The authors of [27] looked at the numerical stability of the least squares estimation algorithms and the derived solutions.

Common precision orbit determination algorithms use double precision arithmetic. The
representation uses a 53-bit mantissa, equivalent to more than 15 decimal digits of precision [151].
Is this accuracy sufficient for precision orbit determination within the solar system? At solar
system barycentric distances between 1 and 10 billion kilometers (10^{12} – 10^{13} m), 15 decimal
digits of accuracy translates into a positional error of 1 cm or less. Therefore, we can conclude
that double precision arithmetic is adequate in principle for modeling the orbits of Pioneer 10
and 11 in the outer solar system in a solar system barycentric reference frame. However, one
must still be concerned about cumulative errors and the stability of the employed numerical
algorithms.

The leading source for computational errors in finite precision arithmetic is the addition of quantities of different magnitudes, causing a loss of least significant digits in the smaller quantity. In extreme cases, this can lead to serious instabilities in numerical algorithms. Software codes that perform matrix operations are especially vulnerable to such stability issues, as are algorithms that use finite differences for solving systems of differential equations numerically.

While it is difficult to prove that a particular solution is not a result of a numerical instability, it is extremely unlikely that two independently-developed programs could produce compatible results that are nevertheless incorrect, as a result of computational error. Therefore, verifying a result using independently-developed software codes is a reliable way to exclude numerical instabilities as a possible error source, and also to put a limit on any numerical errors.

In view of the above, given the excellent agreement in various implementations of the modeling software,
the authors of [27] concluded that differences in analyst choices (parameterization of clocks, data editing,
modeling options, etc.) give rise to coordinate discrepancies only at the level of 0.3 cm. This number
corresponds to an uncertainty in estimating the anomalous acceleration on the order of 8 × 10^{–14} m/s^{2},
which was found to be negligible for the investigation.

Analysis identified, however, a slightly larger error to contend with. After processing, Doppler residuals at JPL were rounded to 15 and later to 14 significant figures. When the Block 5 receivers came online in 1995, Doppler output was further rounded to 13 significant digits. According to [27], this roundoff results in the estimate for the numerical uncertainty of

The accuracy of navigational codes that are used to model the motion of spacecraft is limited by the accuracy of the mathematical models employed by the programs to model the solar system. The two programs used in the investigation – JPL’s ODP/Sigma modeling software and The Aerospace Corporation’s POEAS/CHASMP software package – used different parameter estimation procedures, employed different realizations of the Earth’s orientation parameters, used different planetary ephemerides, and different data editing strategies. While it is possible that some of the differences were partially masked by maneuver estimations, internal consistency checks indicated that the two solutions were consistent at the level of one part in , implying an acceleration error [27].

The consistency of the models was verified by comparing separately the Pioneer 11 results and the
Pioneer 10 results for the three intervals studied in [27]. The models differed, respectively, by (0.25, 0.21,
0.23, 0.02) m/s^{2}. Assuming that these errors are uncorrelated, [27] computed the combined effect on
anomalous acceleration as

The velocity change that results from a propulsion maneuver cannot be modeled exactly. Mechanical uncertainties, fuel properties and impurities, valve performance, and other factors all contribute uncertainties. The authors of [27] found that for a typical maneuver, the standard error in the residuals is . Given 28 maneuvers during the Pioneer 10 study period of 11.5 years, a mismodeling of this magnitude would contribute an error to the acceleration solution with a magnitude of . Assuming a normal distribution around zero with a standard deviation of for each single maneuver, a total of maneuvers yields a total error of

due to maneuver mismodeling.

In addition to the constant anomalous acceleration term, an annual sinusoid has been reported [27, 390]. The peaks of the sinusoid occur when the spacecraft is nearest to the Sun in the celestial sphere, as seen from the Earth, at times when the Doppler noise due to the solar plasma is at a maximum. A parametric fit to this oscillatory term [27, 392] modeled this sinusoid with amplitude , angular velocity , and bias , resulting in post-fit residuals of , averaged over the data interval .

The obtained amplitude and angular velocity can be combined to form an acceleration amplitude: . The likely cause of this apparent acceleration is a mismodeling of the orbital inclination of the spacecraft to the ecliptic plane [27, 392].

[27] estimated the annual contribution to the error budget for . Combining and the magnitude of the annual sinusoidal term for the entire Pioneer 10 data span, they calculated

This number is assumed to be the systematic error from the annual term. [27] also indicated the presence of a significant diurnal term, with a period that is approximately equal
to the sidereal rotation period of the Earth, 23^{h}56^{m}04^{s}.0989. The magnitude of the diurnal term is
comparable to that of the annual term, but the corresponding angular velocity is much larger, resulting in
large apparent accelerations relative to . These large accelerations, however, average out over long
observational intervals, to less than over a year. The origin of the annual and diurnal
terms is likely the same modeling problem [27].

These small periodic modeling errors are effectively masked by maneuvers and plasma noise. However, as they are uncorrelated with the observed anomalous acceleration (characterized by an essentially linear drift, not annual/diurnal sinusoidal signatures), they do not represent a source of systematic error.

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