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Commit f53fcf33 authored by jcandrsn's avatar jcandrsn
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Added the -add-resp option to uq_BP2bvp and uq_bvp2bvp allowing a user to...

Added the -add-resp option to uq_BP2bvp and uq_bvp2bvp allowing a user to specify whether they want the response functions added back to the problem data structure.  Fixed a bug in uq_bvp_gen_samples that prevented the code from finding samples points when multiple stochastic parameters were specified.  Modified uq_coll_add_response, uq_response_evaluation, uq_response_Jacobian, uq_coll_get_idx, and added uq_coll_add_response_adjoint, uq_pce_coefficients_adjoint, uq_int_response_adjoint_evaluation, uq_pce_coefficients_adjoint_dU, uq_int_response_adjoint_Jacobian, to properly handle integral response functions.  Integral response functions require a uniform mesh and cannot handle coco's adaptive mesh functionality in this commit.  Modified the way boundary value Jacobians and second derivatives are handled to make it easier for a user to provide them.  Previously the user needed to specify Jacobians and second derivatives that properly accounted for the size of the sample.  Now users can provide a sort of vectorized encoding of the Jacobian and second derivative and the wrapper function places the information in the correct spot for coco.  Changes made in uq_pce_coefficients_dU and uq_pce_coefficients_dUdU to facilitate this.  Some rearrangement of vector field files in coco_example_runs.  Modifications to demo run files as needed to work with above changes.  Some additional Mathematica calculations required for thesis document and a dead end multiple scales analysis of a duffing oscillator.
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......@@ -4,7 +4,7 @@ funcs = {@F, @F_dU, @F_dP};
% Boundary Conditions
bcs = {};
% Start with a simple case of an undamped inear oscillators
% Start with a simple case of an undamped linear oscillators
pnames = {'A','k','d','w','eps'};
p0 = [1; 1; 0; 1; 0];
......
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