Merge branch 'refac/hd5' into 'main'

Draft: hdf5_init

See merge request naaice/poet!52

src/CMakeLists.txt

@@ -1,8 +1,27 @@
+include(FetchContent)
+FetchContent_Declare(
+  cli11
+  QUIET 
+  GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
+  GIT_TAG v2.4.2
+)
+
+FetchContent_Declare(
+  highfive
+  QUIET
+  GIT_REPOSITORY https://github.com/highfive-devs/highfive.git
+  GIT_TAG v3.0.0
+)
+
+FetchContent_MakeAvailable(cli11)
+FetchContent_MakeAvailable(highfive)
+
 add_library(POETLib
   Init/InitialList.cpp 
   Init/GridInit.cpp 
   Init/DiffusionInit.cpp
   Init/ChemistryInit.cpp
+  IO/checkpoint.cpp
   DataStructures/Field.cpp
   Transport/DiffusionModule.cpp
   Chemistry/ChemistryModule.cpp
@@ -31,17 +50,9 @@ target_link_libraries(
   PUBLIC IPhreeqcPOET
   PUBLIC tug
   PUBLIC MPI::MPI_C 
+  PUBLIC HighFive::HighFive
 )
 
-include(FetchContent)
-FetchContent_Declare(
-  cli11
-  QUIET 
-  GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
-  GIT_TAG v2.4.2
-)
-
-FetchContent_MakeAvailable(cli11)
 
 # add_library(poetlib
 #   Base/Grid.cpp

src/IO/Datatypes.hpp

@@ -0,0 +1,9 @@
+#pragma once 
+
+#include <cstdint>
+#include <DataStructures/Field.hpp>
+
+struct Checkpoint_s {
+    poet::Field &field;
+    uint32_t iteration;
+};

src/IO/HDF5Functions.hpp

@@ -0,0 +1,8 @@
+#pragma once 
+
+#include <string>
+#include "Datatypes.hpp"
+
+int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint);
+
+int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint);

src/IO/checkpoint.cpp

@@ -0,0 +1,28 @@
+#include "IO/Datatypes.hpp"
+#include <cstdint>
+#include <highfive/H5Easy.hpp>
+
+int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint){
+
+    // TODO: errorhandling
+    H5Easy::File file(file_path, H5Easy::File::Overwrite);
+
+
+    H5Easy::dump(file, "/MetaParam/Iterations", checkpoint.iteration);
+    H5Easy::dump(file, "/Grid/Names", checkpoint.field.GetProps());
+    H5Easy::dump(file, "/Grid/Chemistry", checkpoint.field.As2DVector());
+
+    return 0;
+}
+
+int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint){
+
+     H5Easy::File file(file_path, H5Easy::File::ReadOnly);
+
+     checkpoint.iteration = H5Easy::load<uint32_t>(file, "/MetaParam/Iterations");
+
+     checkpoint.field = H5Easy::load<std::vector<std::vector<double>>>(file, "/Grid/Chemistry");
+
+    return 0;
+}
+

src/poet.cpp

@@ -26,6 +26,8 @@
 #include "CLI/CLI.hpp"
 #include "Chemistry/ChemistryModule.hpp"
 #include "DataStructures/Field.hpp"
+#include "IO/Datatypes.hpp"
+#include "IO/HDF5Functions.hpp"
 #include "Init/InitialList.hpp"
 #include "Transport/DiffusionModule.hpp"
 
@@ -393,6 +395,18 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
     // store_result is TRUE)
     call_master_iter_end(R, diffusion.getField(), chem.getField());
 
+    // TODO: write checkpoint
+    // checkpoint struct --> field and iteration
+
+    if (iter == 1) {
+      write_checkpoint("checkpoint1.hdf5",
+                       {.field = chem.getField(), .iteration = iter});
+    } else if (iter == 2) {
+      Checkpoint_s checkpoint_read{.field = chem.getField()};
+      read_checkpoint("checkpoint1.hdf5", checkpoint_read);
+      iter = checkpoint_read.iteration;
+    }
+
     diffusion.getField().update(chem.getField());
 
     MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +

struct_init.org

@@ -0,0 +1,39 @@
+Grid/MemoryOrder (single integer 0=zyx (colmaj); 1=xyz (rowmaj))  
+Grid/Dimensionality (single integer)
+Grid/Cells (uint32_t length=Grid/Dimensionality)
+Grid/Size  (double length=Grid/Dimensionality)
+Grid/ConstantCells (uint32_t array)
+Grid/Porosity/Length  (int 1 (=homog))
+                      (int prod(Grid/Cells))
+Grid/Porosity/Data (double length=Grid/Porosity/Length)
+
+PhreeqcMatrix/Names (string vector)
+PhreeqcMatrix/Data  (double Matrix length(Names)*NumberOfPQC_IDs)
+
+InitialConditions/Names (vector of string (=colnames PhreeqcMatrix))
+InitialConditions/Data  (vector (length Names) of arrays (double length=prod(Cells)))
+
+Diffusion/Names (string vector) transported solutes
+Diffusion/Boundaries/N int matrix N*3=(ind_bound, type, phreeqc_id)  
+Diffusion/Boundaries/W ''
+Diffusion/Boundaries/S ''
+Diffusion/Boundaries/E ''
+Diffusion/Boundaries/T ''
+Diffusion/Boundaries/B ''
+
+Diffusion/InnerBoundaries placeholder
+Diffusion/Alpha
+Diffusion/Alpha/x (double length=1 (=homog))
+                  (double length=prod(Grid/Cells))
+Diffusion/Alpha/y
+Diffusion/Alpha/z
+
+Chemistry
+Chemistry/Database (string)
+Chemistry/Input    (string)
+Chemistry/PhreeqcIDs (int vector)
+Chemistry/Options
+Chemistry/Options/H0O0      (bool)
+Chemistry/Options/WithRedox (bool)
+
+