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initial_conditions.patch
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initial_conditions.patch
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diff --git a/CMakeLists.txt b/CMakeLists.txt
index cdc4615..70e3c0c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -88,6 +88,7 @@ include_directories(
${CUDA_MATH_INCLUDE_DIR}
${RAJA_INCLUDE_DIRS}
${EXTERNAL_INSTALL_DIR}/include
+ ${TINYXML2_INCLUDE_DIR}
)
link_directories(${EXTERNAL_INSTALL_DIR}/lib)
diff --git a/external/CMakeLists.txt b/external/CMakeLists.txt
index 41eefc8..6810fb3 100644
--- a/external/CMakeLists.txt
+++ b/external/CMakeLists.txt
@@ -2,11 +2,13 @@ include( ExternalGTest.cmake )
include( ExternalTabulate.cmake )
include( ExternalRAJA.cmake )
include( ExternalCelero.cmake )
+include( ExternalTinyXML2.cmake )
set( external_libraries
gtest_external
raja_external
tabulate_external
celero_external
+ tinyxml2_external
PARENT_SCOPE
)
diff --git a/external/ExternalTinyXML2.cmake b/external/ExternalTinyXML2.cmake
new file mode 100644
index 0000000..6cacab5
--- /dev/null
+++ b/external/ExternalTinyXML2.cmake
@@ -0,0 +1,20 @@
+#########################################################
+message( STATUS "Building external TinyXML2 project.")
+#########################################################
+
+
+ExternalProject_Add(
+ tinyxml2_external
+ URL "https://github.com/leethomason/tinyxml2/archive/refs/tags/9.0.0.zip"
+ URL_MD5 2a3b1b8acdc1a0bd15e4010d91c505f8
+
+ SOURCE_DIR ${CMAKE_BINARY_DIR}/external/tinyxml2/
+ BINARY_DIR ${CMAKE_BINARY_DIR}/external/tinyxml2-build/
+ INSTALL_DIR ${EXTERNAL_INSTALL_DIR}
+ CMAKE_ARGS -D CMAKE_INSTALL_PREFIX=${EXTERNAL_INSTALL_DIR} -D tinyxml2_BUILD_TESTING=Off -DBUILD_SHARED_LIBS=On
+)
+
+ExternalProject_Get_Property(tinyxml2_external source_dir)
+
+set(TINYXML2_INCLUDE_DIR ${CMAKE_BINARY_DIR}/external/tinyxml2/ CACHE PATH "")
+set(TINYXML2_LIBRARIES ${CMAKE_BINARY_DIR}/external/tinyxml2-build/libtinyxml2.so CACHE PATH "")
diff --git a/file_io/CMakeLists.txt b/file_io/CMakeLists.txt
index 4e90ae6..f84d3d7 100644
--- a/file_io/CMakeLists.txt
+++ b/file_io/CMakeLists.txt
@@ -1,9 +1,10 @@
set(fileio_src
vtk_solution_writer.cpp
+ vtk_solution_reader.cpp
)
add_library(fileio ${LIBTYPE} ${fileio_src})
-target_link_libraries(fileio logger)
+target_link_libraries(fileio logger "${TINYXML2_LIBRARIES}")
add_dependencies(fileio ${external_libraries})
diff --git a/file_io/vtk_solution_reader.cpp b/file_io/vtk_solution_reader.cpp
new file mode 100644
index 0000000..b03b4a9
--- /dev/null
+++ b/file_io/vtk_solution_reader.cpp
@@ -0,0 +1,142 @@
+#include "vtk_solution_reader.hpp"
+
+#include "data_structures/solution_state.hpp"
+#include "logger/logger.hpp"
+#include "tinyxml2.h"
+
+#include <boost/algorithm/string.hpp>
+#include <boost/algorithm/string/split.hpp>
+#include <boost/lexical_cast.hpp>
+
+#include <iostream>
+
+
+CartesianDomainDefinition
+VTKSolutionReader::getCartesianDomain()
+{
+ tinyxml2::XMLDocument doc;
+ auto timer = Logger::get().timer("VTKSolutionReader::getCartesianDomain() reading " + filename_);
+
+ doc.LoadFile(filename_.c_str());
+
+ const char* value_attribute = doc.FirstChildElement("VTKFile")
+ ->FirstChildElement("StructuredGrid")
+ ->FirstChildElement("Piece")
+ ->FirstAttribute()
+ ->Value();
+ std::string attribute_string(value_attribute);
+ // remove unwanted leading or trailing whitespace
+ boost::trim_if(attribute_string, boost::is_any_of("\t "));
+
+
+ // split by spsaces
+ std::vector<std::string> tokens;
+ boost::algorithm::split(tokens, attribute_string, boost::is_any_of("\t "), boost::token_compress_on);
+
+ // cast to ints, will throw on failure
+ const int nxbeg = boost::lexical_cast<int>(tokens[0]);
+ const int nxend = boost::lexical_cast<int>(tokens[1]);
+ const int nybeg = boost::lexical_cast<int>(tokens[2]);
+ const int nyend = boost::lexical_cast<int>(tokens[3]);
+ const int nzbeg = boost::lexical_cast<int>(tokens[4]);
+ const int nzend = boost::lexical_cast<int>(tokens[5]);
+
+ Logger::get().FatalAssert(nxbeg == 0, "VTKSolutionReader nxbeg == 0");
+ Logger::get().FatalAssert(nybeg == 0, "VTKSolutionReader nybeg == 0");
+ Logger::get().FatalAssert(nzbeg == 0, "VTKSolutionReader nzbeg == 0");
+
+ CartesianDomainDefinition domain;
+ domain.nx = nxend;
+ domain.ny = nyend;
+ dimension_ = 2;
+ if (nzend == nzbeg) {
+ domain.nz = 0;
+ }
+ else {
+ domain.nz = nzend;
+ dimension_ = 3;
+ }
+
+ auto dataarray = doc.FirstChildElement("VTKFile")
+ ->FirstChildElement("StructuredGrid")
+ ->FirstChildElement("Piece")
+ ->FirstChildElement("CellData")
+ ->FirstChildElement("DataArray")
+ ->GetText();
+
+ // printf("Points GetText: %s\n", dataarray);
+ std::string cell_data_string(dataarray);
+ // remove unwanted leading or trailing whitespace
+ boost::trim_if(cell_data_string, boost::is_any_of("\t \n"));
+
+ std::vector<std::string> cell_data_tokens;
+ boost::algorithm::split(cell_data_tokens, cell_data_string, boost::is_any_of("\t\n "), boost::token_compress_on);
+
+ // for (auto it = c
+ auto points_array = doc.FirstChildElement("VTKFile")
+ ->FirstChildElement("StructuredGrid")
+ ->FirstChildElement("Piece")
+ ->FirstChildElement("Points")
+ ->FirstChildElement("DataArray")
+ ->GetText();
+
+ std::string points_data_string(points_array);
+ boost::trim_if(points_data_string, boost::is_any_of("\t \n"));
+ std::vector<std::string> point_data_tokens;
+ boost::algorithm::split(point_data_tokens, points_data_string, boost::is_any_of("\t\n "), boost::token_compress_on);
+
+
+ const int npoints = point_data_tokens.size() / 3;
+ Logger::get().FatalAssert(npoints == pow(nxend + 1, dimension_), "VTKSolutionReader npoints == (nxend+1)^dim");
+
+
+ std::vector<double> x, y, z;
+ for (size_t i = 0; i < point_data_tokens.size(); i += 3) {
+ x.push_back(boost::lexical_cast<double>(point_data_tokens[i]));
+ y.push_back(boost::lexical_cast<double>(point_data_tokens[i + 1]));
+ z.push_back(boost::lexical_cast<double>(point_data_tokens[i + 2]));
+ }
+
+ domain.xbeg = *min_element(x.begin(), x.end());
+ domain.xend = *max_element(x.begin(), x.end());
+ domain.ybeg = *min_element(y.begin(), y.end());
+ domain.zbeg = *min_element(z.begin(), z.end());
+
+ return domain;
+}
+
+void
+VTKSolutionReader::setSolution(const IndexArray& interior_indices, SolutionState& state)
+{
+ tinyxml2::XMLDocument doc;
+ auto timer = Logger::get().timer("VTKSolutionReader::setSolution() reading " + filename_);
+ doc.LoadFile(filename_.c_str());
+
+ auto solnarray = doc.FirstChildElement("VTKFile")
+ ->FirstChildElement("StructuredGrid")
+ ->FirstChildElement("Piece")
+ ->FirstChildElement("CellData")
+ ->FirstChildElement("DataArray")
+ ->GetText();
+
+ std::string cell_data_string(solnarray);
+ // remove unwanted leading or trailing whitespace
+ boost::trim_if(cell_data_string, boost::is_any_of("\t \n"));
+
+ std::vector<std::string> cell_data_tokens;
+ boost::algorithm::split(cell_data_tokens, cell_data_string, boost::is_any_of("\t\n "), boost::token_compress_on);
+
+
+ std::vector<double> solution(cell_data_tokens.size());
+ for (size_t i = 0; i < solution.size(); ++i) {
+ solution[i] = boost::lexical_cast<double>(cell_data_tokens[i]);
+ }
+
+
+ auto idx = read_access_host(interior_indices);
+ auto sol = write_access_host(state.getVec(0));
+
+ for (int i = 0; i < idx.size(); ++i) {
+ sol[idx[i]] = solution[i];
+ }
+}
diff --git a/file_io/vtk_solution_reader.hpp b/file_io/vtk_solution_reader.hpp
new file mode 100644
index 0000000..98405f1
--- /dev/null
+++ b/file_io/vtk_solution_reader.hpp
@@ -0,0 +1,23 @@
+#pragma once
+
+
+#include "spatial_discretization/spatial_discretization.hpp"
+#include "data_structures/managed_array.hpp"
+
+
+class SolutionState;
+
+
+class VTKSolutionReader /* : inherit public InitialConditions? better, move that into /initialization */ {
+ public:
+ VTKSolutionReader(const std::string& filename) : filename_(filename) {}
+
+ CartesianDomainDefinition getCartesianDomain();
+
+ void setSolution(const IndexArray& interior_indices, SolutionState& state);
+
+ private:
+ const std::string filename_;
+
+ int dimension_;
+};
diff --git a/file_io/vtk_solution_writer.cpp b/file_io/vtk_solution_writer.cpp
index 436a42c..38bd6cb 100644
--- a/file_io/vtk_solution_writer.cpp
+++ b/file_io/vtk_solution_writer.cpp
@@ -5,24 +5,23 @@
#include <limits>
#include "data_structures/solution_state.hpp"
+#include "governing_equations/cahn_hilliard/cahn_hilliard_state.hpp"
#include "logger/logger.hpp"
#include "spatial_discretization/discretization_2d_cart.hpp"
#include "spatial_discretization/discretization_3d_cart.hpp"
-#include "governing_equations/cahn_hilliard/cahn_hilliard_state.hpp"
-void write_solution_to_vtk(const SolutionState& state, const SpatialDiscretization& geom, std::string filename_withoutext)
+void
+write_solution_to_vtk(const SolutionState& state, const SpatialDiscretization& geom, std::string filename_withoutext)
{
try {
const auto& g2d = dynamic_cast<const Discretization2DCart&>(geom);
write_solution_to_vtk_2d(state, g2d, filename_withoutext);
}
- catch(...)
- {
+ catch (...) {
const auto& g3d = dynamic_cast<const Discretization3DCart&>(geom);
write_solution_to_vtk_3d(state, g3d, filename_withoutext);
}
-
}
@@ -37,21 +36,22 @@ write_solution_to_vtk_2d(const SolutionState& state, const Discretization2DCart&
const CahnHilliardState& cstate = dynamic_cast<const CahnHilliardState&>(state);
- const int ni = geom.ni();
- auto x = read_access_host(geom.x());
- auto y = read_access_host(geom.y());
- auto val = read_access_host(cstate.c());
+ const int ni = geom.ni();
+
+ auto x = read_access_host(geom.xvertex());
+ auto y = read_access_host(geom.yvertex());
+ auto val = read_access_host(cstate.c());
fout << "<VTKFile type=\"StructuredGrid\" version=\"1.0\" byte_order=\"LittleEndian\">\n";
- fout << " <StructuredGrid WholeExtent=\"0 " << ni - 1 << " 0 " << ni - 1 << " 0 0\">\n";
- fout << " <Piece Extent=\" 0 " << ni - 1 << " 0 " << ni - 1 << " 0 0\">\n";
+ fout << " <StructuredGrid WholeExtent=\"0 " << ni << " 0 " << ni << " 0 0\">\n";
+ fout << " <Piece Extent=\" 0 " << ni << " 0 " << ni << " 0 0\">\n";
fout << " <PointData>\n";
fout << " </PointData>\n";
fout << " <CellData>\n";
fout << " <DataArray type=\"Float64\" Name=\"c\" format=\"ascii\">\n";
- for (int i = 0; i < ni - 1; ++i) {
- for (int j = 0; j < ni - 1; ++j) {
+ for (int i = 0; i < ni; ++i) {
+ for (int j = 0; j < ni; ++j) {
fout << std::setprecision(std::numeric_limits<double>::digits10 + 1) << val(i, j) << "\n";
}
}
@@ -61,8 +61,8 @@ write_solution_to_vtk_2d(const SolutionState& state, const Discretization2DCart&
fout << " <DataArray type=\"Float64\" Name=\"Points\" NumberOfComponents=\"3\" "
"format=\"ascii\">\n";
- for (int i = 0; i < ni; ++i) {
- for (int j = 0; j < ni; ++j) {
+ for (int i = 0; i < ni + 1; ++i) {
+ for (int j = 0; j < ni + 1; ++j) {
fout << std::setprecision(std::numeric_limits<double>::digits10 + 1) << x(i, j) << " " << y(i, j) << " 0.0\n";
}
}
@@ -87,22 +87,22 @@ write_solution_to_vtk_3d(const SolutionState& state, const Discretization3DCart&
const CahnHilliardState3D& cstate = dynamic_cast<const CahnHilliardState3D&>(state);
const int ni = geom.ni();
- auto x = read_access_host(geom.x());
- auto y = read_access_host(geom.y());
- auto z = read_access_host(geom.z());
+ auto x = read_access_host(geom.xvertex());
+ auto y = read_access_host(geom.yvertex());
+ auto z = read_access_host(geom.zvertex());
auto val = read_access_host(cstate.c());
fout << "<VTKFile type=\"StructuredGrid\" version=\"1.0\" byte_order=\"LittleEndian\">\n";
- fout << " <StructuredGrid WholeExtent=\"0 " << ni - 1 << " 0 " << ni - 1 << " 0 " << ni-1 << "\">\n";
- fout << " <Piece Extent=\" 0 " << ni - 1 << " 0 " << ni - 1 << " 0 " << ni-1 << "\">\n";
+ fout << " <StructuredGrid WholeExtent=\"0 " << ni << " 0 " << ni << " 0 " << ni << "\">\n";
+ fout << " <Piece Extent=\" 0 " << ni << " 0 " << ni << " 0 " << ni << "\">\n";
fout << " <PointData>\n";
fout << " </PointData>\n";
fout << " <CellData>\n";
fout << " <DataArray type=\"Float64\" Name=\"c\" format=\"ascii\">\n";
- for (int i = 0; i < ni - 1; ++i) {
- for (int j = 0; j < ni - 1; ++j) {
- for (int k = 0; k < ni - 1; ++k){
+ for (int i = 0; i < ni; ++i) {
+ for (int j = 0; j < ni; ++j) {
+ for (int k = 0; k < ni; ++k) {
fout << std::setprecision(std::numeric_limits<double>::digits10 + 1) << val(i, j, k) << "\n";
}
}
@@ -113,10 +113,11 @@ write_solution_to_vtk_3d(const SolutionState& state, const Discretization3DCart&
fout << " <DataArray type=\"Float64\" Name=\"Points\" NumberOfComponents=\"3\" "
"format=\"ascii\">\n";
- for (int i = 0; i < ni; ++i) {
- for (int j = 0; j < ni; ++j) {
- for (int k = 0; k < ni; ++k) {
- fout << std::setprecision(std::numeric_limits<double>::digits10 + 1) << x(i, j, k) << " " << y(i, j, k) << " " << z(i,j,k) << "\n";
+ for (int i = 0; i < ni + 1; ++i) {
+ for (int j = 0; j < ni + 1; ++j) {
+ for (int k = 0; k < ni + 1; ++k) {
+ fout << std::setprecision(std::numeric_limits<double>::digits10 + 1) << x(i, j, k) << " " << y(i, j, k) << " "
+ << z(i, j, k) << "\n";
}
}
}
diff --git a/governing_equations/CMakeLists.txt b/governing_equations/CMakeLists.txt
index f32699f..d3bcb39 100644
--- a/governing_equations/CMakeLists.txt
+++ b/governing_equations/CMakeLists.txt
@@ -3,7 +3,9 @@ set(governing_equations_src
cahn_hilliard/cahn_hilliard_initial_conditions.cpp
residual_calculator.cpp
cahn_hilliard/cahn_hilliard_solution_monitor.cpp
- cahn_hilliard/cahn_hilliard_3d_fd.cpp)
+ cahn_hilliard/cahn_hilliard_3d_fd.cpp
+ initial_conditions_from_file.cpp
+ )
if(MADG_USE_CUDA)
diff --git a/governing_equations/initial_conditions_from_file.cpp b/governing_equations/initial_conditions_from_file.cpp
new file mode 100644
index 0000000..5ce9ae6
--- /dev/null
+++ b/governing_equations/initial_conditions_from_file.cpp
@@ -0,0 +1,11 @@
+#include "initial_conditions_from_file.hpp"
+
+#include "time_integrable_rhs.hpp"
+#include "file_io/vtk_solution_reader.hpp"
+
+
+void
+InitialConditionsFromFile::set(const TimeIntegrableRHS& rhs, SolutionState& state) const
+{
+ reader_.setSolution(rhs.interiorIndices(), state);
+}
diff --git a/governing_equations/initial_conditions_from_file.hpp b/governing_equations/initial_conditions_from_file.hpp
new file mode 100644
index 0000000..277dfcd
--- /dev/null
+++ b/governing_equations/initial_conditions_from_file.hpp
@@ -0,0 +1,19 @@
+#pragma once
+
+
+#include "governing_equations/initial_conditions.hpp"
+
+class VTKSolutionReader;
+
+
+class InitialConditionsFromFile : public InitialConditions {
+ public:
+ InitialConditionsFromFile(VTKSolutionReader& reader) : reader_(reader) {}
+
+ virtual ~InitialConditionsFromFile() = default;
+
+ void set(const TimeIntegrableRHS&, SolutionState& state) const override;
+
+ private:
+ VTKSolutionReader& reader_;
+};
diff --git a/initialization/puppeteer.cpp b/initialization/puppeteer.cpp
index d148c0d..7452c3d 100644
--- a/initialization/puppeteer.cpp
+++ b/initialization/puppeteer.cpp
@@ -1,5 +1,6 @@
#include "puppeteer.hpp"
+#include "file_io/vtk_solution_reader.hpp"
#include "file_io/vtk_solution_writer.hpp"
#include "governing_equations/cahn_hilliard/cahn_hilliard_2d_fd.hpp"
#include "governing_equations/cahn_hilliard/cahn_hilliard_3d_fd.hpp"
@@ -7,6 +8,7 @@
#include "governing_equations/cahn_hilliard/cahn_hilliard_parameters.hpp"
#include "governing_equations/cahn_hilliard/cahn_hilliard_solution_monitor.hpp"
#include "governing_equations/initial_conditions.hpp"
+#include "governing_equations/initial_conditions_from_file.hpp"
#include "governing_equations/residual_calculator.hpp"
#include "logger/logger.hpp"
#include "spatial_discretization/discretization_2d_cart.hpp"
@@ -24,6 +26,12 @@ Puppeteer::Puppeteer(const std::vector<std::string>& cmd_line)
Logger::get().initLogFile(Options::get().log_file());
Logger::get().InfoMessage(parser.getConfigurationFileTemplate());
+ const auto init_cond_file = Options::get().initial_condition_file();
+ if (init_cond_file != "none") {
+ solution_reader_ = std::make_unique<VTKSolutionReader>(init_cond_file);
+ Logger::get().InfoMessage("Using initial conditions file " + init_cond_file);
+ }
+
//
// construct the primary simulation components
//
@@ -72,23 +80,27 @@ Puppeteer::geomFactory()
{
const int nhalo = 2; // should be dependent on equation and order / stencil size
+ CartesianDomainDefinition domain;
+
+ if (solution_reader_) {
+ domain = solution_reader_->getCartesianDomain();
+ }
+ else {
+ domain.nx = Options::get().domain_resolution();
+ domain.ny = domain.nx;
+ domain.nz = domain.nx;
+ domain.xbeg = Options::get().domain_x_begin();
+ domain.xend = Options::get().domain_x_end();
+ domain.ybeg = Options::get().domain_x_begin();
+ domain.zbeg = Options::get().domain_x_begin();
+ }
+
const int dim = Options::get().dimension();
switch (dim) {
case 2:
- return std::make_unique<Discretization2DCart>(
- Options::get().domain_resolution(),
- nhalo,
- Options::get().domain_x_begin(),
- Options::get().domain_x_end(),
- Options::get().domain_x_begin());
+ return std::make_unique<Discretization2DCart>(domain, nhalo);
case 3:
- return std::make_unique<Discretization3DCart>(
- Options::get().domain_resolution(),
- nhalo,
- Options::get().domain_x_begin(),
- Options::get().domain_x_end(),
- Options::get().domain_x_begin(),
- Options::get().domain_x_begin());
+ return std::make_unique<Discretization3DCart>(domain, nhalo);
default:
Logger::get().FatalMessage("Only dimensions 2 and 3 supported.");
}
@@ -126,8 +138,13 @@ Puppeteer::initialConditionsFactory()
Logger::get().FatalAssert(
Options::get().equation_type() == "cahn-hilliard", "Only equation_type=cahn-hilliard currently supported.");
- CahnHilliardParameters params;
- return std::make_unique<CahnHilliardInitialConditions>(params);
+ if (solution_reader_) {
+ return std::make_unique<InitialConditionsFromFile>(*solution_reader_);
+ }
+ else {
+ CahnHilliardParameters params;
+ return std::make_unique<CahnHilliardInitialConditions>(params);
+ }
}
diff --git a/initialization/puppeteer.hpp b/initialization/puppeteer.hpp
index 5dcd3ba..f10f6cf 100644
--- a/initialization/puppeteer.hpp
+++ b/initialization/puppeteer.hpp
@@ -11,6 +11,7 @@ class TimeIntegrableRHS;
class SpatialDiscretization;
class InitialConditions;
class TimeIntegrator;
+class VTKSolutionReader;
class Puppeteer {
@@ -26,11 +27,12 @@ class Puppeteer {
std::unique_ptr<TimeIntegrableRHS> rhs_;
std::unique_ptr<InitialConditions> initial_conditions_;
std::unique_ptr<TimeIntegrator> time_integrator_;
+ std::unique_ptr<VTKSolutionReader> solution_reader_;
- static std::unique_ptr<TimeIntegrableRHS> rhsFactory(SpatialDiscretization&);
- static std::unique_ptr<SpatialDiscretization> geomFactory();
- static std::unique_ptr<InitialConditions> initialConditionsFactory();
- static std::unique_ptr<TimeIntegrator> timeIntegratorFactory(TimeIntegrableRHS&);
+ static std::unique_ptr<TimeIntegrableRHS> rhsFactory(SpatialDiscretization&);
+ std::unique_ptr<SpatialDiscretization> geomFactory();
+ std::unique_ptr<InitialConditions> initialConditionsFactory();
+ static std::unique_ptr<TimeIntegrator> timeIntegratorFactory(TimeIntegrableRHS&);
void attachTimeObservers(TimeIntegrator&);
void attachResidualObservers(TimeIntegrator&, TimeIntegrableRHS&);
diff --git a/program_options/program_options.hpp b/program_options/program_options.hpp
index d0917c4..7c2bb0d 100644
--- a/program_options/program_options.hpp
+++ b/program_options/program_options.hpp
@@ -23,6 +23,7 @@ class Options
// file options
const std::string& config_file() const { return config_file_; }
const std::string& solution_output_file() const { return solution_output_file_; }
+ const std::string& initial_condition_file() const { return initial_condition_file_; }
const std::string& log_file() const { return log_file_; }
int log_frequency() const { return log_frequency_; }
@@ -63,6 +64,7 @@ class Options
// file options
std::string config_file_;
std::string solution_output_file_;
+ std::string initial_condition_file_;
std::string log_file_;
int log_frequency_;
diff --git a/program_options/program_options_parser.cpp b/program_options/program_options_parser.cpp
index 43f4ec7..9b5ef9d 100644
--- a/program_options/program_options_parser.cpp
+++ b/program_options/program_options_parser.cpp
@@ -85,6 +85,9 @@ ProgramOptionsParser::ProgramOptionsParser()
"solution_output_file",
po::value<std::string>(&Options::get().solution_output_file_),
"Solution output file name, without file extension.")(
+ "initial_condition_file",
+ po::value<std::string>(&Options::get().initial_condition_file_)->default_value("none"),
+ "Filename containing and initial solution. Overrides input values if not 'none'.")(
"log_file",
po::value<std::string>(&Options::get().log_file_)->default_value("maDGiCart"),
"Solution output file name, without file extension.")(
diff --git a/spatial_discretization/discretization_2d_cart.cpp b/spatial_discretization/discretization_2d_cart.cpp
index f2c84a5..1883d8c 100644
--- a/spatial_discretization/discretization_2d_cart.cpp
+++ b/spatial_discretization/discretization_2d_cart.cpp
@@ -2,12 +2,7 @@
#include <memory>
-Discretization2DCart::Discretization2DCart(
- int ni,
- int nhalo,
- double xbeg,
- double xend,
- double ybeg)
+Discretization2DCart::Discretization2DCart(int ni, int nhalo, double xbeg, double xend, double ybeg)
: SpatialDiscretization("Discretization2DCart"),
ni_(ni),
nhalo_(nhalo),
@@ -16,7 +11,9 @@ Discretization2DCart::Discretization2DCart(
interior_indices_(*this, "InteriorIndices", ni * ni),
boundary_indices_(*this, "BoundaryIndices", (ni + 2 * nhalo) * nhalo_ * 2 + ni * nhalo_ * 2),
x_coord_(*this, "CoordinateX", ni, ni, nhalo),
- y_coord_(*this, "CoordinateY", ni, ni, nhalo)
+ y_coord_(*this, "CoordinateY", ni, ni, nhalo),
+ x_vertex_coord_(*this, "VertexCoordinateX", ni + 1, ni + 1, nhalo),
+ y_vertex_coord_(*this, "VertexCoordinateY", ni + 1, ni + 1, nhalo)
{
{
auto idx_list = write_access_host(interior_indices_);
@@ -66,15 +63,29 @@ Discretization2DCart::Discretization2DCart(
}
}
- auto x = write_access_host(x_coord_);
- auto y = write_access_host(y_coord_);
- const real_wp xc_beg = xbeg+0.5*dx_;
- const real_wp yc_beg = ybeg+0.5*dx_;
+ {
+ auto xv = write_access_host(x_vertex_coord_);
+ auto yv = write_access_host(y_vertex_coord_);
- for (int i = -nhalo; i < ni+nhalo; ++i){
- for (int j = -nhalo; j < ni+nhalo; ++j){
- x(i,j) = xc_beg + real_wp(i)*dx_;
- y(i,j) = yc_beg + real_wp(j)*dx_;
+ for (int i = -nhalo; i < ni + nhalo + 1; ++i) {
+ for (int j = -nhalo; j < ni + nhalo + 1; ++j) {
+ xv(i, j) = xbeg + dx_ * real_wp(i);
+ yv(i, j) = ybeg + dx_ * real_wp(j);
+ }
+ }
+ }
+
+ {
+ auto xv = read_access_host(x_vertex_coord_);
+ auto yv = read_access_host(y_vertex_coord_);
+ auto x = write_access_host(x_coord_);
+ auto y = write_access_host(y_coord_);
+
+ for (int i = -nhalo; i < ni + nhalo; ++i) {
+ for (int j = -nhalo; j < ni + nhalo; ++j) {
+ x(i, j) = 0.5 * (xv(i, j) + xv(i + 1, j));
+ y(i, j) = 0.5 * (yv(i, j) + yv(i, j + 1));
+ }
}
}
}
@@ -179,8 +190,9 @@ Discretization2DCart::biharmonic(const ManagedArray2D<real_wp>& state_in, Manage
f.getIJ(idx[ii], i, j);
del4f(i, j) = (f(i, j + 2) + 2.0 * f(i - 1, j + 1) - 8.0 * f(i, j + 1) + 2.0 * f(i + 1, j + 1) + f(i - 2, j) -
- 8.0 * f(i - 1, j) + 20.0 * f(i, j) - 8.0 * f(i + 1, j) + f(i + 2, j) + 2.0 * f(i - 1, j - 1) -
- 8.0 * f(i, j - 1) + 2.0 * f(i + 1, j - 1) + 1.0 * f(i, j - 2)) / dx4;
+ 8.0 * f(i - 1, j) + 20.0 * f(i, j) - 8.0 * f(i + 1, j) + f(i + 2, j) + 2.0 * f(i - 1, j - 1) -
+ 8.0 * f(i, j - 1) + 2.0 * f(i + 1, j - 1) + 1.0 * f(i, j - 2)) /
+ dx4;
});
}
diff --git a/spatial_discretization/discretization_2d_cart.hpp b/spatial_discretization/discretization_2d_cart.hpp
index 54bd009..21809b1 100644
--- a/spatial_discretization/discretization_2d_cart.hpp
+++ b/spatial_discretization/discretization_2d_cart.hpp
@@ -8,6 +8,12 @@ class Discretization2DCart : public SpatialDiscretization {
public:
Discretization2DCart(int ni, int nhalo, double xbeg, double xend, double ybeg);
+ Discretization2DCart(const CartesianDomainDefinition& domain, int nhalo)
+ : Discretization2DCart(domain.nx, nhalo, domain.xbeg, domain.xend, domain.ybeg)
+ {
+ }
+
+
~Discretization2DCart() = default;
const IndexArray& interiorIndices() const { return interior_indices_; }
@@ -15,10 +21,10 @@ class Discretization2DCart : public SpatialDiscretization {
std::unique_ptr<ManagedArray2D<real_wp>> createRealArray() const;
- int ni() const { return ni_; }
- int nhalo() const { return nhalo_; }
+ int ni() const { return ni_; }
+ int nhalo() const { return nhalo_; }
double dx() const { return dx_; }
- int nInteriorPoints() const { return ni()*ni(); }
+ int nInteriorPoints() const { return ni() * ni(); }
void applyPeriodicBoundaryConditions(ManagedArray2D<real_wp>& state) const;
@@ -30,14 +36,20 @@ class Discretization2DCart : public SpatialDiscretization {
const ManagedArray2DOwning<real_wp>& x() const { return x_coord_; }
const ManagedArray2DOwning<real_wp>& y() const { return y_coord_; }
+ const ManagedArray2DOwning<real_wp>& xvertex() const { return x_vertex_coord_; }
+ const ManagedArray2DOwning<real_wp>& yvertex() const { return y_vertex_coord_; }
+
private:
- const int ni_;
- const int nhalo_;
- const int ninhalo_;
+ const int ni_;
+ const int nhalo_;
+ const int ninhalo_;
const double dx_;
- IndexArray interior_indices_;
- IndexArray boundary_indices_;
+ IndexArray interior_indices_;
+ IndexArray boundary_indices_;
ManagedArray2DOwning<real_wp> x_coord_;
ManagedArray2DOwning<real_wp> y_coord_;
+
+ ManagedArray2DOwning<real_wp> x_vertex_coord_;
+ ManagedArray2DOwning<real_wp> y_vertex_coord_;
};
diff --git a/spatial_discretization/discretization_3d_cart.cpp b/spatial_discretization/discretization_3d_cart.cpp
index 3b21258..153b326 100644
--- a/spatial_discretization/discretization_3d_cart.cpp
+++ b/spatial_discretization/discretization_3d_cart.cpp
@@ -11,7 +11,10 @@ Discretization3DCart::Discretization3DCart(int ni, int nhalo, double xbeg, doubl
periodic_receiver_indices_(*this, "PeriodicReceiverIndices", (pow(ninhalo_, 3) - pow(ni_, 3))),
x_coord_(*this, "CoordinateX", ni, ni, ni, nhalo),
y_coord_(*this, "CoordinateY", ni, ni, ni, nhalo),
- z_coord_(*this, "CoordinateZ", ni, ni, ni, nhalo)
+ z_coord_(*this, "CoordinateZ", ni, ni, ni, nhalo),
+ x_vertex_coord_(*this, "VertexCoordinateX", ni + 1, ni + 1, ni + 1, nhalo),
+ y_vertex_coord_(*this, "VertexCoordinateY", ni + 1, ni + 1, ni + 1, nhalo),
+ z_vertex_coord_(*this, "VertexCoordinateZ", ni + 1, ni + 1, ni + 1, nhalo)
{
{
auto idx_list = write_access_host(interior_indices_);
@@ -27,22 +30,37 @@ Discretization3DCart::Discretization3DCart(int ni, int nhalo, double xbeg, doubl
}
}
+ {
+ auto xv = write_access_host(x_vertex_coord_);
+ auto yv = write_access_host(y_vertex_coord_);
+ auto zv = write_access_host(z_vertex_coord_);
+
+ for (int i = -nhalo; i < ni + nhalo + 1; ++i) {
+ for (int j = -nhalo; j < ni + nhalo + 1; ++j) {
+ for (int k = -nhalo; k < ni + nhalo + 1; ++k) {
+ xv(i, j, k) = xbeg + dx_ * real_wp(i);
+ yv(i, j, k) = ybeg + dx_ * real_wp(j);
+ zv(i, j, k) = zbeg + dx_ * real_wp(k);
+ }
+ }
+ }
+ }
+
{
+ auto xv = read_access_host(x_vertex_coord_);
+ auto yv = read_access_host(y_vertex_coord_);
+ auto zv = read_access_host(z_vertex_coord_);
auto x = write_access_host(x_coord_);
auto y = write_access_host(y_coord_);
auto z = write_access_host(z_coord_);
- const real_wp xc_beg = xbeg + 0.5 * dx_;
- const real_wp yc_beg = ybeg + 0.5 * dx_;
- const real_wp zc_beg = zbeg + 0.5 * dx_;
-
for (int i = -nhalo; i < ni + nhalo; ++i) {
for (int j = -nhalo; j < ni + nhalo; ++j) {
for (int k = -nhalo; k < ni + nhalo; ++k) {
- x(i, j, k) = xc_beg + real_wp(i) * dx_;
- y(i, j, k) = yc_beg + real_wp(j) * dx_;
- z(i, j, k) = zc_beg + real_wp(k) * dx_;
+ x(i, j, k) = 0.5*(xv(i, j, k) + xv(i+1, j, k));
+ y(i, j, k) = 0.5*(yv(i, j, k) + yv(i, j+1, k));
+ z(i, j, k) = 0.5*(zv(i, j, k) + zv(i, j, k+1));
}
}
}
diff --git a/spatial_discretization/discretization_3d_cart.hpp b/spatial_discretization/discretization_3d_cart.hpp
index 0d697e1..caf3bb8 100644
--- a/spatial_discretization/discretization_3d_cart.hpp
+++ b/spatial_discretization/discretization_3d_cart.hpp
@@ -7,17 +7,22 @@ class Discretization3DCart : public SpatialDiscretization {
public:
Discretization3DCart(int ni, int nhalo, double xbeg, double xend, double ybeg, double zbeg);
+ Discretization3DCart(const CartesianDomainDefinition& domain, int nhalo)
+ : Discretization3DCart(domain.nx, nhalo, domain.xbeg, domain.xend, domain.ybeg, domain.zbeg)
+ {
+ }
+
~Discretization3DCart() = default;
const IndexArray& interiorIndices() const { return interior_indices_; }
-// const IndexArray& boundaryIndices() const { return boundary_indices_; }
+ // const IndexArray& boundaryIndices() const { return boundary_indices_; }
std::unique_ptr<ManagedArray3D<real_wp>> createRealArray() const;
- int ni() const { return ni_; }
- int nhalo() const { return nhalo_; }
+ int ni() const { return ni_; }
+ int nhalo() const { return nhalo_; }
double dx() const { return dx_; }
- int nInteriorPoints() const { return interior_indices_.size(); }
+ int nInteriorPoints() const { return interior_indices_.size(); }
void applyPeriodicBoundaryConditions(ManagedArray3D<real_wp>& state) const;
@@ -29,10 +34,14 @@ class Discretization3DCart : public SpatialDiscretization {
const ManagedArray3DOwning<real_wp>& y() const { return y_coord_; }
const ManagedArray3DOwning<real_wp>& z() const { return z_coord_; }
+ const ManagedArray3DOwning<real_wp>& xvertex() const { return x_vertex_coord_; }
+ const ManagedArray3DOwning<real_wp>& yvertex() const { return y_vertex_coord_; }
+ const ManagedArray3DOwning<real_wp>& zvertex() const { return z_vertex_coord_; }
+
private:
- const int ni_;
- const int nhalo_;
- const int ninhalo_;
+ const int ni_;
+ const int nhalo_;
+ const int ninhalo_;
const double dx_;
IndexArray interior_indices_;
@@ -43,4 +52,8 @@ class Discretization3DCart : public SpatialDiscretization {
ManagedArray3DOwning<real_wp> x_coord_;
ManagedArray3DOwning<real_wp> y_coord_;
ManagedArray3DOwning<real_wp> z_coord_;
+
+ ManagedArray3DOwning<real_wp> x_vertex_coord_;
+ ManagedArray3DOwning<real_wp> y_vertex_coord_;
+ ManagedArray3DOwning<real_wp> z_vertex_coord_;
};
diff --git a/spatial_discretization/spatial_discretization.hpp b/spatial_discretization/spatial_discretization.hpp
index ccfe944..5d1d3ad 100644
--- a/spatial_discretization/spatial_discretization.hpp
+++ b/spatial_discretization/spatial_discretization.hpp
@@ -3,6 +3,18 @@
#include "data_structures/managed_array_owner.hpp"
+struct CartesianDomainDefinition {
+ int nx;
+ int ny;
+ int nz;
+ double xbeg;
+ double xend;
+ double ybeg;
+ double zbeg;
+};
+
+
+
class SpatialDiscretization : public ManagedArrayOwner {
public:
SpatialDiscretization(std::string classname)
diff --git a/testing/unit_tests/CMakeLists.txt b/testing/unit_tests/CMakeLists.txt
index 53195d5..e633a09 100644
--- a/testing/unit_tests/CMakeLists.txt
+++ b/testing/unit_tests/CMakeLists.txt
@@ -4,7 +4,7 @@ add_executable(unit_testing
governing_equations/cahn_hilliard_2d_fd_test.cpp
time_stepping/cahn_hilliard_regression_test.cpp
spatial_discretization/discretization_3d_cart_test.cpp
- governing_equations/cahn_hilliard_3d_fd_test.cpp)
+ governing_equations/cahn_hilliard_3d_fd_test.cpp file_io_test.cpp)
add_dependencies(unit_testing ${external_libraries})
diff --git a/testing/unit_tests/file_io_test.cpp b/testing/unit_tests/file_io_test.cpp
new file mode 100644
index 0000000..dc4b9cf
--- /dev/null
+++ b/testing/unit_tests/file_io_test.cpp
@@ -0,0 +1,157 @@
+#include <gtest/gtest.h>
+
+#include "typedefs.hpp"
+
+#include "data_structures/exec_includes.hpp"
+#include "file_io/vtk_solution_reader.hpp"
+#include "file_io/vtk_solution_writer.hpp"
+#include "governing_equations/cahn_hilliard/cahn_hilliard_2d_fd.hpp"
+#include "governing_equations/cahn_hilliard/cahn_hilliard_3d_fd.hpp"
+#include "spatial_discretization/discretization_2d_cart.hpp"
+
+
+TEST(FileIO, Discretization2DCartWriteAndRead)
+{
+ const std::string filename_without_ext = "fileio_unittest";
+ const std::string filename_with_ext = filename_without_ext + ".vts";
+
+ const int N = 16;
+ const int Nhalo = 2;
+ const double xbeg = -2;
+ const double xend = 3;
+ const double ybeg = -1;
+
+
+ Discretization2DCart geom(N, Nhalo, xbeg, xend, ybeg);
+ CahnHilliardParameters ch_params;
+ CahnHilliard2DFD rhs(geom, ch_params);
+
+ // write a specific solution file to disk
+ {
+ auto state = rhs.createSolutionState();
+
+
+ auto c = write_access_host(dynamic_cast<CahnHilliardState&>(*state).c());
+
+ auto x = read_access_host(geom.x());
+ auto y = read_access_host(geom.y());
+ auto idx = read_access_host(geom.interiorIndices());
+
+
+ maDGForAllHost(ii, 0, idx.size(), {
+ int i;
+ int j;
+ c.getIJ(idx[ii], i, j);
+ c(i, j) = sin(x(i, j)) * cos(y(i, j));
+ });
+
+ write_solution_to_vtk(*state, geom, filename_without_ext);
+ }
+
+
+ // read back the solution file
+ {
+ VTKSolutionReader file_reader(filename_with_ext);
+
+ const auto domain_defn = file_reader.getCartesianDomain();
+ EXPECT_EQ(domain_defn.nx, N);
+ EXPECT_EQ(domain_defn.ny, N);
+ EXPECT_EQ(domain_defn.nz, 0);
+ EXPECT_EQ(domain_defn.xbeg, xbeg);
+ EXPECT_EQ(domain_defn.xend, xend);
+ EXPECT_EQ(domain_defn.ybeg, ybeg);
+ EXPECT_EQ(domain_defn.zbeg, 0);
+
+ auto input_state = rhs.createSolutionState();
+ file_reader.setSolution(geom.interiorIndices(), *input_state);
+
+
+ auto x = read_access_host(geom.x());
+ auto y = read_access_host(geom.y());
+ auto idx = read_access_host(geom.interiorIndices());
+ auto c = read_access_host(dynamic_cast<CahnHilliardState&>(*input_state).c());
+
+ maDGForAllHost(ii, 0, idx.size(), {
+ int i;
+ int j;
+ c.getIJ(idx[ii], i, j);
+ EXPECT_NEAR(c(i, j), sin(x(i, j)) * cos(y(i, j)), 1.e-16);
+ });
+ }
+}
+
+
+TEST(FileIO, Discretization3DCartWriteAndRead)
+{
+ const std::string filename_without_ext = "fileio3d_unittest";
+ const std::string filename_with_ext = filename_without_ext + ".vts";
+
+ const int N = 16;
+ const int Nhalo = 2;
+ const double xbeg = -2;
+ const double xend = 3;
+ const double ybeg = -1;
+ const double zbeg = 1;
+
+
+ Discretization3DCart geom(N, Nhalo, xbeg, xend, ybeg, zbeg);
+ CahnHilliardParameters ch_params;
+ CahnHilliard3DFD rhs(geom, ch_params);
+
+ // write a specific solution file to disk
+ {
+ auto state = rhs.createSolutionState();
+
+
+ auto c = write_access_host(dynamic_cast<CahnHilliardState3D&>(*state).c());
+
+ auto x = read_access_host(geom.x());
+ auto y = read_access_host(geom.y());
+ auto z = read_access_host(geom.z());
+ auto idx = read_access_host(geom.interiorIndices());
+
+
+ maDGForAllHost(ii, 0, idx.size(), {
+ int i;
+ int j;
+ int k;
+ c.getIJK(idx[ii], i, j, k);
+ c(i, j, k) = sin(x(i, j, k)) * cos(y(i, j, k)) * cos(z(i, j, k));
+ });
+
+ write_solution_to_vtk(*state, geom, filename_without_ext);
+ }