add initial MFEM db plugin

git-svn-id: http://visit.ilight.com/svn/visit/trunk/src@23703 18c085ea-50e0-402c-830e-de6fd14e8384

config-site/aztec1.cmake

@@ -177,6 +177,11 @@ ITAPS_LINK_DIRECTORIES(GRUMMP ${VISITHOME}/itaps/1.4/GRUMMP/0.6.5/${VISITARCH}/l
 ##
 #VISIT_OPTION_DEFAULT(VISIT_MANTA_DIR ${VISITHOME}/manta/2540/${VISITARCH})
 
+##
+## MFEM 
+##
+VISIT_OPTION_DEFAULT(VISIT_MFEM_DIR ${VISITHOME}/mfem/68e941f8fe/${VISITARCH})
+
 ##
 ## Mili
 ##

databases/CMakeLists.txt

@@ -277,6 +277,7 @@ CHECK_THIRDPARTY_DEPENDENT_PLUGINS(HDF4     Cosmos ZeusMP)
 CHECK_THIRDPARTY_DEPENDENT_PLUGINS(MDSPLUS  MDSplus)
 CHECK_THIRDPARTY_DEPENDENT_PLUGINS(MILI     Mili)
 CHECK_THIRDPARTY_DEPENDENT_PLUGINS(UINTAH   Uintah)
+CHECK_THIRDPARTY_DEPENDENT_PLUGINS(MFEM     MFEM)
 IF (WIN32)
     CHECK_THIRDPARTY_DEPENDENT_PLUGINS(ZLIB     VCellMTMD)
 ENDIF (WIN32)

databases/MFEM/CMakeLists.txt

+# DO NOT EDIT THIS FILE! THIS FILE IS AUTOMATICALLY GENERATED BY xml2cmake
+PROJECT(MFEM)
+
+INCLUDE(${VISIT_SOURCE_DIR}/CMake/PluginMacros.cmake)
+
+SET(COMMON_SOURCES
+MFEMPluginInfo.C
+MFEMCommonPluginInfo.C
+)
+
+SET(LIBI_SOURCES 
+MFEMPluginInfo.C
+)
+
+SET(LIBM_SOURCES
+MFEMMDServerPluginInfo.C
+${COMMON_SOURCES}
+avtMFEMFileFormat.C
+JSONRoot.C
+)
+
+SET(LIBE_SOURCES
+MFEMEnginePluginInfo.C
+${COMMON_SOURCES}
+avtMFEMFileFormat.C
+JSONRoot.C
+)
+
+INCLUDE_DIRECTORIES(
+${CMAKE_CURRENT_SOURCE_DIR}
+${MFEM_INCLUDE_DIR}
+${VISIT_INCLUDE_DIR}/third_party_builtin
+${VISIT_COMMON_INCLUDES}
+${VISIT_INCLUDE_DIR}/avt/DBAtts/MetaData
+${VISIT_INCLUDE_DIR}/avt/DBAtts/SIL
+${VISIT_INCLUDE_DIR}/avt/Database/Database
+${VISIT_INCLUDE_DIR}/avt/Database/Formats
+${VISIT_INCLUDE_DIR}/avt/Database/Ghost
+${VISIT_INCLUDE_DIR}/avt/FileWriter
+${VISIT_INCLUDE_DIR}/avt/Filters
+${VISIT_INCLUDE_DIR}/avt/MIR/Base
+${VISIT_INCLUDE_DIR}/avt/MIR/Tet
+${VISIT_INCLUDE_DIR}/avt/MIR/Zoo
+${VISIT_INCLUDE_DIR}/avt/Math
+${VISIT_INCLUDE_DIR}/avt/Pipeline/AbstractFilters
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Data
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Pipeline
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Sinks
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Sources
+${VISIT_INCLUDE_DIR}/avt/VisWindow/VisWindow
+${VISIT_INCLUDE_DIR}/visit_vtk/full
+${VISIT_INCLUDE_DIR}/visit_vtk/lightweight
+${EAVL_INCLUDE_DIR} 
+${VTK_INCLUDE_DIRS} 
+)
+
+
+LINK_DIRECTORIES(${VISIT_LIBRARY_DIR} ${EAVL_LIBRARY_DIR} ${VTK_LIBRARY_DIRS} ${MFEM_LIBRARY_DIR} )
+
+ADD_LIBRARY(IMFEMDatabase ${LIBI_SOURCES})
+TARGET_LINK_LIBRARIES(IMFEMDatabase visitcommon)
+SET(INSTALLTARGETS IMFEMDatabase)
+
+IF(NOT VISIT_ENGINE_ONLY AND NOT VISIT_DBIO_ONLY)
+    ADD_LIBRARY(MMFEMDatabase ${LIBM_SOURCES}    )
+    TARGET_LINK_LIBRARIES(MMFEMDatabase visitcommon avtdbatts avtdatabase_ser ${MFEM_LIB} )
+    ADD_TARGET_DEFINITIONS(MMFEMDatabase MDSERVER)
+    SET(INSTALLTARGETS ${INSTALLTARGETS} MMFEMDatabase)
+ENDIF(NOT VISIT_ENGINE_ONLY AND NOT VISIT_DBIO_ONLY)
+
+ADD_LIBRARY(EMFEMDatabase_ser ${LIBE_SOURCES})
+TARGET_LINK_LIBRARIES(EMFEMDatabase_ser visitcommon avtdatabase_ser avtpipeline_ser ${MFEM_LIB} )
+ADD_TARGET_DEFINITIONS(EMFEMDatabase_ser ENGINE)
+SET(INSTALLTARGETS ${INSTALLTARGETS} EMFEMDatabase_ser)
+
+IF(VISIT_PARALLEL)
+    ADD_PARALLEL_LIBRARY(EMFEMDatabase_par ${LIBE_SOURCES})
+    TARGET_LINK_LIBRARIES(EMFEMDatabase_par visitcommon avtdatabase_par avtpipeline_par ${MFEM_LIB} )
+    ADD_TARGET_DEFINITIONS(EMFEMDatabase_par ENGINE)
+    SET(INSTALLTARGETS ${INSTALLTARGETS} EMFEMDatabase_par)
+ENDIF(VISIT_PARALLEL)
+
+VISIT_INSTALL_DATABASE_PLUGINS(${INSTALLTARGETS})
+VISIT_PLUGIN_TARGET_RTOD(databases ${INSTALLTARGETS})
+VISIT_PLUGIN_TARGET_FOLDER(databases MFEM ${INSTALLTARGETS})
+

databases/MFEM/JSONRoot.C

+/*****************************************************************************
+*
+* Copyright (c) 2000 - 2014, Lawrence Livermore National Security, LLC
+* Produced at the Lawrence Livermore National Laboratory
+* LLNL-CODE-442911
+* All rights reserved.
+*
+* This file is  part of VisIt. For  details, see https://visit.llnl.gov/.  The
+* full copyright notice is contained in the file COPYRIGHT located at the root
+* of the VisIt distribution or at http://www.llnl.gov/visit/copyright.html.
+*
+* Redistribution  and  use  in  source  and  binary  forms,  with  or  without
+* modification, are permitted provided that the following conditions are met:
+*
+*  - Redistributions of  source code must  retain the above  copyright notice,
+*    this list of conditions and the disclaimer below.
+*  - Redistributions in binary form must reproduce the above copyright notice,
+*    this  list of  conditions  and  the  disclaimer (as noted below)  in  the
+*    documentation and/or other materials provided with the distribution.
+*  - Neither the name of  the LLNS/LLNL nor the names of  its contributors may
+*    be used to endorse or promote products derived from this software without
+*    specific prior written permission.
+*
+* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT  HOLDERS AND CONTRIBUTORS "AS IS"
+* AND ANY EXPRESS OR  IMPLIED WARRANTIES, INCLUDING,  BUT NOT  LIMITED TO, THE
+* IMPLIED WARRANTIES OF MERCHANTABILITY AND  FITNESS FOR A PARTICULAR  PURPOSE
+* ARE  DISCLAIMED. IN  NO EVENT  SHALL LAWRENCE  LIVERMORE NATIONAL  SECURITY,
+* LLC, THE  U.S.  DEPARTMENT OF  ENERGY  OR  CONTRIBUTORS BE  LIABLE  FOR  ANY
+* DIRECT,  INDIRECT,   INCIDENTAL,   SPECIAL,   EXEMPLARY,  OR   CONSEQUENTIAL
+* DAMAGES (INCLUDING, BUT NOT  LIMITED TO, PROCUREMENT OF  SUBSTITUTE GOODS OR
+* SERVICES; LOSS OF  USE, DATA, OR PROFITS; OR  BUSINESS INTERRUPTION) HOWEVER
+* CAUSED  AND  ON  ANY  THEORY  OF  LIABILITY,  WHETHER  IN  CONTRACT,  STRICT
+* LIABILITY, OR TORT  (INCLUDING NEGLIGENCE OR OTHERWISE)  ARISING IN ANY  WAY
+* OUT OF THE  USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+* DAMAGE.
+*
+*****************************************************************************/
+
+// ************************************************************************* //
+//                                 JSONRoot.C                                //
+// ************************************************************************* //
+
+
+#include <fstream>
+#include "rapidjson/document.h"
+
+
+#include "JSONRoot.h"
+
+#include <iostream>
+using namespace std;
+
+
+// ****************************************************************************
+//  Method: JSONRootPath Constructor
+//
+//  Purpose: Inits an instance of a JSONRootPath object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootPath::JSONRootPath()
+:path("")
+{
+}
+
+// ****************************************************************************
+//  Method: JSONRootPath Destructor
+//
+//  Purpose: Cleans up an instance of a JSONRootPath object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootPath::~JSONRootPath()
+{
+}
+
+// ****************************************************************************
+//  Method: JSONRootPath::Expand
+//
+//  Purpose: Maps a doman id to is file system or in db path.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+std::string
+JSONRootPath::Expand(int domain) const
+{
+    //
+    // TODO: handle domain id mapping (likley printf style expansion)
+    //
+    
+    return path;
+}
+
+// ****************************************************************************
+//  Method: JSONRootPath::Set
+//
+//  Purpose: Sets the base pattern for a path.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+void 
+JSONRootPath::Set(const string &path)
+{
+    this->path = path;
+}
+
+// ****************************************************************************
+//  Method: JSONRootEntry Constructor
+//
+//  Purpose: Inits an instance of a JSONRootEntry object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootEntry::JSONRootEntry()
+{
+
+}
+
+// ****************************************************************************
+//  Method: JSONRootEntry Destructor
+//
+//  Purpose: Cleans up an instance of a JSONRootEntry object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootEntry::~JSONRootEntry()
+{
+
+}
+// ****************************************************************************
+//  Method: JSONRootEntry::Path
+//
+//  Purpose: Returns the path object associated with this entry.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootPath &
+JSONRootEntry::Path()
+{
+    return path;
+}
+
+// ****************************************************************************
+//  Method: JSONRootEntry::Tags
+//
+//  Purpose: Returns the names of the tags associated with this entry.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+void
+JSONRootEntry::Tags(std::vector<std::string> &tag_names) const
+{
+    tag_names.clear();
+    for(map<string,string>::const_iterator itr = tags.begin();
+        itr!=tags.end();
+        itr++)
+        {
+            tag_names.push_back(itr->first);
+        }
+}
+
+// ****************************************************************************
+//  Method: JSONRootEntry::HasTag
+//
+//  Purpose: Returns if this entry has a tag with the given name.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+bool
+JSONRootEntry::HasTag(const std::string &tag_name) const
+{
+  
+   return (tags.find(tag_name) != tags.end());
+}
+
+// ****************************************************************************
+//  Method: JSONRootEntry::Tag
+//
+//  Purpose:
+//     Returns the tag with the given name. 
+//     The tag is created if it doesn't already exist.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+std::string &
+JSONRootEntry::Tag(const std::string &tag_name)
+{
+    return tags[tag_name];
+}
+
+
+// ****************************************************************************
+//  Method: JSONRootDataSet Constructor
+//
+//  Purpose: Inits an instance of a JSONRootEntry object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootDataSet::JSONRootDataSet()
+{};
+
+// ****************************************************************************
+//  Method: JSONRootDataSet Destructor
+//
+//  Purpose: Cleans up an instance of a JSONRootEntry object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRootDataSet::~JSONRootDataSet()
+{};
+
+
+// ****************************************************************************
+//  Method: JSONRootDataSet::NumberOfDomains
+//
+//  Purpose: Returns the number of domains in the dataset.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+int
+JSONRootDataSet::NumberOfDomains() const
+{
+    return ndomains;
+}
+   
+// ****************************************************************************
+//  Method: JSONRootDataSet::SetNumberOfDomains
+//
+//  Purpose: Sets the number of domains in the dataset.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************                     
+void         
+JSONRootDataSet::SetNumberOfDomains(int ndomains)
+{
+    this->ndomains = ndomains;
+}
+
+// ****************************************************************************
+//  Method: JSONRootDataSet::Mesh
+//
+//  Purpose: Returns the mesh entry associated with this mesh. 
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************   
+JSONRootEntry   &
+JSONRootDataSet::Mesh()
+{
+    return mesh;
+}
+      
+// ****************************************************************************
+//  Method: JSONRootDataSet::Fields
+//
+//  Purpose: Returns the names of the fields associated with this dataset.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************         
+void
+JSONRootDataSet::Fields(std::vector<std::string> &field_names) const
+{
+    field_names.clear();
+    for(map<string,JSONRootEntry>::const_iterator itr = fields.begin();
+        itr!=fields.end();
+        itr++)
+        {
+            field_names.push_back(itr->first);
+        }
+}
+
+// ****************************************************************************
+//  Method: JSONRootDataSet::Field
+//
+//  Purpose: 
+//     Returns the field with the given name. 
+//     The field is created if it doesn't already exist.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// **************************************************************************** 
+JSONRootEntry  &
+JSONRootDataSet::Field(const std::string &field_name)
+{
+    return fields[field_name];
+}
+
+// ****************************************************************************
+//  Method: JSONRoot Constructor
+//
+//  Purpose: Inits an instance of a JSONRootEntry object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRoot::JSONRoot()
+{
+
+}
+
+// ****************************************************************************
+//  Method: JSONRoot Constructor 
+//
+//  Purpose: Inits a JSONRoot object using the ParseJSON() method.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// **************************************************************************** 
+JSONRoot::JSONRoot(const std::string &json_root)
+{
+    ParseJSON(json_root);
+}
+
+// ****************************************************************************
+//  Method: JSONRoot Destructor
+//
+//  Purpose: Cleans up  an instance of a JSONRootEntry object.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// ****************************************************************************
+JSONRoot::~JSONRoot()
+{
+
+}
+
+// ****************************************************************************
+//  Method: JSONRootDataSet::DataSets
+//
+//  Purpose: Returns the names of the datasets in this root file.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// **************************************************************************** 
+void
+JSONRoot::DataSets(vector<string> &dset_names) const
+{
+    dset_names.clear();
+    for(map<string,JSONRootDataSet>::const_iterator itr = dsets.begin();
+        itr!=dsets.end();
+        itr++)
+        {
+            dset_names.push_back(itr->first);
+        }
+}
+
+// ****************************************************************************
+//  Method: JSONRootDataSet::DataSet
+//
+//  Purpose:
+//     Returns the dataset with the given name. 
+//     The dataset is created if it doesn't already exist.
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// **************************************************************************** 
+JSONRootDataSet &
+JSONRoot::DataSet(const std::string &dset_name)
+{
+    return dsets[dset_name];
+}
+
+// ****************************************************************************
+//  Method: JSONRootDataSet::NumberOfDataSets
+//
+//  Purpose: Returns the number of datasets described by this root file.
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// **************************************************************************** 
+int
+JSONRoot::NumberOfDataSets() const
+{
+    return dsets.size();
+}
+
+
+// ****************************************************************************
+//  Method: JSONRoot::ParseJSON
+//
+//  Purpose: Parses a JSON string into this JSONRoot object. 
+//
+//
+//  Programmer:  Cyrus Harrison
+//  Creation:    Thu Jun 12 16:02:35 PDT 2014
+//
+// **************************************************************************** 
+void 
+JSONRoot::ParseJSON(const std::string &json_root)
+{
+    // clear existing structure
+    dsets.clear();
+
+    // open root file and read its contents
+    ifstream iroot;
+    iroot.open(json_root.c_str());
+    std::string json((std::istreambuf_iterator<char>(iroot)), 
+                      std::istreambuf_iterator<char>());
+
+    // parse with rapidjson
+    rapidjson::Document document;
+    if(document.Parse<0>(json.c_str()).HasParseError())
+    {
+        // TODO: Throw VisIt Exception
+        cout << "ERROR PARSING JSON DATA" <<endl;
+    }
+
+    if(document.IsObject())
+    {
+        // handle datasets
+        if (document.HasMember("dsets"))
+        {
+            const rapidjson::Value &json_dsets = document["dsets"];
+            for (rapidjson::Value::ConstMemberIterator dsets_itr = json_dsets.MemberBegin(); 
+                 dsets_itr != json_dsets.MemberEnd(); ++dsets_itr)
+            {
+                string curr_dset_name = dsets_itr->name.GetString();
+                JSONRootDataSet &curr_dset = DataSet(curr_dset_name);
+                const rapidjson::Value &json_dset = dsets_itr->value;
+                // handle # of domains, meshes w/ tags
+                curr_dset.SetNumberOfDomains(json_dset["domains"].GetInt());
+                curr_dset.Mesh().Path().Set(json_dset["mesh"]["path"].GetString());
+                if(json_dset["mesh"].HasMember("tags"))
+                {
+                    const rapidjson::Value &mesh_tags = json_dset["mesh"]["tags"];
+                    for (rapidjson::Value::ConstMemberIterator tags_itr = mesh_tags.MemberBegin(); 
+                         tags_itr != mesh_tags.MemberEnd(); ++tags_itr)
+                    {      
+                        curr_dset.Mesh().Tag(tags_itr->name.GetString()) = tags_itr->value.GetString();
+                    }
+                }
+                // handle fields
+                if(json_dset.HasMember("fields"))
+                {
+                    const rapidjson::Value &json_fields =json_dset["fields"];
+                    for (rapidjson::Value::ConstMemberIterator fields_itr = json_fields.MemberBegin(); 
+                         fields_itr != json_fields.MemberEnd(); ++fields_itr)
+                     {
+                        const rapidjson::Value &json_field = fields_itr->value;
+                        string curr_field_name = fields_itr->name.GetString();
+                        JSONRootEntry &curr_field = curr_dset.Field(curr_field_name);
+                        curr_field.Path().Set(json_field["path"].GetString());
+                        const rapidjson::Value &json_tags = json_field["tags"];
+                        for (rapidjson::Value::ConstMemberIterator tags_itr = json_tags.MemberBegin(); 
+                             tags_itr != json_tags.MemberEnd(); ++tags_itr)
+                        {      
+                            curr_field.Tag(tags_itr->name.GetString()) = tags_itr->value.GetString();
+                        }
+                     }
+                 }
+            }
+        }
+    }
+}
+
+// ****************************************************************************
+//  Method: JSONRoot::ToJson
+//
+//  Purpose: Constructs a std::string with JSON that represent the JSONRoot.
+//
+//