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Instructions for Modifying Dakota's Input Specification
Specification Change Table of Contents

To modify Dakota's input specification (for maintenance or addition of new input syntax), specification maintenance mode must be enabled at Dakota configure time with the -DENABLE_SPEC_MAINT option, e.g.,

./cmake -DENABLE_SPEC_MAINT:BOOL=ON ..

This will enable regeneration of NIDR and Dakota components which must be updated following a spec change.

New XML specification

The authoritative source for valid Dakota input grammar is now dakota/src/dakota.xml. The schema defining valid content for this XML file is in dakota/src/dakota.xsd. In the transition period (until parser work is complete), Dakota input grammar will be edited in the .xml file and translated using Java to dakota/src/dakota.input.nspec for consumption by the Dakota build process.

Process overview for updating the XML input definition:

XML Build Requirements

Editing the XML and then compiling Dakota requires

XML Editing Tools

The following tools will make editing dakota.input.xml easier.

XML Features (with map to NIDR)

Out of necessity, the initial Dakota XML dakota.xml closely mirrors dakota.input.nspec. Valid Dakota input grammar is constrained by dakota.xml, an XML document which must validate against dakota.xsd. The top-level element of interest is <input>, which is comprised of a sequence of content elements (keywords, alternates, etc.), which may themselves contain additional child content elements. The key content types are:

Deprecated: Modify dakota.input.nspec

The master input specification dakota.input.nspec in Dakota/src is the primary file to update when making a specification change. It uses the following syntactic elements:

Warning
  • Do not skip this step. Attempts to modify the NIDR_keywds.hpp file in Dakota/src without using the NIDR table generator are very error-prone. Moreover, the input specification provides a reference to the allowable inputs of a particular executable and should be kept in synch with the parser files; modifying the parser files independent of the input specification creates, at a minimum, undocumented features.
  • All keywords in dakota.input.nspec are lower case by convention. All user inputs are converted to lower case by the parser prior to keyword match testing, resulting in case insensitive parsing.
  • Since the NIDR parser allows abbreviation of keywords, you must avoid adding a keyword that could be misinterpreted as an abbreviation for a different keyword within the same top-level keyword, such as "environment" and "method". For example, adding the keyword "expansion" within the method specification would be a mistake if the keyword "expansion_factor" already was being used in this specification.
  • The NIDR input is somewhat order-dependent, allowing the same keyword to be reused multiple times in the specification. This often happens with aliases, such as lower_bounds, upper_bounds and initial_point. Ambiguities are resolved by attaching a keyword to the most recently seen context in which it could appear, if such exists, or to the first relevant context that subsequently comes along in the input file. With the earlier IDR parser, non-exclusive specifications (those not in mutually exclusive blocks) were required to be unique. That is why there are such aliases for initial_point as cdv_initial_point and ddv_initial_point: so older input files can be used with no or fewer changes.

Rebuild generated files

When configured with -DENABLE_SPEC_MAINT, performing a make in Dakota/src will regenerate all files which derive from dakota.input.nspec, including NIDR_keywds.hpp, dakota.input.summary, NIDR_guikywds.h, and dakota.input.desc. If you commit changes to a source repository, be sure to commit any automatically generated files in addition to any modified in the following steps. It is not strictly necessary to run make at this point in the sequence, and in fact may generate errors if necessary handlers aren't yet available.

Update NIDRProblemDescDB.cpp in Dakota/src

Many keywords have data associated with them: an integer, a floating-point number, a string, or arrays of such entities. Data requirements are specified in dakota.input.nspec by the tokens INTEGER, REAL, STRING, INTEGERLIST, REALLIST, STRINGLIST. (Some keywords have no associated data and hence no such token.) After each keyword and data token, the dakota.input.nspec file specifies functions that the NIDR parser should call to record the appearance of the keyword and deal with any associated data. The general form of this specification is

{ startfcn, startdata, stopfcn, stopdata }

i.e., a brace-enclosed list of one to four functions and data pointers, with trailing entities taken to be zero if not present; zero for a function means no function will be called. The startfcn must deal with any associated data. Otherwise, the distinction between startfcn and stopfcn is relevant only to keywords that begin a group of keywords (enclosed in parentheses or square brackets). The startfcn is called before other entities in the group are processed, and the stop function is called after they are processed. Top-level keywords often have both startfcn and stopfcn; stopfcn is uncommon but possible for lower-level keywords. The startdata and (if needed) stopdata values are usually pointers to little structures that provide keyword-specific details to generic functions for startfcn and stopfcn. Some keywords that begin groups (such as "approx_problem" within the top-level "environment" keyword) have no need of either a startfcn or a stopfcn; this is indicated by "{0}".

Most of the things within braces in dakota.input.nspec are invocations of macros defined in NIDRProblemDescDB.cpp. The macros simplify writing dakota.input.nspec and make it more readable. Most macro invocations refer to little structures defined in NIDRProblemDescDB.cpp, usually with the help of other macros, some of which have different definitions in different parts of NIDRProblemDescDB.cpp. When adding a keyword to dakota.input.nspec, you may need to add a structure definition or even introduce a new data type. NIDRProblemDescDB.cpp has sections corresponding to each top-level keyword. The top-level keywords are in alphabetical order, and most entities in the section for a top-level keyword are also in alphabetical order. While not required, it is probably good practice to maintain this structure, as it makes things easier to find.

Any integer, real, or string data associated with a keyword are provided to the keyword's startfcn, whose second argument is a pointer to a Values structure, defined in header file nidr.h.

Example 1: if you added the specification:

    [method_setting REAL {method_setting_start, &method_setting_details} ]

you would provide a function

void NIDRProblemDescDB::
method_setting_start(const char *keyname, Values *val, void **g, void *v)
{ ... }

in NIDRProblemDescDB.cpp. In this example, argument &method_setting_details would be passed as v, val->n (the number of values) would be 1 and *val->r would be the REAL value given for the method_setting keyword. The method_setting_start function would suitably store this value with the help of method_setting_details.

For some top-level keywords, g (the third argument to the startfcn and stopfcn) provides access to a relevant context. For example, method_start (the startfcn for the top-level method keyword) executes

DataMethod *dm = new DataMethod;
g = (void*)dm;

(and supplies a couple of default values to dm). The start functions for lower-level keywords within the method keyword get access to dm through their g arguments. Here is an example:

void NIDRProblemDescDB::
method_str(const char *keyname, Values *val, void **g, void *v)
{
(*(DataMethod**)g)->**(String DataMethod::**)v = *val->s;
}

In this example, v points to a pointer-to-member, and an assignment is made to one of the components of the DataMethod object pointed to by *g. The corresponding stopfcn for the top-level method keyword is

void NIDRProblemDescDB::
method_stop(const char *keyname, Values *val, void **g, void *v)
{
DataMethod *p = *(DataMethod**)g;
delete p;
}

which copies the now populated DataMethod object to the right place and cleans up.

Example 2: if you added the specification

    [method_setting REALLIST {{N_mdm(RealL,methodCoeffs)}

then method_RealL (defined in NIDRProblemDescDB.cpp) would be called as the startfcn, and methodCoeffs would be the name of a (currently nonexistent) component of DataMethod. The N_mdm macro is defined in NIDRProblemDescDB.cpp; among other things, it turns RealL into NIDRProblemDescDB::method_RealL. This function is used to process lists of REAL values for several keywords. By looking at the source, you can see that the list values are val->r[i] for 0 <= i < val->n.

Update ProblemDescDB.cpp in Dakota/src

Augment/update get_<data_type>() functions

The next update step involves extending the database retrieval functions in ProblemDescDB.cpp. These retrieval functions accept an identifier string and return a database attribute of a particular type, e.g., a RealVector:

const RealVector& get_rv(const String& entry_name);

The implementation of each of these functions contains tables of possible entry_name values and associated pointer-to-member values. There is one table for each relevant top-level keyword, with the top-level keyword omitted from the names in the table. Since binary search is used to look for names in these tables, each table must be kept in alphabetical order of its entry names. For example,

...
else if ((L = Begins(entry_name, "model."))) {
if (dbRep->methodDBLocked)
Locked_db();
#define P &DataModelRep::
static KW<RealVector, DataModelRep> RVdmo[] = { // must be sorted
{"nested.primary_response_mapping", P primaryRespCoeffs},
{"nested.secondary_response_mapping", P secondaryRespCoeffs},
{"surrogate.kriging_conmin_seed", P krigingConminSeed},
{"surrogate.kriging_correlations", P krigingCorrelations},
{"surrogate.kriging_max_correlations", P krigingMaxCorrelations},
{"surrogate.kriging_min_correlations", P krigingMinCorrelations}};
#undef P
KW<RealVector, DataModelRep> *kw;
if ((kw = (KW<RealVector, DataModelRep>*)Binsearch(RVdmo, L)))
return dbRep->dataModelIter->dataModelRep->*kw->p;
}

is the "model" portion of ProblemDescDB::get_rv(). Based on entry_name, it returns the relevant attribute from a DataModel object. Since there may be multiple model specifications, the dataModelIter list iterator identifies which node in the list of DataModel objects is used. In particular, dataModelList contains a list of all of the data_model objects, one for each time a top-level model keyword was seen by the parser. The particular model object used for the data retrieval is managed by dataModelIter, which is set in a set_db_list_nodes() operation that will not be described here.

There may be multiple DataMethod, DataModel, DataVariables, DataInterface, and/or DataResponses objects. However, only one specification is currently allowed so a list of DataEnvironment objects is not needed. Rather, ProblemDescDB::environmentSpec is the lone DataEnvironment object.

To augment the get_<data_type>() functions, add table entries with new identifier strings and pointer-to-member values that address the appropriate data attributes from the Data class object. The style for the identifier strings is a top-down hierarchical description, with specification levels separated by periods and words separated with underscores, e.g., "keyword.group_specification.individual_specification". Use the dbRep->listIter->attribute syntax for variables, interface, responses, and method specifications. For example, the method_setting example attribute would be added to get_drv() as:

{"method_name.method_setting", P methodSetting},

inserted at the beginning of the RVdmo array shown above (since the name in the existing first entry, i.e., "nested.primary_response_mapping", comes alphabetically after "method_name.method_setting").

Update Corresponding Data Classes

In this step, we extend the Data class definitions (DataEnvironment, DataMethod, DataModel, DataVariables, DataInterface, and/or DataResponses) to include the new attributes referenced in Update NIDRProblemDescDB.cpp in Dakota/src and Augment/update get_<data_type>() functions.

Update the Data class header file

Add a new attribute to the public data for each of the new specifications. Follow the style guide for class attribute naming conventions (or mimic the existing code).

Update the .cpp file

Define defaults for the new attributes in the constructor initialization list. Add the new attributes to the assign() function for use by the copy constructor and assignment operator. Add the new attributes to the write(MPIPackBuffer&), read(MPIUnpackBuffer&), and write(ostream&) functions, paying careful attention to the use of a consistent ordering.

Use get_<data_type>() Functions

At this point, the new specifications have been mapped through all of the database classes. The only remaining step is to retrieve the new data within the constructors of the classes that need it. This is done by invoking the get_<data_type>() function on the ProblemDescDB object using the identifier string you selected in Augment/update get_<data_type>() functions. For example:

const String& interface_type = problem_db.get_string("interface.type");

passes the "interface.type" identifier string to the ProblemDescDB::get_string() retrieval function, which returns the desired attribute from the active DataInterface object.

Warning
Use of the get_<data_type>() functions is restricted to class constructors, since only in class constructors are the data list iterators (i.e., dataMethodIter, dataModelIter, dataVariablesIter, dataInterfaceIter, and dataResponsesIter) guaranteed to be set correctly. Outside of the constructors, the database list nodes will correspond to the last set operation, and may not return data from the desired list node.

Update the Documentation

Doxygen comments should be added to the Data class headers for the new attributes, and the reference manual sections describing the portions of dakota.input.nspec that have been modified should be updated. In particular, the reference manual tables summarizing keywords provide help data to the Jaguar user interface so need to be kept updated.