Minor - turn off some debug output.


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2046 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Added more hooks to create_groups and some checks for path_valid in the
HDF5 data stream.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2047 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Made a number of modifications to the adaptive importance sampling algorithm.  Modified the number of samples per batch on a surrogate to be the number requested on the surrogate in the input file.  The converge_cov() function now only runs for MMAIS.  The AIS algorithm now correctly picks a new representative point at each iteration.  If no points are found in the failure domain, then the closest point is used.  The previous representative points are no longer considered candidates for future batches.

git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2048 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Update spec for importance sampling refinement:
> probability_refinement is now the preferred keyword (aliased to previous
  sample_refinement) for use in PCE, SC, and local reliability.
> probability_refinement now includes an optional "refinement_samples" spec
  that is independent of the "samples" spec for PCE and SC.  It currently 
  defaults to 1000, which should be relatively fast in combination with
  default maxIterations = 100.
Affects no tests as we currently have no probability_refinement coverage 
(additions planned).

Also cleaned up the sample apportionment logic in NonDAdaptImpSampling::
generate_samples() to preclude possible out-of-bounds errors (still could
omit some refinement samples due to integer truncation).


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2049 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Update importance sampling refinement docs in Ref Manual.  Minor DEBUG block
removals from NonDAdaptImpSampling::initialize() for consistency.


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2050 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Additions of a framework for Mohamed to add the "Opt Darts" 
algorithm, which will be somewhat similar to DIRECT. 
For now, the new class is called OptDartsOptimizer, although 
we can change this. 



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2051 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Tweaked Brian Adam's monostate class which adds support for writing variable
length string data type in HDF5 binary files.

ToDo:
1.  Ensure resource is properly closed when IO client no longer needs 
the monostate managing the hid_t. (may require transition to singleton pattern)
2.  Add support for reading variable length strings
3.  More rigrous testing.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2052 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Added test for HDF5 write of variable length string.  Should've been committed
along with the code in rev 2052.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2053 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Checkpoint incremental progress in HDF5 IO helper constructor cleanup.
The class is still relatively simple, so allow default constructible,
copy constructible, and assignment.

Added a new constructor argument, a boolean:  db_is_incore so that
a single constructor can manage both incore and file stream DB cases.

NOTE:  in this check-pointed version the support for the incore case is
disabled!

ToDo -- ASAP:  restore support for the incore DB case.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2054 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Restored in-core HDF5 driver case.
Request review by Brian Adams.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2055 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Added test for in-core, memory storage of HDF5 data with persistence to file
when program terminates.  Also, covers default constructor case for the HDF5 IO
Helper class.

ToDo:  Add test for a collection (std::vector) of HDF5 IO Helper objects.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2056 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Corrected interface to incore, HDF5 DB test function.



git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2057 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Add output of the number of grid samples for PCE and SC when dakota is in 
-check mode.  Feature requested by Jeremy Templeton, among others (important 
for estimating HPC resources when using sparse grids).


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2058 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Further updates to the adaptive importance sampling.  Repeated function evaluations have been eliminated and portions of the code have been consolidated to reduce redundancy.  In particular, select_init_rep_points() has been incorporated into select_rep_points(RealVectorArray samples, Real fail_tol) using the fail_tol argument.  Also, the actual evaluation of the model has been extracted into a separate function.  Currently, the response values are being stored in a RealVector, but Mike is going to look into reducing this extra storage cost.

git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2059 aa0779c3-6ec2-4b84-a212-a405c134cd8d
HDF5 improvements to write/read vlen strings, arrays of vlen strings

 * Finish migration from fixed length to variable length string datatype, including: remove derived datatype, class member, ctor args.

 * For now, remove various extra demos with variable length strings, and instead just use LT interface where possible.

 * Update test cases to reflect variable length string and the start of a reader for StringArray, which is incomplete (test just checks size of array, but not contents for now).





git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2060 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Fixed a bug in the allocation of an array that was causing a seg fault on cases where MMAIS was being performed on a surrogate model.

git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2061 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Refactor for approximation scalability when handling large response QoI 
data sets.  Mirrors Pecos revision 886.  Approximation data is now split 
into shared data (managed within new SharedApproxData class hierarchy) and 
per QoI data (managed within the previous but now streamlined Approximation 
class hierarchy).  SharedApproxData is similar in intent to SharedVariablesData
(subject of a previous Dakota refactor), although the latter does not require a
mirrored class hierarchy.  At this point, SharedApproxData is specialized for
Pecos and Surfpack -- Taylor, TANA3, and GaussProc can be added in time.

Note: this commit introduces instability, but it will be stabilized ASAP.
Regression PCE in particular needs additional work, but the least squares 
case should be operational soon.


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2062 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Patch for Surfpack tests (e.g., SBO, SBNLS).  Don't require reimplementation
of SharedApproxData::build() as SharedSurfpackApproxData currently has no
shared run-time initialization tasks.


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2063 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Patch for derivative logic for non-global approximations (Taylor and TANA3).
Completes restoration of SBO and SBNLS tests (all dakota_sbo_*.in and 
dakota_sbnls_*.in are now clean).


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2064 aa0779c3-6ec2-4b84-a212-a405c134cd8d
Patch for GPAIS: don't require reimplementation of SharedApproxData::pop().


git-svn-id: https://software.sandia.gov/svn/public/dakota/core/trunk@2065 aa0779c3-6ec2-4b84-a212-a405c134cd8d