant structures Some of these structures are understood cusps for instance signify sudden changes in the pulsar s spin rate during a glitch sinusoidal oscillations can represent unmodelled companions such as planets or the pulsar precessing However many of the structures seen in the residuals are still not understood and are known as timing noise To obtain the most accurate pulsar s positional and proper motion parameters and dispersion measure it is essential to remove this timing noise This has traditionally been carried out by fitting higher order pulsar rotational derivative terms More recently Hobbs et al 2004 described a method for fitting harmonically related sinusoids 5 3 Default values 6 Observation files For each pulsar an arrival time file must be created that contains all the site arrival times i e the pulse arrival time at the observatory for each observation These files can take the form
43. s parameter or whether this parameter should be held constant 0 default hold constant 1 fit These labels are described in Table 2 An example of a parameter file for PSR J0437 4715 taken from the catalogue and fitting for various parameters PSRJ J0437 4715 RAJ 04 37 15 7865145 1 7 000e 07 DECJ 47 15 08 461584 1 8 000e 06 DM 2 6469 1 000e 04 PEPOCH 51194 000 FO 173 6879489990983 1 3 000e 13 Fi 1 728314E 15 1 1 600e 20 PMRA 121 438 6 000e 03 PMDEC 71 438 7 000e 03 BINARY DD PB 5 741046 1 3 000e 06 ECC 1 9186E 5 1 5 000e 09 A1 3 36669157 1 1 400e 07 TO 51194 6239 1 8 000e 04 10 Table 1 Observatory details x y Z Mnemonic Clock 882589 65 4924872 32 3943729 348 GBT gbt 4752329 7000 2790505 9340 3200483 7470 NARRABRI atca 2390490 0 5564764 0 1994727 0 ARECIBO ao 228310 702 4631922 905 4367064 059 NANSHAN nanshan 4460892 6 2682358 9 3674756 0 DSS 43 tid43 4554231 5 2816759 1 3454036 3 PARKES pks 3822252 643 153995 683 5086051 443 JODRELL jb 1601192 5041981 4 3554871 4 VLA vla 4324165 81 165927 11 4670132 83 NANCAY ncy 4033949 5 486989 4 4900430 8 EFFELSBERG eff 3822252 643 153995 683 5086051 443 JODRELLM4 jbm4 881856 58 4925311 86 3943459 70 GB300 gb300 882872 57 4924552 73 3944154 92 GB140 gb140 882315 33 4925191 41 3943414 05 GB853 gb853 383395 727 173759 585 5077751 313 MKIII j 3817176 557 162921 170 5089462 046 TABLEY k 3828714 504 169458 987 5080647 749 DARNHALL l 3859711 492 201995 08
44. se on x axis 6 plot year on x axis x redo fit h display this help g change the graphics terminal right mouse button delete TOA left mouse button identify TOA c clear highlights start zoom region finish zoom region simulate new arrival times unzoom et hn 13 7 errors To be written 13 8 fake It is often necessary to simulate timing residuals that would be expected to be measured for a particular pulsar TEMPO2 contains a plug in package to do this FAKE automatically generates a set of TOAs between dates specified by the user The arrival times are defined to be at transit and so only the pulsar s right ascension is used in this calculation The pre fit timing residuals are then formed using a parameter file containing the simulated pulsar s position spin parameters binary parameters etc and 25 subtracted from the original simulated arrival times This procedure is iterated until the residuals are Zero These arrival times can subsequently be modified by 1 the addition of Gaussian noise and 2 the addition of simulated timing noise Upon running the fake plugin the user is asked to provide The number of days between observations The number of observations on a given day The maximum absolute hour angle allowed Whether the user required random or regular hour angle coverage The initial MJD for the simulated TOAs The final MJD for the simulated TOAs The rms of Gaussian noise to be added to the TOAs Whe
45. ssumed that clock offsets and drift rates are small enough that if t t f t then t t f t The spacing of the dates need not be any specific value or even be regular For most purposes roughly daily values are suitable All files ending in clk in TEMP02 clock are read by TEMPO2 when it starts executing Then given a TOA to transform it obtains the name of the clock against which it was measured based upon name specified in the observatory database 4 5 given the observatory code recorded in the TOA file Given the source and destination clocks TEMPO2 must then choose a selection of clock correction tables from clk files to use for the transformation This is firstly attempted by consulting the list of pre defined transformation paths which are defined using CLK CORR CHAIN entries in the parameter file For example the following tells TEMPO2 to convert from UTC PKS to TT TAI using tables defined in pks2gps clk gps2utc clk utc2tai clk and tai2tt tai clk CLK CORR CHAIN pks2gps gps2utc utc2tai tai2tt tai This parameter may be specified multiple times EMPO2 will attempt to apply each path in the order in which they were specified which may fail if the MJD of the TOA is outside the range of component tables If no applicable pre defined paths are found TEMPO2 find the best possible path using all of the available tables Here best means the path for which the sum of badness values is minimized Tie bre
46. t value and the difference between the pre and post fit values A flag indicates whether the parameter was included in the fit For binary systems the default output format also provides details on the binary model and lists if possible the mass function minimum median and maximum companion masses the total system mass and the inclination angle An example is given below Results for PSR J0437 4715 RMS pre fit residual 6 895 us RMS post fit residual 0 096 us Number of points in fit 367 PARAMETER Pre fit Post fit Uncertainty Difference Fit RAJ rad 1 2097885336826 1 20978853474746 2 1206e 11 1 0649e 09 Y RAJ hms 04 37 15 7865 04 37 15 7865146 2 916e 07 1 4643e 05 DECJ rad 0 824709094076948 0 824709094473468 1 5157e 11 3 9652e 10 Y DECJ dms 47 15 08 4615 47 15 08 46158 3 1264e 06 8 1788e 05 FO s 1 173 68794630603 173 687946306032 9 5579e 15 2 3306e 12 Y Fi s 2 1 728e 15 1 72831367406148e 15 2 3325e 22 3 1367e 19 Y PEPOCH MJD 51194 0001248168 51194 0001248168 0 0 N POSEPOCH MJD 51194 0001248168 51194 0001248168 0 0 N DMEPOCH MJD 51194 51194 0 0 N DM cm 3 pc 2 64690012312213 2 64690012312213 0 0 N PMRA mas yr 121 43799811708 121 43799811708 0 0 N PMDEC mas yr 71 4379988923397 71 4379988923397 0 0 N PX mas 7 19 7 19 0 0 N SINI 0 6788 0 6788 0 0 N PB d 5 741046089 5 74104608900813 1 0437e 11 8 1286e 12 Y TO MJD 51194 6240248265 51194 6240248265 0 0 N A1 1t s 3 36669162220122 3 3666
47. tain 5 6 whitespace separated parameters These are in order the x y and z geocentric coordinates in metres a one word name for the observatory a few character mnemonic and optionally the name of the clock associated with the observatory used to refer to the relevant clock correction tables If not supplied the clock name is constructed as UTC xxx where xxx is the observatory mnemonic For full accuracy observatory coordinates should be specified in the International Terrestrial Reference System Geodetic coordinates as optionally used by TEMPO given as latitude and longitude in degrees in the form dddmmss ss and height in metres may be specified in which case TEMPO2 will detect this and convert them to the ITRF on the assumption that they refer to the GRS80 geoid The converted coordinates are displayed and execution is halted for the user to add the converted coordinates to the observatories database or not the accuracy of the conversion and the assumption of GRS80 may be dubious NOTE The mnemonics in observatories dat have not been finalised Please let G Hobbs or R Edwards know if you prefer another mnemonic for your observatory The current observatory file is listed in Table 1 5 Parameter files The parameter files have the same design as in the earlier tempo implementations Each of the pulsar parameters has a label a value and may have an uncertainty on the value and a flag indicating whether TEMPO2 should fit for thi
48. tch off calculation of the interplanetary medium NITS Number of iterations for the fitting routines DILATEFREQ Whether or not to apply gravitational redshift and time dila tion to observing frequency Y N IBOOT Number of iterations used in the bootstrap fitting method PLANET SHAPIRO CORRECT_TROPOSPHERE NE1AU TIMEEPH T2CMETHOD CLK CORR CHAIN EPHEM TZRMJD TZRSITE NSPAN or TSPAN TZRFRQ START FINISH EPHVER TRACK Whether or not to apply tropospheric delay corrections The electron density at 1 AU due to the solar wind Which time ephemeris to use IF99 FB90 Method for transforming from terrestrial to celestial frame IAU2000B TEMPO Clock correction chain s to use Sect 4 1 Which solar system ephemeris to use 12 Table 3 Binary parameters that can be entered in a parameter file Label Description Units BINARY Binary model BT ELL1 DD MSS Al Projected semi major axis of orbit lt sec PB Orbital period days ECC or E Eccentricity of orbit TO Epoch of periastron MJD OM Longitude of periastron degrees TASC Epoch of ascending node MJD EPS1 ECC x sin OM for ELL1 model EPS2 ECCx cos OM for ELL1 model OMDOT Rate of advance of periastron deg yr PBDOT 1st time derivative of binary period 10712 A1DOT or XDOT Rate of change of projected semi major axis 10 12 SINI Sine of inclination angle M2 Companion mass solar masses XPBDOT Rate of change of orbital period minus GR prediction A1DOT
49. the latest EOPs The user may op tionally select to emulate the algorithm of tempo which neglects polar motion and uses an out of date precession nutation model for transforming the observatory coordinates to the celestial frame using the T2C METHOD parameter in this case TEMPO2 clock ut1 dat in the same format as the corresponding file for tempo is used 4 3 Time ephemeris The pulse arrival times at the observatory at transformed to the arrival time at the solar system barycentre SSB In this transformation the Einstein delay which describes the combined effect of gravitiatonal redshift and time dilation due to the motion of the Earth and other bodies must be taken in to account This transformation converts the site arrival time from TT to a coordinate time at the SSB known as Barycentric Coordinate Time TCB Optionally for backward compatibility with tempo the user may also choose to use a scaled version of this frame in which the mean drift relative to TT is divided out this is nominally but incorrectly see Paper II referred to as TDB This is accomplished by specifying UNITS TDB in the parameter file The Einstein delay is computed using a polynomial approximation to the numerical evaulation of the time dilation integral as provided by Irwin amp Fukushima 1999 It lives in TEMP02 ephemeris TIMEEPH short te405 For reproducing results obtained with tempo the user may also chose to use the Fairhead amp Bretagnon 199
50. the pre and post fit timing residuals for multiple pulsar simultaneously o e 29 8 Example of the STRIDEFIT graphical interface plug in which calculates the pulsar s disper sion measure as a function fo time 2 222 ll rs 30 List of Tables OUR NN A Observatory details c xou id ve A AA WU E Ue eu de ee ees Rd 11 Pulsar parameters that can be entered in a parameter file s 12 Binary parameters that can be entered in a parameter file sss 13 Flags in arrival time files uo xe oe cg mox on X Y de 3ed Ue A dew opor eim Roe Y 16 Commands that may be included in an arrival time file 00 17 1 INTRODUCTION TEMPO2 is a new version of the TEMPO pulsar timing software An overview of the software is provided in Hobbs Edwards amp Manchester 2006 MNRAS 369 655 A second paper provides mathematical details of the algorithms used in the software Edwards Hobbs amp Manchester 2006 currently available from astro ph A third paper will describe how TEMPO2 can be used to simulate the effects of gravitational waves on pulsar timing residuals A summary of the basic features can also be found in Hobbs Edwards amp Manchester 2006 in press CHJAA This document provides full usage instructions for TEMPO2 2 Obtaining and installing tempo2 The TEMPO2 software and documentation can be obtained from http www atnf csiro au research pulsar ppta tempo2 Click on the Downl
51. ther red noise should be added to simulate timing noise If the red noise option is selected the user is also requested to provide The power law index for the red noise The power law amplitude A random number seed Whether the residuals should be smoothed Whether a cubic should be added to the residuals The red noise is simulated as a shot noise process obtained by summing many sinusoids with random phase but with amplitudes given by the requested power law spectrum The following example simulates a pulsar with a large proper motion 1 o s og ww Produce a parameter file similar to called testfake par PSRJ J1730 2304 RAJ 17 30 21 6483 DECJ 23 04 31 4 POSEPOCH 51500 0 PMRA 200 PEPOCH 51500 0 FO 123 110289179797 Fi 3 0631E 16 DM 9 611 CLK UTC NIST EPHEM DE200 Run tempo2 gr fake testfake par Follow on screen instructions The fake plug in will produce an arrival time file called testfake simulate In the parameter file change the PMRA back to zero Run tempo2 gr plk f testfake par testfake simulate The result should be similar to that shown in Figure 5 note this code was based om the fake software originally developed by Duncan Lorimer and updated by Simon Johnston 13 9 gorilla To be written 26 J1750 2504 e Lg l x NL J la T ey 5 z or a Zu ao 4 L E Ps lt lt e d MES Pt E D E E z n a oe Doc ootb 3 P a i IRA L A 5
52. using this interface 13 5 compareRes To be written 13 6 delays This interface allows the user to inspect the clock corrections and propagation time delays that TEMPO2 has applied in order to obtain barycentric arrival times See Figure 4 tempo2 gr delays f mypar par mytim tim The following key strokes are possible q quit y 1 Cy followed by 1 plot first clock correction y 2 Cy followed by 2 plot second clock correction y 3 plot third clock correction y 4 plot fourth clock correction y 5 plot fifth clock correction y 6 plot UT1 y 7 plot Shapiro delay due to Sun y 8 plot dispersion delay in solar system y 9 plot dispersion delay in ISM y 0 plot Roemer delay y a plot pre fit residuals y b plot post fit residuals y c plot Shapiro delay due to Jupiter 24 J1810 2005 4x10 2x107 Shapiro delay s atl T Ee e o amp uie sg MPt uso Se Eg Ph oue e pe Pp e e ee ty ep p E si ae pe ae ep 0 50 100 150 200 250 300 350 400 Day of year Figure 4 The solar system Shapiro delay for PSR J1810 2005 shown using the DELAYS graphical interface plug in y d plot Shapiro delay due to Saturn y e plot Shapiro delay due to Uranus y f plot Shapiro delay due to Neptune y g plot total planetary Shapiro delay y h plot tropospheric propagation delay 1 plot TOA number on x axis 2 plot MJD day on x axis 3 plot observing frequency on x axis 4 plot day of year on x axis 5 plot binary pha
53. z amp amp amp amp amp amp amp amp amp amp amp amp amp amp amp amp amp amp 18 02 05 33496 12 21 24 03 72 6 79 066424253435 18 4 574E 16 13 52855 52855 52855 149 666066 0 69888924320 20 3 718853847 52595 795078543 1 0412e 06 2 3924e 06 52605 162 53565 334 0 52883 440856822 1390 Options are also available to increase the uncertainties by a given factor To change the parameters listed to change the string displayed if a parameter has not been set and to change the number of decimal places output 12 2 general2 This output format is similar to the GENERAL output described above However this output provides access to values calculated for each observation sat bat clockO gt clock4 the the the the the shapiroJ shapiroS shapiroV shapiroU shapiroN Shapiro delay due Shapiro delay due Shapiro delay due Shapiro delay due Shapiro delay due site arrival times barycentric arrival times various clock correction values shapiro the solar Shapiro delay to to to to to tropo the tropospheric delay roemer the solar system Roemer correction to TT tt delay Juptier Saturn Venus Uranus Neptune 21 tt2tb correction from TT to TB fearth ssb magnitude of vector from Earth to barycentre fearth ssbi magnitude of x component from Earth to barycentre fearth ssb2 magnitude of y component fr
Download Pdf Manuals
Related Search