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Merge pull request #59 from tboudreaux/feature/mixedPolytrope

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Static 3D FEM Polytropic Model
This commit is contained in:
Emily Boudreaux
2025-06-12 04:11:03 -04:00
committed by GitHub
parent d33a46490f 8dd0890d60
commit af7d519e9a
4 changed files with 91 additions and 42 deletions
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2
build-config/meson.build
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@@ -5,6 +5,8 @@ subdir('yaml-cpp')
subdir('quill') subdir('quill')
subdir('boost') subdir('boost')
subdir('opatIO') subdir('opatIO')
subdir('mpi')
subdir('hypre')
subdir('pybind') subdir('pybind')
# Set the config file error handling options # Set the config file error handling options

40
src/composition/private/composition.cpp
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@@ -1,3 +1,23 @@
/* ***********************************************************************
//
// Copyright (C) 2025 -- The 4D-STAR Collaboration
// File Author: Emily Boudreaux
// Last Modified: March 26, 2025
//
// 4DSSE is free software; you can use it and/or modify
// it under the terms and restrictions the GNU General Library Public
// License version 3 (GPLv3) as published by the Free Software Foundation.
//
// 4DSSE is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
// See the GNU Library General Public License for more details.
//
// You should have received a copy of the GNU Library General Public License
// along with this software; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// *********************************************************************** */
#include "composition.h" #include "composition.h"
#include "quill/LogMacros.h" #include "quill/LogMacros.h"
@@ -10,7 +30,7 @@
#include "atomicSpecies.h" #include "atomicSpecies.h"
using namespace composition; namespace serif::composition {
CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(chemSpecies::species.at("H-1")), m_initialized(false) {} CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(chemSpecies::species.at("H-1")), m_initialized(false) {}
@@ -527,10 +547,24 @@ Composition Composition::operator+(const Composition& other) const {
return mix(other, 0.5); return mix(other, 0.5);
} }
std::ostream& composition::operator<<(std::ostream& os, const Composition& composition) { std::ostream& operator<<(std::ostream& os, const GlobalComposition& comp) {
os << "Global Composition: \n";
os << "\tSpecific Number Density: " << comp.specificNumberDensity << "\n";
os << "\tMean Particle Mass: " << comp.meanParticleMass << "\n";
return os;
}
std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry) {
os << "<" << entry.m_symbol << " : m_frac = " << entry.mass_fraction() << ">";
return os;
}
std::ostream& operator<<(std::ostream& os, const Composition& composition) {
os << "Composition: \n"; os << "Composition: \n";
for (const auto& [symbol, entry] : composition.m_compositions) { for (const auto& [symbol, entry] : composition.m_compositions) {
os << entry << "\n"; os << entry << "\n";
} }
return os; return os;
} }
} // namespace serif::composition

39
src/composition/public/composition.h
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@@ -1,3 +1,23 @@
/* ***********************************************************************
//
// Copyright (C) 2025 -- The 4D-STAR Collaboration
// File Author: Emily Boudreaux
// Last Modified: March 26, 2025
//
// 4DSSE is free software; you can use it and/or modify
// it under the terms and restrictions the GNU General Library Public
// License version 3 (GPLv3) as published by the Free Software Foundation.
//
// 4DSSE is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
// See the GNU Library General Public License for more details.
//
// You should have received a copy of the GNU Library General Public License
// along with this software; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// *********************************************************************** */
#ifndef COMPOSITION_H #ifndef COMPOSITION_H
#define COMPOSITION_H #define COMPOSITION_H
@@ -13,7 +33,7 @@
#include "atomicSpecies.h" #include "atomicSpecies.h"
namespace composition{ namespace serif::composition {
/** /**
* @brief Represents the global composition of a system. This tends to be used after finalize and is primarily for internal use. * @brief Represents the global composition of a system. This tends to be used after finalize and is primarily for internal use.
*/ */
@@ -22,12 +42,7 @@ namespace composition{
double meanParticleMass; ///< The mean particle mass of the composition (\sum_{i} \frac{n_i}{m_i}. where n_i is the number fraction of the ith species and m_i is the mass of the ith species). double meanParticleMass; ///< The mean particle mass of the composition (\sum_{i} \frac{n_i}{m_i}. where n_i is the number fraction of the ith species and m_i is the mass of the ith species).
// Overload the output stream operator for GlobalComposition // Overload the output stream operator for GlobalComposition
friend std::ostream& operator<<(std::ostream& os, const GlobalComposition& comp) { friend std::ostream& operator<<(std::ostream& os, const GlobalComposition& comp);
os << "Global Composition: \n";
os << "\tSpecific Number Density: " << comp.specificNumberDensity << "\n";
os << "\tMean Particle Mass: " << comp.meanParticleMass << "\n";
return os;
}
}; };
/** /**
@@ -154,10 +169,7 @@ namespace composition{
* @param entry The CompositionEntry to output. * @param entry The CompositionEntry to output.
* @return The output stream. * @return The output stream.
*/ */
friend std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry) { friend std::ostream& operator<<(std::ostream& os, const CompositionEntry& entry);
os << "<" << entry.m_symbol << " : m_frac = " << entry.mass_fraction() << ">";
return os;
}
}; };
/** /**
@@ -190,7 +202,8 @@ namespace composition{
*/ */
class Composition { class Composition {
private: private:
Probe::LogManager& m_logManager = Probe::LogManager::getInstance(); serif::config::Config& m_config = serif::config::Config::getInstance();
serif::probe::LogManager& m_logManager = serif::probe::LogManager::getInstance();
quill::Logger* m_logger = m_logManager.getLogger("log"); quill::Logger* m_logger = m_logManager.getLogger("log");
bool m_finalized = false; ///< True if the composition is finalized. bool m_finalized = false; ///< True if the composition is finalized.
@@ -450,6 +463,6 @@ namespace composition{
Composition operator+(const Composition& other) const; Composition operator+(const Composition& other) const;
}; };
}; }; // namespace serif::composition
#endif // COMPOSITION_H #endif // COMPOSITION_H

52
tests/composition/compositionTest.cpp
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@@ -25,13 +25,13 @@ TEST_F(compositionTest, isotopeMasses) {
} }
TEST_F(compositionTest, constructor) { TEST_F(compositionTest, constructor) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
EXPECT_NO_THROW(composition::Composition comp); EXPECT_NO_THROW(serif::composition::Composition comp);
} }
TEST_F(compositionTest, registerSymbol) { TEST_F(compositionTest, registerSymbol) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
EXPECT_NO_THROW(comp.registerSymbol("H-1")); EXPECT_NO_THROW(comp.registerSymbol("H-1"));
EXPECT_NO_THROW(comp.registerSymbol("He-4")); EXPECT_NO_THROW(comp.registerSymbol("He-4"));
EXPECT_THROW(comp.registerSymbol("H-19"), std::runtime_error); EXPECT_THROW(comp.registerSymbol("H-19"), std::runtime_error);
@@ -45,8 +45,8 @@ TEST_F(compositionTest, registerSymbol) {
} }
TEST_F(compositionTest, setGetComposition) { TEST_F(compositionTest, setGetComposition) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
@@ -71,8 +71,8 @@ TEST_F(compositionTest, setGetComposition) {
} }
TEST_F(compositionTest, setGetNumberFraction) { TEST_F(compositionTest, setGetNumberFraction) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1", false); comp.registerSymbol("H-1", false);
comp.registerSymbol("He-4", false); comp.registerSymbol("He-4", false);
@@ -88,8 +88,8 @@ TEST_F(compositionTest, setGetNumberFraction) {
} }
TEST_F(compositionTest, subset) { TEST_F(compositionTest, subset) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
comp.setMassFraction("H-1", 0.6); comp.setMassFraction("H-1", 0.6);
@@ -97,14 +97,14 @@ TEST_F(compositionTest, subset) {
EXPECT_NO_THROW(comp.finalize()); EXPECT_NO_THROW(comp.finalize());
std::vector<std::string> symbols = {"H-1"}; std::vector<std::string> symbols = {"H-1"};
composition::Composition subsetComp = comp.subset(symbols, "norm"); serif::composition::Composition subsetComp = comp.subset(symbols, "norm");
EXPECT_TRUE(subsetComp.finalize()); EXPECT_TRUE(subsetComp.finalize());
EXPECT_DOUBLE_EQ(subsetComp.getMassFraction("H-1"), 1.0); EXPECT_DOUBLE_EQ(subsetComp.getMassFraction("H-1"), 1.0);
} }
TEST_F(compositionTest, finalizeWithNormalization) { TEST_F(compositionTest, finalizeWithNormalization) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
comp.setMassFraction("H-1", 0.3); comp.setMassFraction("H-1", 0.3);
@@ -115,8 +115,8 @@ TEST_F(compositionTest, finalizeWithNormalization) {
} }
TEST_F(compositionTest, finalizeWithoutNormalization) { TEST_F(compositionTest, finalizeWithoutNormalization) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
comp.setMassFraction("H-1", 0.5); comp.setMassFraction("H-1", 0.5);
@@ -127,8 +127,8 @@ TEST_F(compositionTest, finalizeWithoutNormalization) {
} }
TEST_F(compositionTest, getComposition) { TEST_F(compositionTest, getComposition) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
comp.setMassFraction("H-1", 0.6); comp.setMassFraction("H-1", 0.6);
@@ -142,8 +142,8 @@ TEST_F(compositionTest, getComposition) {
} }
TEST_F(compositionTest, setCompositionMode) { TEST_F(compositionTest, setCompositionMode) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
comp.setMassFraction("H-1", 0.6); comp.setMassFraction("H-1", 0.6);
@@ -164,8 +164,8 @@ TEST_F(compositionTest, setCompositionMode) {
} }
TEST_F(compositionTest, hasSymbol) { TEST_F(compositionTest, hasSymbol) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp; serif::composition::Composition comp;
comp.registerSymbol("H-1"); comp.registerSymbol("H-1");
comp.registerSymbol("He-4"); comp.registerSymbol("He-4");
comp.setMassFraction("H-1", 0.6); comp.setMassFraction("H-1", 0.6);
@@ -179,27 +179,27 @@ TEST_F(compositionTest, hasSymbol) {
} }
TEST_F(compositionTest, mix) { TEST_F(compositionTest, mix) {
Config::getInstance().loadConfig(EXAMPLE_FILENAME); serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
composition::Composition comp1; serif::composition::Composition comp1;
comp1.registerSymbol("H-1"); comp1.registerSymbol("H-1");
comp1.registerSymbol("He-4"); comp1.registerSymbol("He-4");
comp1.setMassFraction("H-1", 0.6); comp1.setMassFraction("H-1", 0.6);
comp1.setMassFraction("He-4", 0.4); comp1.setMassFraction("He-4", 0.4);
EXPECT_NO_THROW(comp1.finalize()); EXPECT_NO_THROW(comp1.finalize());
composition::Composition comp2; serif::composition::Composition comp2;
comp2.registerSymbol("H-1"); comp2.registerSymbol("H-1");
comp2.registerSymbol("He-4"); comp2.registerSymbol("He-4");
comp2.setMassFraction("H-1", 0.4); comp2.setMassFraction("H-1", 0.4);
comp2.setMassFraction("He-4", 0.6); comp2.setMassFraction("He-4", 0.6);
EXPECT_NO_THROW(comp2.finalize()); EXPECT_NO_THROW(comp2.finalize());
composition::Composition mixedComp = comp1 + comp2; serif::composition::Composition mixedComp = comp1 + comp2;
EXPECT_TRUE(mixedComp.finalize()); EXPECT_TRUE(mixedComp.finalize());
EXPECT_DOUBLE_EQ(mixedComp.getMassFraction("H-1"), 0.5); EXPECT_DOUBLE_EQ(mixedComp.getMassFraction("H-1"), 0.5);
EXPECT_DOUBLE_EQ(mixedComp.getMassFraction("He-4"), 0.5); EXPECT_DOUBLE_EQ(mixedComp.getMassFraction("He-4"), 0.5);
composition::Composition mixedComp2 = comp1.mix(comp2, 0.25); serif::composition::Composition mixedComp2 = comp1.mix(comp2, 0.25);
EXPECT_TRUE(mixedComp2.finalize()); EXPECT_TRUE(mixedComp2.finalize());
EXPECT_DOUBLE_EQ(mixedComp2.getMassFraction("H-1"), 0.45); EXPECT_DOUBLE_EQ(mixedComp2.getMassFraction("H-1"), 0.45);
EXPECT_DOUBLE_EQ(mixedComp2.getMassFraction("He-4"), 0.55); EXPECT_DOUBLE_EQ(mixedComp2.getMassFraction("He-4"), 0.55);