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This pull request introduces improvements to the thermobarometry inversion framework in BurnMan, focusing on how uncertainties in pressure and temperature ("state uncertainties") are handled and incorporated into misfit calculations.
Updates
tools.thermobarometry.assemblage_affinity_covariance_matrix()andtools.thermobarometry.assemblage_affinity_misfit(). Including state uncertainties increases the total uncertainties and decreases the misfit corresponding to reaction affinities.tools.thermobarometry.assemblage_state_misfit()function to calculate a misfit based on prior state (P, T) and uncertainties.tools.thermobarometry.estimate_conditions()to optionally use the newtools.thermobarometry.assemblage_state_misfit()function. This also fixes a bug - the old code internally calculated Cov([P, T])^-1 using pinv, which because of the inherent difference in scales resulted in an erroneous zero eigenvalue.examples/example_optimal_thermobarometry.pyand output to use the newtools.thermobarometry.assemblage_state_misfit()function. The change in output reflects the bug fix described above.tests.test_tools.pycovering the new functionality.burnman/optimize/linear_fitting.py