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timspainNERSCtimspainNERSC
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Merge pull request #53 from nextsimdg/feat_mvm
Minimum viable model
2 parents b579f34 + 0535990 commit 83f2bfb

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‎.gitignore‎

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/.settings/*
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/src/modules/generated/moduleLoader*.ipp
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/*/src/modules/generated/moduleLoader*.ipp
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/run/restart.nc
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/run/nextsim
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/run/.DS_Store

‎CMakeLists.txt‎

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@@ -4,14 +4,20 @@ set(CMAKE_CXX_STANDARD 11)
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project(framework_dg)
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set (NETCDF_CXX "YES")
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find_package(netCDF REQUIRED)
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if ("${CMAKE_HOST_SYSTEM_NAME}" STREQUAL "Darwin")
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set(NSDG_NetCDF_Library "netcdf-cxx4")
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else()
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set(NSDG_NetCDF_Library "netcdf_c++4")
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endif()
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find_package(Boost COMPONENTS program_options REQUIRED)
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find_package(Catch2 REQUIRED)
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# To add netCDF to a target:
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# target_include_directories(target PUBLIC ${netCDF_INCLUDE_DIR})
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# target_link_directories(target PUBLIC ${netCDF_LIB_DIR})
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# target_link_libraries(target LINK_PUBLIC netcdf-cxx4)
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# target_link_libraries(target LINK_PUBLIC "${NSDG_NetCDF_Library}")
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# Set the location of the ipp files used by ModuleLoader for the main build
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set(ModuleLoaderIppTargetDirectory
@@ -53,8 +59,10 @@ target_include_directories(nextsim PRIVATE
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"${Boost_INCLUDE_DIRS}"
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"${ModuleLoaderIppTargetDirectory}"
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"${NextsimIncludeDirs}"
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"${netCDF_INCLUDE_DIR}"
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)
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target_link_libraries(nextsim LINK_PUBLIC ${Boost_LIBRARIES})
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target_link_directories(nextsim PUBLIC "${netCDF_LIB_DIR}")
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target_link_libraries(nextsim LINK_PUBLIC ${Boost_LIBRARIES} "${NSDG_NetCDF_Library}")
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#The parse_modules target is inherited from src
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add_dependencies(nextsim parse_modules)

‎core/src/CMakeLists.txt‎

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@@ -11,19 +11,37 @@ set(BaseSources
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"ConfiguredModule.cpp"
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"CommandLineParser.cpp"
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"ModuleLoader.cpp"
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"ElementData.cpp"
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"PrognosticData.cpp"
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"ExternalData.cpp"
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"DevGridIO.cpp"
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"DevStep.cpp"
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"StructureFactory.cpp"
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)
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list(TRANSFORM BaseSources PREPEND "${CMAKE_CURRENT_SOURCE_DIR}/")
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set(ModuleDir "${CMAKE_CURRENT_SOURCE_DIR}/modules")
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set(StructureModuleSources
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"DevGrid.cpp"
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)
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set(ModuleSources
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"${StructureModuleSources}"
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)
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list(TRANSFORM ModuleSources PREPEND "${ModuleDir}/")
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set(NextsimSources
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"${NextsimSources}"
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"${BaseSources}"
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"${ModuleSources}"
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PARENT_SCOPE)
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set(NextsimIncludeDirs
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"${NextsimIncludeDirs}"
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"${ModuleDir}"
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"${CMAKE_CURRENT_SOURCE_DIR}"
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PARENT_SCOPE)
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‎core/src/DevGridIO.cpp‎

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/*!
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* @file DevGridIO.cpp
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*
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* @date Jan 14, 2022
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* @author Tim Spain <timothy.spain@nersc.no>
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*/
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#include "include/DevGridIO.hpp"
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#include "include/DevGrid.hpp"
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#include "include/ElementData.hpp"
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#include "include/IStructure.hpp"
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#include <cstddef>
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#include <ncDim.h>
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#include <ncDouble.h>
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#include <ncFile.h>
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#include <ncVar.h>
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#include <map>
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#include <vector>
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namespace Nextsim {
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// Forward declarations
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enum class StringName {
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METADATA_NODE,
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DATA_NODE,
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STRUCTURE,
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X_DIM,
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Y_DIM,
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Z_DIM,
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};
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std::string hiceName = "hice";
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std::string ciceName = "cice";
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std::string hsnowName = "hsnow";
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std::string ticeName = "tice";
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std::string sstName = "sst";
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std::string sssName = "sss";
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typedef std::map<StringName, std::string> NameMap;
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void initGroup(std::vector<ElementData>& data, netCDF::NcGroup& grp, const NameMap& nameMap);
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void dumpGroup(const std::vector<ElementData>& data, netCDF::NcGroup& grp, const NameMap& nameMap);
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// See https://isocpp.org/wiki/faq/pointers-to-members#macro-for-ptr-to-memfn
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#define CALL_MEMBER_FN(object, ptrToMember) ((object).*(ptrToMember))
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// pointer to a member of PrognosticData that takes no arguments and returns a
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// double. See https://isocpp.org/wiki/faq/pointers-to-members#typedef-for-ptr-to-memfn
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typedef double (PrognosticData::*ProgDoubleFn)() const;
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// Map between variable names and retrieval functions
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// See https://isocpp.org/wiki/faq/pointers-to-members#array-memfnptrs
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// clang-format off
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static const std::map<std::string, ProgDoubleFn> variableFunctions
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= { { hiceName, &PrognosticData::iceThickness },
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{ ciceName, &PrognosticData::iceConcentration },
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{ hsnowName, &PrognosticData::snowThickness },
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{ sstName, &PrognosticData::seaSurfaceTemperature },
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{ sssName, &PrognosticData::seaSurfaceSalinity } };
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// clang-format on
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void DevGridIO::init(std::vector<ElementData>& data, const std::string& filePath) const
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{
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NameMap nameMap = {
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{ StringName::METADATA_NODE, IStructure::metadataNodeName() },
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{ StringName::DATA_NODE, IStructure::dataNodeName() },
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{ StringName::STRUCTURE, DevGrid::structureName },
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{ StringName::X_DIM, DevGrid::xDimName },
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{ StringName::Y_DIM, DevGrid::yDimName },
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{ StringName::Z_DIM, DevGrid::nIceLayersName },
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};
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netCDF::NcFile ncFile(filePath, netCDF::NcFile::read);
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initGroup(data, ncFile, nameMap);
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ncFile.close();
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}
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void DevGridIO::dump(const std::vector<ElementData>& data, const std::string& filePath) const
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{
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NameMap nameMap = {
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{ StringName::METADATA_NODE, IStructure::metadataNodeName() },
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{ StringName::DATA_NODE, IStructure::dataNodeName() },
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{ StringName::STRUCTURE, DevGrid::structureName },
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{ StringName::X_DIM, DevGrid::xDimName },
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{ StringName::Y_DIM, DevGrid::yDimName },
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{ StringName::Z_DIM, DevGrid::nIceLayersName },
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};
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netCDF::NcFile ncFile(filePath, netCDF::NcFile::replace);
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dumpGroup(data, ncFile, nameMap);
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ncFile.close();
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}
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void initMeta(std::vector<ElementData>& data, const netCDF::NcGroup& metaGroup)
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{
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int nx = DevGrid::nx;
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data.resize(nx * nx);
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}
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void initData(std::vector<ElementData>& data, const netCDF::NcGroup& dataGroup)
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{
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// Get the number of ice layers from the ice temperature data
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const int layersDim = 2;
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int nLayers = dataGroup.getVar(ticeName).getDim(layersDim).getSize();
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int nx = DevGrid::nx;
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for (int i = 0; i < nx; ++i) {
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for (int j = 0; j < nx; ++j) {
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int linearIndex = i * nx + j;
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double hice;
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double cice;
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double hsnow;
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double sst;
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double sss;
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std::vector<std::size_t> loc = { std::size_t(i), std::size_t(j) };
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dataGroup.getVar(hiceName).getVar(loc, &hice);
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dataGroup.getVar(ciceName).getVar(loc, &cice);
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dataGroup.getVar(hsnowName).getVar(loc, &hsnow);
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dataGroup.getVar(sstName).getVar(loc, &sst);
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dataGroup.getVar(sssName).getVar(loc, &sss);
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// Retrieve ice temperature data
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std::vector<double> tice(nLayers);
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for (int l = 0; l < nLayers; ++l) {
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std::vector<std::size_t> loc3 = { loc[0], loc[1], std::size_t(l) };
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dataGroup.getVar(ticeName).getVar(loc3, &tice[l]);
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}
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data[linearIndex]
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= PrognosticGenerator().hice(hice).cice(cice).sst(sst).sss(sss).hsnow(hsnow).tice(
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tice);
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}
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}
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for (auto fnNamePair : variableFunctions) {
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const std::string& name = fnNamePair.first;
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netCDF::NcVar var(dataGroup.getVar(name));
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}
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}
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void initGroup(std::vector<ElementData>& data, netCDF::NcGroup& grp, const NameMap& nameMap)
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{
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netCDF::NcGroup metaGroup(grp.getGroup(nameMap.at(StringName::METADATA_NODE)));
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netCDF::NcGroup dataGroup(grp.getGroup(nameMap.at(StringName::DATA_NODE)));
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initMeta(data, metaGroup);
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initData(data, dataGroup);
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}
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void dumpMeta(
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const std::vector<ElementData>& data, netCDF::NcGroup& metaGroup, const NameMap& nameMap)
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{
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metaGroup.putAtt(IStructure::typeNodeName(), nameMap.at(StringName::STRUCTURE));
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}
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/*
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* Uses a pointer-to-member-function to access the data in PrognosticData
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* element by element. Please see the references in the comments associated
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* with ProgDoubleFn and CALL_MEMBER_FN for more details.
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*/
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std::vector<double> gather(const std::vector<ElementData>& data, ProgDoubleFn pFunc)
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{
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std::vector<double> gathered(data.size());
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for (int i = 0; i < data.size(); ++i) {
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gathered[i] = CALL_MEMBER_FN(data[i], pFunc)();
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}
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return gathered;
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}
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void dumpData(
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const std::vector<ElementData>& data, netCDF::NcGroup& dataGroup, const NameMap& nameMap)
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{
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int nx = DevGrid::nx;
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// Create the dimension data, since it has to be in the same group as the
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// data or the parent group
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netCDF::NcDim xDim = dataGroup.addDim(nameMap.at(StringName::X_DIM), nx);
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netCDF::NcDim yDim = dataGroup.addDim(nameMap.at(StringName::Y_DIM), nx);
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std::vector<netCDF::NcDim> dims2 = { xDim, yDim };
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for (auto fnNamePair : variableFunctions) {
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const std::string& name = fnNamePair.first;
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netCDF::NcVar var(dataGroup.addVar(name, netCDF::ncDouble, dims2));
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std::vector<double> gathered = gather(data, variableFunctions.at(name));
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var.putVar(gathered.data());
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}
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int nLayers = data[0].nIceLayers();
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netCDF::NcDim zDim = dataGroup.addDim(nameMap.at(StringName::Z_DIM), nLayers);
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std::vector<netCDF::NcDim> dims3 = { xDim, yDim, zDim };
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netCDF::NcVar iceT(dataGroup.addVar(ticeName, netCDF::ncDouble, dims3));
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// Gather the three dimensional data explicitly (until there is more than
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// one three dimensional dataset).
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std::vector<double> tice(data.size() * nLayers);
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for (int i = 0; i < data.size(); ++i) {
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int ii = nLayers * i;
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for (int l = 0; l < nLayers; ++l) {
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tice[ii + l] = data[i].iceTemperature(l);
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}
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}
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iceT.putVar(tice.data());
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}
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void dumpGroup(
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const std::vector<ElementData>& data, netCDF::NcGroup& headGroup, const NameMap& nameMap)
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{
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netCDF::NcGroup metaGroup = headGroup.addGroup(nameMap.at(StringName::METADATA_NODE));
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netCDF::NcGroup dataGroup = headGroup.addGroup(nameMap.at(StringName::DATA_NODE));
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dumpMeta(data, metaGroup, nameMap);
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dumpData(data, dataGroup, nameMap);
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}
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} /* namespace Nextsim */

‎core/src/DevStep.cpp‎

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/*!
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* @file DevStep.cpp
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*
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* @date Jan 12, 2022
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* @author Tim Spain <timothy.spain@nersc.no>
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*/
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#include "include/DevStep.hpp"
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#include "include/IPrognosticUpdater.hpp"
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#include "include/PrognosticData.hpp"
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namespace Nextsim {
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void DevStep::iterate(const Iterator::Duration& dt)
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{
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PrognosticData::setTimestep(dt);
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for (pStructure->cursor = 0; pStructure->cursor; ++pStructure->cursor) {
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auto& data = *pStructure->cursor;
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data.updateDerivedData(data, data, data);
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data.calculate(data, data, data);
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data.updateAndIntegrate(data);
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}
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}
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} /* namespace Nextsim */

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