Issue: ODA-350 Improved KalmanFilterTests. Now it can handle arbitrary order of XML sections. OpenDATestSupport contains new method for reading/parsing output file and removing all special characters Issue: ODA-350 Fixed two model_efdc_dll tests such that they run on Mac as well Issue: ODA-350 Create new Mac binaries (PPC + X86_64) and universal binary for EFDC-dll Added a "sort" step before the regexp comparison in NoosStochObserverTest.java, as the parent containers have no inherent internal order. Fix broken tests. Issue: ODA-350 Fixed test for running on Mac. a) removed hash codes b) improved test (order of exchange Items was not defined) Fix loading of opendabridge.dll when running ant "test". Test DudWithConstraint has been replaced and deleted in a previous commit. Issue: ODA-350 Added darwin (mac) binaries Fix loading of opendabridge.dll when running oda_run_gui.bat Compiled on TeamCity: Test revert 4588 to fix native tests. Trying to fix the core tests, undo changes from 4588 and check TeamCity. Core testscript which is compatible with TeamCity. Ant target test needs not build, those 3 steps are performed as a separate task. Type-O leading to model_glm being build into model_example_blackbox.jar (part2). Type-O leading to model_glm being build into model_example_blackbox.jar. Added pre-compile core libraries to OpenDA 2.2. Extended Ant build to include new models in OpenDA 2.2. Removed Java 1.6 from OpenDA 2.2. Pre-release update: Upgraded OpenDA version number to 2.2. Branching OpenDA 2.2 for release preparation. Added check on empty list (null) of dir.s in project root Issue: 349 - add an optional flag in efdcModelFactoryConfig.xml for indicating if ControlsGateWaterLevel is used: true - default value of the flag is "false" so that older configuration can work without any modification - add checks in EfdcModelInstance.createModelExchangeItems(): if useGateWaterLevel==false, then don't create controlGateWaterLevel exchangeItem Issue: TOOLS-21593 Merged revision(s) 4658 from public/branches/OpenDA_2_1 Fix log messages for non-set observation filter working directory Issue: TOOLS-7739 Issue: TOOLS-7739 / TOOLS-21593 Merged revision(s) 4594, 4598, 4657 from public/branches/OpenDA_2_1: To reduce memory usage, the application runner was extended with a query for the input- and output items that are really used in the computation Fix in query for the actually used input- and output items Fix in determining BB stoch. model items that indeed are accessed TeamCity file permission check. Set properties to Java 1.7. Set ignored libraries. Issue: ODA-348 Dud with constraints: add check if pInit==upper_bound in initialize(). Add a corresponding unit test. Core and Observers Castor files are build on the TeamCity build server: removed compiled files. Issue: ODA-348 Bug in BasedDudCoreOptimizer solved. Native ddl's and lib are now build on TeamCity. Copy JRE 1.7 in build step. Minor adaptation for Rolf's use of the SimpleStochModel. Moved Ant build target to Java 1.7 and included Java 1.7 JRE Issue: ODA-333 Issue: ODA-347 repaired case-sensitive links to xml-example files Added test-case for DUD with constraints various small changes Add glm lake model Buildserver complains of missing slahes in the other projects. Buildserver complains of missing slahes in libheat_stoch.vfproj Correction for calling-depedent autocorrection features, modifying the presence of path separators. TeamCity compilation process could not find libheat_stoch.lib. Correction to libheat_stoch.lib target location specification. Issue: ODA-346 Add logging info for chgdir calls. Issue: ODA-323 Example of using DELSA based on DAMFlow. Issue: ODA-323 First version of DELSA implementation. Only regular grid is supported on the parameter space. Added dummy module project_view.iml so that all folders and files in public are visible in IntelliJ project view. Issue: ODA-346 Fix issue with messages prefix for GNU. Add linux binaries. Issue: 346 Include secnds.for for AIX compatibility Add logging to messages.log for FEWS messages Add Windows binary Enable Unit test for toxics Issue: ODA-346 Add shared libraries for linux Issue: ODA-346 Set numbers to single precision when they are stored in single precision vars Issue: ODA-346 Add seconds to AIX makefile. Issue: ODA-346 Add missing OpenMP loops Add dtime.for for AIX compatibility Initialize LAYER = 0.0 Issue: ODA-346 Update makefile to include model_gateser_time_series.f90 Issue: ODA-346 Add check on instance identifier. Fix bug in model_make_step.f90 Issue: ODA-346 Include exchange item in documentation ODA-325 Compare ascii-files with tolerance on numbers in the strings. Add this option in the file compare of some test which were failing due to tiny rounding errors ODA-325 Added special testPCC to ant build. Disabling those test that are not working (for a reason) on the Mac PPC build/test server Issue: ODA-XXX Improved message in ArrayExchangeItem Issue: ODA-XXX Made timehorizon of MapsNoiseModel protected such that we can easily create a noise model based on this default implementation Bug fixes by Arjo Segers for the generation of f90 interfaces Updated documentation. Issue: ODA-346 Merge change from Nier in RESTOUT.for Write jre version to screen. Correction to timeframe management. Added support for single timestep addition to NetcdfScalarTimeSeriesExchangeItem. Issue: ODA-346 Add fixes for time administration. Issue: ODA-346 Add support for ControlsGateWaterLevel exchange item. Calibration test did not reach correct value of 9.0 exactly, but remains slightly smaller 8.9. Name of Dud_parameterConstraints.oda was inconsistent with Dud_parameterConstraint.tst Try to fix native build on teamcity. In this attempt using autoreconf_fix.sh Issue: ODA-345 Operation "multiply" for noise model is corrected, i.e. by initializing the vector of factors with 1 and then add the noise to the factors. ODA-344: GeometryUtils: Fixed bug in bilinear interpolation. ODA-344: GeometryUtils: Implemented bilinear interpolation and unit test. ODA-344: Added example code in the form of an unused and only partially implemented class LocalizationExampleModelInstance. ODA-344: GeometryUtils: added unit test. ODA-344: GeometryUtils: removed package org.openda.model_bmi.geometry. ODA-344: GeometryUtils: moved GeometryUtils from org.openda.model_bmi.geometry to org.openda.utils.geometry. ODA-344: GeometryUtils: added new package org.openda.utils.geometry. ODA-344: Removed Delft_Util.jar again. ODA-344: GeometryUtils: Calculating Cohn weights now also works for WGS84 lat,lon coordinates. ODA-344: Changed GeometryUtils to use Cohn's formula for localization weights. ODA-344: IoObjectStochObserver: implemented IoObjectStochObserver.IoObjectStochObsDescriptions#getValueProperties for exchangeItems with rectangular grids. To improve performance of getValueProperties always convert rectangular grids to curvilinear grids internally. ODA-344: Comments only. ODA-344: Made EnKFSeq work for localization method Hamill. This only works when using valueProperties to get the "x" and "y" coordinates from the observationDescriptions object in method getObservedLocalization in the modelInstance. ODA-344: Comments only. ODA-344: Added code to GeometryUtils to get observed values and get localization weights for grid observations. This code treats each observed grid cell as a separate observation location. Fixed initialization of inserted model factory WflowPythonToJavaAdapterTest: Fixed unit test. ODA-344: Comments only. Corrected openda.ipr file. ODA-344: Fixed build. ODA-344: Added new GeometryUtils and Delft_Util.jar. ODA-344: Added model_bmi. This is still work in progress. Issue: ODA-53 Switched to new version of IKVM (needed for higher versions of java) Added website documentation to new OpenDA doc. Issue: ODA-341 Implement the method loadPersistentState of EnSR. ODA-339: Fixed bug in BBModelInstance#finish where ioObjects were flushed and cleared, but dataObjects not. ODA-339: Fixed bug in BBModelInstance where ioObjects and dataObjects were not flushed before saving the state. This is needed so that before the state is saved, the state exchangeItems are finished (if they are used). This way the saved state will represent the latest data from the memory, instead of previous data that happened to be still present in the state files. Issue: ODA-339 Fixed bug in BBModelInstance where ioObjects and dataObjects were not cleared before restoring a previous state. This is needed so that after a previous state has been restored, the state exchangeItems are initialized again from scratch (when they are used). This way the state exchangeItems will represent the data from the restored state, instead of previous data that happened to be still present in the memory. Reverted 4532 (fix in choice for creating observation descriptions not working) Fix in choice for creating observation descriptions (costa based / datools based) Issue: ODA-xxxx removed chmod on non-existing directory, attempt to repair Build Java for Linux end users on Teamcity; added chmod for linux64_gnu Issue: ODA-333 some improvements after testing with model_simona_blackbox Issue: ODA-337 In case of sequentual simulation we do not wite the extended state (localization) to the result writer because: 1 This causes problems using the netcdf writer when the number of obs changes per assimilation step 2 Outpur of sequetial and normal assimilation is more similar Issue: ODA-337 Improved output of localization masks and gains to resultwriter for the case where we do sequential assimilation. Issue: ODA-337 Improved output of localization masks and gains to resultwriter for the case where we do sequential assimilation. Issue: ODA-xxx Removed unused import statements that caused an error in Teamcity unit tests. Issue: ODA-333 added documentation for option parameterConstraints, based on internship report Yvonne Ruckstuhl. Issue: ODA-333 new option to specify limits on parameters in Dud algorithm (parameterConstraints) ODA-339: Comments only. Issue: ODA-327 Comments only. ODA-339: NoiseModel: improved error message. Described config workaround in the comments in the code. Issue: ODA-327 Partly fixed unit tests. Issue: ODA-327 Corrected openda.ipr file. Issue: ODA-327 Updated comments for unit tests that use JEPP. Issue: ODA-327 Updated openda.ipr file. Issue: ODA-310 Add comments on wflow unit tests about the environment variables required for running the unit test. This should be set manually by the programmer in their development environment. Issue: ODA-337 Initial commit for testing: We now have a new localization method "autoZhang". Some reorganization of classes was needed to fit in this method in a nice OO way NOTE: no documentation, no proper configuration in this implementation Issue: ODA-189 Minor improvements on output/error messages ODA-189 Disabled assimilation of temperature (can be switched on with a boolean in both(!) NemoModelInstance.java and NemoNetcdfStochObserver.java Improved update timestep for model_tva. Diamond operator not supported yet. added "compile" file for automake Issue: ODA-xxxx New attempt to fix makefiles, previous one used to modern autmake Issue: ODA-XXXX Native makefiles where broken (explicit --gnu flag and automake version). Added zipFile get method to FileBasedModelState. Issue: ODA-299 Fixed problems with cleaning op Delft3D-Flow-OpenDA-DLL. FlowDll methods static, to make more explicit that the DLL is only loaded once. The DLL's initialize and finalize calls can now be called per modelfactory. Issue: ODA-240 bugfix cta_metinfo.setRegGrid is used externally.w Issue: ODA-240 Extend f90 headers and make exports more explicit in c-includes. This is an attempt to replace f77 with f90 binding for delft3d. Issue: ODA-189 explicit close of files in NEMO wrapper Issue: ODA-331 Improve the functionality for writing output to netCDF. Issue: ODA-189 Fixed two bugs in NEMO netcdf observer ->returning times for single day does now only return a single time ->Incorrect loop filtering dummy/outside domain observations Issue: ODA-331 Add a functionality to write output to a netcdf file. Issue: ODA-335 Implement method evaluatePDF of the IoObjectStochObserver. Issue: ODA-331 Add a functionality to write output to a netcdf file. Issue: ODA-334 When running models in parallel using threads we see that the data assimilation process takes 1/3 of the CPU (on a two core system). This behaviour is cased the thread polling whether a model run/compute is done Solution: configurable sleep in thread. ->Documentation is updated as well TimeZone fix for Delwaq his files. Issue: ODA-332 Fixed ElmDiv of native (tree) vectors. Changed y=x/y bij y=y/x such that the computations are similar to the PointwiseDivision of the java/OpenDA (tree)vectors. The connection between java-c has been (re) activated such that we no longer get a non-supported runtime exception. Issue: ODA-189 Different behaviour (fixed) for sequentual analysis (assimilating observations one at a time). the computation/output of pred_a_linear can be switched on and off in the analysis. This is used bu EnKFSeq to switch the output off and handle pred_a_linear by iteself. Issue: ODA-189 NEMO: -remove sat observations which are outside the domain -Fix problem whith JMD conversion mm is minute not moth Issue: ODA-330 Modifications related to saveInternalState and restoreInternalState for Particle Filter and FileBasedModelState (e.g. wflow/openstream) Issue: ODA-327 Comments only. Issue: ODA-327 Updated PythonBridgeTest unit test. Issue: ODA-327 Added python interfaces. Issue: ODA-327 Added first version of PythonBridgeStochModelFactory. Issue: ODA-327 Updated PythonBridgeTest unit test. Issue: ODA-314 Added dummy chapters to administrate what is still missing. All bullets in file Verbeteren_doc_lijst.txt (version dec 2013) are included. Issue: ODA-314 Aanvulling op de documentatie. Wflow: Updated unit test. Issue: ODA-310 Use StringBuffer in VectorDouble().toString() to solve the problem of "running slowly" when writing the noise vector into a file for restart. Issue: ODA-325 Fixed EFDC DLL unit tests for Mac (tested on intel hopefully working on PCC as wel) Issue: ODA-327 Updated unit test and iml files. Issue: ODA-189 Assimilate satellite observations in NEMO model using a netcdf observer and use extended model interface to handle the observation in a model specific implementation and not using the default black box configuration/matching Issue: ODA-189 Output which observation is assimilated in sequential assimilation of observations Issue: ODA-189 Changed some variables in the black box model instance and factory to protected such that we can extend these classes for models implementing the extended model interface (own localization and observation operator) Issue: ODA-314 Added references via \cite-commands instead of typed text. Issue: ODA-327 Updated python_bridge files. Issue: ODA-310 Update open stream / wflow python scripts. Fixed iml files. Issue: ODA-XXX Fixed syntax error in Intelij project file, introduced in commit 4419 Issue: ODA-327 Added first version of OpenDA Python bridge (this is still work in progress). Issue: ODA-279 Added x64 project files for C# bridging and MikeShe model Issue: ODA-279 Clean-up/upgrade of Karup test for MikeShe Issue: ODA-281 Allow bias correction on only a limited number of observations Issue: ODA-327 Added directory structure for java-c-python bridge Issue: ODA-327 Added references to include files Issue: ODA-328 Added configuration file for example run Issue: ODA-325 Changed vector comparisons in to "String" for to element by element comparisons using a treshhold. in Unit tests Issue: ODA-279 Changed and added test configurations for the mikeShe Karup model Issue: ODA-279 Changed and added test configurations for the mikeShe Karup model Issue: ODA-325 Fixed test 13 from Lorenz96Model. This test was too sensitive for small rounding errors comparing double arrays as strings Issue: ODA-328 Initial check-in of gain regularisation option for EnKF, DEnKF etc TODO: * check columns of gain * adjust schema files Issue: ODA-279 Added (matlab) tools to create initial ensembles for the MikeSHE model. Currently a setup is available for the Karup model_mikeshe/tests/generateEns native build fixes runned fix for automake Share project "public" into "https://repos.deltares.nl/repos/openda/public" Issue: ODA-325 Added mac binaries ppc/x86_64 for EFDC dll model Issue: ODA-325 Replaced mac binaries of SWAN with universal binaries Issue: ODA-321 Correct some errors related to load, restore, release of stochModelState (model restart files and noise files) for DudEnKF. Issue: ODA-310 Redesign schemas: replacing attributes of scalar output file names with elements to allow easier extension in the future. Issue: ODA-XXX Improved error message when predicted values of the model cannot be matched to the observed values in the black box wrapper. The error will now contain the missing times in MJD as well and will show for which times (in MJD) the model did predict values. This makes debugging much easier. Issue: ODA-314 Documentation: Getting started chapter Issue: ODA-314 Added documentation from CTA memo 200802(The Costa Workbench) on toymodels, calibration and data assimilation algorithms. Issue: ODA-314 removed option \ifpdf from style file, because of name clash error in MikTex Issue: ODA-314 bb_cookbook.tex: added svn:keywords and prepared document for include in documentation. No content review yet. Issue: ODA-314 rmi_thread.tex: added svn:keywords and prepared document for include in documentation. No content review yet. Issue: ODA-310 Redesign schemas: cleaning up unnecessary elements. Issue: ODA-321 Activate restarts of DudENSR, DudEnKF and ParticleFilter. Issue: ODA-310 Improvement: use List instead of Map,Dimension> for station ids. Issue: ODA-310 Modification on NetcdfUtils requires modification on EfdcNetcdfDataObject too. Issue: ODA-310 I forgot to commit WflowModelFactoryConfigReader also. --> Modifications on Netcdf-related classes to support extra option for wflow: it is now possible to write scalar output in netCDF. Issue: ODA-310 Modification on NetcdfUtils requires modification on EfdcNetcdfDataObject too. Issue: ODA-326 ODA-326: Fixed bug where reading/writing time series in WDM files did not work when Windows 7 Language for non-Unicode programs was set to Korean (Korea). Issue: ODA-189 removed stochObserver directory of the NEMO sat test case. This directory contained too much files. The content is now available as a tgz file which need to be unpacked before running the model. Issue: ODA-310 Modifications on Netcdf-related classes to support extra option for wflow: it is now possible to write scalar output in netCDF. Issue: ODA-310 Extra option for wflow: it is now possible to write scalar output in netCDF. ODA-325 Fixed os selction. Old mac version return "Darwin" for OS name in java and not "Mac" Updates for model Delwaq. Issue: ODA-322 ThreadStochModelFactory.java now implements ITimeHorizon. Added config script for apple PowerPC Issue: ODA-310 Recompile castor of wflow with java1.6 to solve the problem of java.lang.UnsupportedClassVersionError occurred in TeamCity. Issue: ODA-279 Support for writing stoch observers in C# (initial dynamic loading from oda-file of C# class) Issue: ODA-320 Fixed problem with id, ignored in main noos configuration file Issue: ODA-314 Added user documentation for the ResultWriter. Issue: ODA-314 New windows native binaries after changing project files Issue: ODA-314 Fixed microsoft dev studio project files after moving the source of the example models Issue: ODA-310 An extra optional entry is added on the wflowModelFactoryConfig.xsd to allow user to choose state variables (based on their exchange item IDs) to be written to the model output and analysis netcdf files. The corresponding model wrapper files, including the xsd file, are modified to support this new entry. Issue: 279 Initial version DHIStochObserver implementation in C# Issue: ODA-209 Add 64bit jep.dll. wflow model adapter is modified to work with jep-3.1.0 64bit (it turns out that windows version of 64bit jep.getValue returns a Long instead of Integer, hence it is necessary to modify the wrapper). Issue: ODA-314 documentation from ./core/native/doc added to OpenDA_documentation.tex, contents still to be reviewed. ODA-314 Renamed directory containing native model examples from exaples to models. Changed configure flag --with/--without-examples in to --with/--without-models ODA-314 Removed old, partially non working tests Issue: ODA-314 added svn:keywords and prepared document for \include{} in OpenDA_documentation.tex. No content review yet. Issue: ODA-314 Removed empty directory ./core/native/doc Issue: ODA-314 Moved doxygen to core/doc, updated file Doxygen and generated new .html files for ../../native/include. Issue: ODA-314 Moved documentation on running costa in parallel and model_builders to /core/doc. No latex changes made yet. Issue: ODA-314 Moved information to old_and_to_be_moved_before_release/, deleted unused files Issue: ODA-314 Moved documentation: the source code for the modelcombiner was removed from core/native/src/cta/ in r1260. Issue: ODA-314 created directory for outdated documentation Issue: ODA-317 Added forgotten files. Issue: ODA-316 Added forgotten file. Issue: ODA-317: Modification of period with height in swan TPAR boundary. ISsue: ODA-316 Added support for setting the standarddeviation of the observations errors as a fraction of the observed value. Also combinations with standardDeviation are allowed. Issue: ODA-314 Adapted style file: references per \input{}, command \odachapter changed Start of openda.bib Added chapter on bias_modelling, including svn:keywords Issue: ODA-281 Added additional check for user error in input In the previous version the user could trigger en exception/crash providing wrong input Issue: ODA-162 Extend dupuitPFile*.java (i.e. adding new exchange items) to make it possible to calibrate parameter sPolder in model file dupuit.P. Issue: ODA-313 A small bug is found in SimulationKwadraticCostFunction while testing the Levenberg-Marquardt algorithm implementation: costTotal is written after background cost component is added to the residual cost component. Issue: ODA-314 first version of main file OpenDA_documetation.tex added, latex style files and text of GNU Free Documentation License. Issue: ODA-313 First version of the Levenberg-Marquardt algorithm implementation: SimpleLeastSquaresCostFunctionWithState for unit test, checking especially if uncertainty estimate is OK. Issue: ODA-313 First version of the Levenberg-Marquardt algorithm implementation: test case with DAMflow model, with error estimate of the state vector. Issue: ODA-313 First version of the Levenberg-Marquardt algorithm implementation: test case with DAMflow model. Issue: ODA-313 First version of the Levenberg-Marquardt algorithm implementation. Issue: ODA-162 Extend dupuitGFile*.java (i.e. adding new exchange items) to make it possible to calibrate all parameters in model file dupuit.G. Issue: ODA-276 Trying to fix problems with test-driver Issue: ODA-276 Add model_reactive_advection tests. Issue: ODA-276 Issue: ODA-276 Fix svn problem in model_nemo Issue: ODA-279 Cleaning up, removed hard paths in Karup test and added scripts for creating initial restart files. This is needed because restart files from various MikeShe versions are not compatible. Issue: ODA-304 Modify D3dResults.java to allow user to make an exchangeItem for each output pair variable-location in a TRIH file. Issue: ODA-209 Intermediate product: jep-3.1.0 32bit, and wflow/OpenStream wrapper adjusted to work with PCRaster4.0. (So far, PCRaster4.0 32 bit is available; as soon as the 64bit version available, a new dll will be made/tested. Issue: ODA-189 Added NEMO benchmark test New attempt to get headless testing working on Mac Updated ant build script for Darwin headless testing Replaced some vector.toString comparisons with regular experssions. For example : not: assertEquals("[1.233343454534,324234234234]",vec.toString()); but AssertTrue(vec.toString().matches("(.*)1.2333434545(.*),3242342342(.*)")) Removed serialVersionUID for serializable classes. No serialVersionUID needed because OpenDA only uses serialization for running different instances of the same code in parallel. Issue: ODA-297 Downgraded Makefiles for older autconf Issue: ODA-297 Added missing makefiles Issue: ODA-297 Added missing make-file Issue: ODA-297 Linux: Changed configure script of native such that system installation of libsqlite3 can be used. new flag --disable-system-sqlite3 can be used to force compilation of OpenDA version of libsqlite3 (which is now a dynamic library) Issue: ODA-298 spatie te veel in setup_openda.bat (laatste text regel) Issue: ODA-288 Fix an issue that when no modelExchangeItemIds are defined for a noiseModel exchangeItem, would result in adding a null pointer as modelEchangeItemId. Issue: ODA-267 Add win32 binaries for model_efdc_dll. Issue: ODA-296 Initial implementation of Sequential assimilation for EnKF and DEnkf. We now have two new filter classes: DEnKFSeq and EnKFSeq These filters augment the state with the predictions and assimilate the observation one at a time New tests have been added for the simple_lorenz96 for these filters and the test criteria are made more strict for all simple_lorenz96 tests. Issue: ODA-288 Improve error when noise model exchange item is used but not defined in the config files. Issue: ODA-288 Deprecate NoiseModelExchangeItemConfig constructor, as it is unclear what happens when both modelExchangeItemId (used) and modelExchangeItemIds (ignored) are passed as arguments. Add two new constructors with either have modelExchangeItemId or modelExchangeItemIds as argument. Use new constructor in BBStochModelConfigReader. Issue: ODA-288 Fix a bug in NoiseModelExchangeItemConfig which causes that the modelExchangeItems are not remembered when parsing the config. As a result no noise was added to the modelExchangeItems. Fixed all swan unit tests on Mac OS-X * Added mac executables for tests * Added linux executable to configurations * updated existing mac executables with a version that statically links libgfortran (more robust) Issue: ODA-295 Attempt to fix startup scripts for windows. TimeSeriesNoiseModelInstance: Moved actual addition of noise to a separate routine. Cosmatic and handy for extending this class. Issue: ODA-293 ODA-293: EfdcModelInstance: fixed bug where output data of last timeStep was not written to model_output.nc file for a single black box model run. Added model_reactive_advection, model_nemo and model_delwaq to target "clean" in build.xml file. Issue: ODA-288 added ini4j.jar, parser for INI file format Issue: ODA-294 OpenDA version string is now taken from meta-info in jar file Java 1.6 version of the new castor files. Issue: ODA-292 Possibility to -set initial value for regularisationConstant -use regularisationConstnat as parameter (not only offset or log product) Increase max number of parameters shown in gui to 100 Issue: ODA-290 Added and configured Mac swan binaries for all SWAN "tests" oda_test.sh is now happy on Mac Issue: ODA-278 Include OpenMP configuration in Visual Studio 2008 solution. Updated windows build. Issue: ODA-278 Set correct flag for openmp in combination with gnu compilers. Issue: ODA-278 Add openmp target to Makefile. Fixed test (no comparison of strings but of values instead, to avoid accuracy problems) Issue: ODA-189 property eol-style: native set Fixed test (no comparison of files any more, but of values, to avoid accuracy problems) ODA-272 Fix line length. Issue: ODA-272 Initial support for drifters (floating TOXICS). Add libEfdcOrig.a as a depency in the makefile for libEFDC.so. Added tst files for model_nemo. Issue: ODA-276 Put a file in empty folders for core/tests/native_heat to keep teamcity happy. Issue: ODA-276 Deactivated old swan tests. Issue: ODA-276 Test if the empty folders give problems on teamcity. Issue: ODA-276\Reactivate EfdcRestartTest and deactivate Delft3dResultsTest to see if this causes the crash on TeamCity. Issue: ODA-276\Deactivate EfdcRestartTest to see if this causes the crash on TeamCity. Small change to start_eclipse.bat Add some missing empty directories for build system. Added temporal averaging option to cost function for calibration. Issue: ODA-276 Fix standalone tests in core. Issue: ODA-287 Initial version of reactive advection model to public. This model has *) changed numerics to solve stability issues *) new noise model *) different (biased) forcings NOTE: no windows executable has been created yet for the new (python) model Issue: ODA-281 Added test input for bias aware model Issue: ODA-281 Improved bias aware model. The user can do a lot of configuration now. Added documentation on the bias aware model. Removed debug output in compute method of black box wrapper Issue: ODA-286 Replaced old AR1 noise model with a new implementation. No detailed testing but the tests (oda_test.sh) still work after this change. Issue: ODA-268 Update of svnkit to beta of version 1.8. This allows the use of tortoise 1.8 Issue: ODA-285 Changed initial random seeds in TestRunner such that they correspond to runs in ApplicationRunner Issue: ODA-267 Shorten line length in openDA_wrapper.f90 Add .FOR support to Makefile. Update AIX version of Makefile. Issue: ODA-267 Add documentation. removed mac binaries from development trunk (should only be generated for releases Turned of junit test to see if this avoids a crash of all junit tests in public on teamcity. Some bug fixes to make junit tests work on windows with eclipse. Changed interface to set native random seed. Seed is changed from long to int. This will allow c-binding to work in a platform independed way Issue: ODA-267 More detailed log messages Issue: ODA-281 Added config files Issue: ODA-281 Intermediate check-in the bias aware model is now prepared for a lot of external configuration Issue: ODA-281 Added constructor to ObserverUtils using the IObservationDescriptions. Issue: ODA-270 Fixed bug with unknown end time Issue: ODA-275 C#: Added interfacing to allow a C# stoch observer to be used as well C#: Support for localization Issue: ODA-281 Bias Awareness: No longer hard-wired to black box wrapper. The user can now specify any model factory. Issue: ODA-270 Revert wrong capitals for loading opendabrigde library. Linux is sensitive to case. Fix description in DoubleExchangeItem for syntaxerror in sobek-wrapper. Fix SwanTimeInfoTest Issue: ODA-270 Fixed some trouble with aliasDefinitions in the BBModelInstance. Aliases are now copied to every modelInstance and evolve independently from there. This allows for changes in time. Known internal aliases: instanceNumber currentTime targetTime startTime and EndTime. Issue: ODA-270 Replacing 64bit dll in win32_ifort directory replaced mpich2mpi.dll by a 64-bit version Issue: ODA-284 Added pdf of black box cookbook Issue: ODA-284 First version of black box cookbook document Update of Delwaq BB wrapper model files. Issue: ODA-272, ODA-278 Add build configuration for OpenMP for Visual Studio. Only one toxic can be active, always pass the single TOX field to the current active toxic exchange item. If spill duration and spill amount are zero, set spill rate to zero. Update of Delwaq BB wrapper. Issue: ODA-297 Fixed small issue with full path names in MikeShe ModelFactory Issue: ODA-281 Bias awareness model some improvements to make first example working (Karup model with MikeShe) Issue: ODA-283 removed netcdf-4.2.jar from NEMO wrapper. The wrapper is now using the toolsUI from OpenDA core Issue: ODA-282 Removing copies of libraries. Accidental commit of linux32_gnu folder. Rebuilt d3d binaries for Windows 32-bit (ifort compiler) fixed test configs activated d3d tests Issue: ODA-240 Cleaning up delft3f kalman test cases. cd "`printf "%b" 0057home0057verlaanm0057deltares0057src0057openda0137201302180057public0057model0137delft3d0057tests0057kalman0137estuary`" Issue: ODA-281 Initial setup of modeling and filtering the bias in observations. Update cta-native-libaries Issue: ODA-267 Do a relative assert in unit test for time step, etc. Disable toxics unit test. Issue: ODA-240 Small bug fix for linux and delft3d native wrapper. Issue: ODA-240 Update openda-wrapper for further testing. Issue: ODA-240 Update openda-wrapper for further testing. Issue: ODA-280 Fixed bugs in 2d-noisemodel. Fixed references to jna Issue: ODA-279 Changed to more recent version of mpi to make it compatible with delt3d. Issue: ODA-279 Revert jna to version 3.3 for team-city. Issue: ODA-279 Revert jna to version 3.3 for team-city. Issue: ODA-279 Remove incompatible copies of mpich libraries. Issue: ODA-272 Add test for toxic exchange items. Issue: 272 XP dll. Issue: ODA-267, ODA-272 Changed check on NTOX for exchange items calls. Improved makefile to support more OSes. Issue: ODA-267 Correct svn:ignore properties. Issue: ODA-267 Set svn:ignore properties on test directories. Issue: ODA-240 Update delft3d libraries for linux64_gnu Issue: ODA-279 Added empty implementation of GetObservedValues and getObservedLocalization to generic OpenMI bridge Issue: ODA-240 Cleaning up delft3d tests. Missing xmlSchemas folder was blocking ant zip. Issue: ODA-279 Fixed some issues in dotnet bridging and mikeshe coupling (mostly references) Issue: ODA-240 Fix river calibration test-case Issue: ODA-240 Fixed calibration_estuary_dd test on linux. Issue: ODA-240 Fixed calibration_estuary test on linux. ODA-240 Disabled one test for now and add linbraries to eclipse search-path. Issue: ODA-279 Initial check-in of mikeshe coupling including two test models. Issue: ODA-240 Update of delft3d libs for linux64_gnu minor textual change in comment Issue: ODA-240 Small issue with symbolic links and delft3d-dll. Issue: ODA-240 Force netcdf3 on all machines. Issue: ODA-240 Update of delft3d libs for linux64_gnu Issue: ODA-207 Updated Delft3d-Flow EnKF wrapper (flow2d3d_openda.dll) to the latest version of to open source version of delft3d. Unit tests now run on Windows (32bit). Added batch file to start IDEA with the right path for unit testing Removed reference to libltdl from libNefisSO. It seems that this is not used anymore. Issue: ODA-240 Try removing -lltdl from nefis library. Effect unknown. Issue: ODA-240 Update of build of linux64_gnu libraries for delft3d on teamcity client. Added handy script oda_matlabconv. Convert an OpenDA matlab result file into a directory with matlab script files for each variable. First converting using this script and then reading the variables that are needed is in general much faster. All files are stored in a directory with the same name as the matlab input file. The files that are generated have the name f_variable_name.m. Sourcing such a file in matlab will declare the variable 'variable_name' Issue: ODA-240 Build of linux64_gnu libraries for delft3d on teamcity client. Issue: ODA-276 Try new build of 64bit libEFDC.so Issue: ODA-240 Add linux64_gnu support for delft3d ddl Ant build failed on missing doc directory. Issue: ODA-240 Fix delft3d junit tests for calibration. Issue: ODA-258 - Noise model is propagated from TSTART to TTARGET directly, instead of per model time step - Add a unit test for testing model.axpyOnState of OpenStreams - Correct bug in IoObjectStochObserver Issue: ODA-278, ODA-272 Update visual studio solution. Add new XP dll Issue: ODA-278, ODA-272 Only one toxic is active and returned depending on the settings in EVENT_TOX2.INP. Toxics boundary exchange items are deactivated. Add OpenMP pragmas. Issue: ODA-278 Merged OpenMP pragmas from IBM code into PC version. Add files from IBM code. Issue: ODA-267 Update makefile for new lib location. Issue: ODA-267 Update scripts to new lib directory. Issue: ODA-276 Replaced EFDC libraries with copies built on an older system. Issue: ODA-276 Add libraries (they were ignored) Issue: ODA-276 Made efdc_dll work in teamcity? Issue: ODA-275 Initial implementation: Extended model interface and support in black box wrapper to handle interpolation to observed values and localization by user defined methods Issue: ODA-225 Changed reference output after bugfix in EnSR. Issue: ODA-227 More robust handling of empty TimeSeriesStochObservers Changed reference output for (partially) empty observers as a result of changes in behaviour introduced in this issue (ODA-227) Issue: ODA-276 Replaced OPENDA_NATIVE_DIR by standard $(top_srcdir) in makefiles Issue: ODA-276 Check in generated makefiles, to see if that fixes teamcity Issue: ODA-189 Some upgrades to NEMO wrapper en test model Improved test model with realistic observations resembling satellite tracks (available at irregular times) Issue: ODA-227 Fixed problem in creating selections of NOOS and timeseries observationdescriptions We had empty/illegal timeseries when some timeseries were empty (no observations) for the given time selection Issue: ODA-276 Makefile did not work for vbuild. Issue: ODA-267 Fix export of supports_exhange_item. Make new XP dll. Issue: ODA-267, ODA-268, ODA-271, ODA-272 Add win32 shared dll, updated proj Add misssing pbm_cut.for Issue: ODA-267 Fix serializable warning about serialversionuid. Remove unnecessary imports. Remove unused variables. Issue: ODA-266, ODA-267, ODA-271, ODA-272 Add linux64_gnu libEFDC.so. Issue: ODA-266, ODA-267, ODA-271, ODA-272 Add method for requesting EFDC dll if exchange item is configured. Add toxics exchange items. Improve switching between template and workdirs in EFDC dll. Add generic module (model_exchange_items) for exchange item related functions and settings. Move exchange item related settings from state and time series to generic module. Replace hardcoded exchange item identifiers by parameters. Improve logging. Issue: ODA-264 Added Free-method to native result writers Issue: ODA-273 Fixed some problems for handling height in NOOS observations - correct initialization and reading of the value -fixed comparison to NaN Note: corresponds to revision10->11 fix in the OpenDA-MikeShe repository Issue: ODA-267 Add a simple native ensemble simulation run using the EFDC shared library. Issue ODA-267 Added tests for the native part of the EFDC model. Issue: ODA-267 Merge new EFDC code with OpenDA compliant shared library. Introduction of model_delwaq in the OpenDA public tree. Corrected various type-Os in the interface documentation. Issue: ODA-258 Rename BBWrappedExchangeItem by BBCollectTimeSeriesExchangeItem. Issue: ODA-189 Changed configuration after solving problem with setting up an initial ensemble by the black box coupler Issue: ODA-269 Use dynamic aliasses for templateDir such that we can use %instanceNumber% in the templateDir as well. This allows us to prepare different work directories for each ensemble member Issue: ODA-189 Added (unused) resources and native_bin folder to the NEMO model directory Issue: ODA-189 Added missing module.properties file for NEMO project Issue: ODA-258 Modify BBStochModelInstance and BBWrappedExchangeItem for the collectPredictorTimeSeries to work also with non-BBModelFactory, e.g. OpenStreams. Issue: ODA-189 Added missing build file for NEMO model wrapper Issue: ODA-189 Added missing build file for NEMO model wrapper Issue: ODA-258 Add flag 'collectPredictorTimeSeries' in the bbStochModel configuration for collecting predictor (in memory) at various time levels. This is useful, for example, for asynchronous KFing. Test has been made using a SWAN example. Issue: ODA-258 Add three new parameters to the sequentialSimulation.xsd for specifying analyses times required for running AsynKF in FEWS. Issue: ODA-258 Add three new parameters for specifying analyses times required for running AsynKF in FEWS. Issue: ODA-267 Moved log files to parent dir. Write debug messages to log instead of stdout. Updated log messages. Issue: ODA-265 Enable unit tests for model_efdc_dll under linux. Issue: ODA-265 Changed JNA protection to false, as it crashes when libjsig.so was not added to LD_PRELOAD. Issue: ODA-264 Added native resultwriting 1) Bridging 2) Java implementation layer 3) Example implementation in F90 4) Test input for Example implementation MS-dev files have not yet been created. Issue: ODA-189 Fixed problem for models without a noise model Issue: ODA-189 Minor changes: -removed whole path to executable -fixed linking opa exe to workdir Issue: ODA-263 Add a 'work around' in the SWAN wrapper for accommodating SWAN simulation in STATIONARY mode. Issue: ODA-189 Setup input for nemo model. Ensemble based kalman filtering with initial ensemble. No noise model! Issue: ODA-189 NEMO model: updated/bugfixes in wrapper code Issue: ODA-189 Intermediate setup of NEMO test (only Darwin executable) and wrapper configuration files Issue: ODA-189 Initial check in of wrapper classes for NEMO model Issue: ODA-261 *Implementation of DEnKF algorithm (including localization) *Changed part of EnKF routines into protected such that DEnKF can be based on EnKF implementation *Changed native_head model to finer resolution *Added input and tests for native_head for EnSR, DEnKF *Changed amount of output for the simple_oscillator test Issue: ODA-262 Updated MS-Dev files as well for changes in opendabridge. Issue: ODA-262 *Set seed of native random generator at start of each test in the TestRunner *Allow native random generator to be initialized from the java code (set seed) *Some reorganization of the native bridging code Note: Only linux/Mac (Windows project files have not been changed in this commit) Issue: ODA-224 Replaced EnKF algorithm with a more modular implementation. Issue: ODA-224 Moved the original EnKF implementation to EnKF old. Will be replaced by a more modular implementation Issue: ODA-252 ODA-252: NetcdfDataObject: fixed type of _FillValue attribute. Removed missing_value and standard_name attributes from written netcdf files and added calendar attribute. Updated WflowModelOpenDaInFewsTest unit tests. Issue:ODA-200 Added support of AnnounceObsValues for parallel (native) runs as well Issue: ODA-200 *Write error to stdout *Improved error message Issue: ODA-256 Added two calibration test-cases for delft3d. Issue: ODA-255 Fixed bug in EnSR changed chi = ( I - psi'*psi ) into chi = ( I + psi'*psi ) Issue: ODA-254 64-bit version of the native code of OpenDA including adjusted external binaries ODA-250: WflowModelInstance: fixed bug where input data was shifted one timeStep for wflow model. Issue: ODA-252 ODA-252: WflowModelInstance: fixed bug. Wflow model expects values to start at upperLeft corner of grid. Issue: ODA-251 ODA-251: for improved performance Issue: ODA-251 ODA-251: WflowModelInstance: improved performance of writing netcdf files. Do not initialize netcdf with fillValues, since these values will all be overwritten anyway. Issue: ODA-252 ODA-252: WflowModelInstance: fixed bug where grid data was flipped upside down (North and South were interchanged). Issue: ODA-252 ODA-252: WflowModelInstance: changed code so that grid cell coordinates are written to output netcdf files for regular grids. Issue: ODA-251 ODA-251: adjustments Onno (taiwan) Issue: ODA-250 ODA-250: WflowModelInstance: fixed bug where input data for forcings was not put into the model for timeSteps after an analysis timeStep. Issue: ODA-248 Fix bug in restart of MapsNoiseModelInstance Issue: ODA-224 Replaced system random generator for native OpenDA by our own implementation. This to allow us to have full control. Issue: ODA-249 Add netcdf restart option for swan in template. Issue: ODA-191 Extend the test example DudWritersWithSelections.oda with the use of regular expression to select result items based on context. Issue: ODA-224 *Improved (error) messages *changed from rand to the (better) random for random generator in native part of OpenDA. Adapted relative paths to bin dir in d3dflowrestart test. Issue: ODA-248 Fixed bug with scaling. Results look ok again. Issue: ODA-248 Speed up of 2d-noise-model including seperability. Issue: ODA-224 Added additional utility routine for computing ensemble standard deviation when mean is already removed ODA-224 Fixed output level of result writer in order to stop tests from faining Problem was introduced in another issue Issue: ODA-209 ODA-209: Wflow: fixed unit tests. Issue: ODA-247, SIMONA-3946 Initialize function handles to CTA_NULL. Issue: ODA-191 Remove old putValue methods and leave only the new putValue available. Correct all related codes and examples. Issue: ODA-53 Fix in model.Update() loop: stop when model is Done. Issue: ODA-246 First edition of runIntellij.bat for running Intellij with the correct OPENDA_BINDIR in PATH. It runs so far only for 'public' part of OpenDA. Issue: ODA-242 The method getTimes() of IoObjectStochObserver is corrected to give the time information in ascending order. Issue: ODA-131 Updated generation script for Fortran 9X binding Issue: ODA-131 Regenerated Fortran 9X binding Issue: ODA-242 IoObjectStochObserver is corrected for the case where observations are available at more than one stations, one value at one station, but at different time levels.