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Merge pull request #29 from tboudreaux/feature/nuclearNetwork

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Added approx8 neuclear network and general nuclear network framework.
This commit is contained in:
Emily Boudreaux
2025-03-21 15:03:15 -04:00
committed by GitHub
parent 8a7c0c7658 552a360064
commit 8f41ee91f2
9 changed files with 1284 additions and 0 deletions
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226
build-config/boost/install.sh Executable file
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#!/usr/bin/env bash
#
# install.sh - Interactive installation script for Boost.
#
# This script checks if Boost is installed (by looking for boost/version.hpp in common locations).
# If not found, it prompts the user to install Boost using the native package manager for:
# - FreeBSD, Ubuntu, Debian, Fedora, Arch, Mint, Manjaro, macOS, OpenSuse, and Nix.
#
# All output is colorized for clarity and logged to meson-log.txt.
set -e
# ANSI color codes.
RED="\033[0;31m"
GREEN="\033[0;32m"
YELLOW="\033[0;33m"
BLUE="\033[0;34m"
NC="\033[0m" # No Color
# Log file.
LOGFILE="4DSSE-install-log.txt"
touch "$LOGFILE"
# Log function: prints to stdout and appends to logfile.
log() {
local message="$1"
# Print the colored message to stdout.
echo -e "$message"
# Strip ANSI escape sequences and append the cleaned message to the log file.
echo -e "$message" | sed -r 's/\x1B\[[0-9;]*[mK]//g' >> "$LOGFILE"
}
check_boost_installed() {
log "${BLUE}[Info] Checking for Boost::numeric and Boost::phoenix using Meson...${NC}"
local tmpDir
if [[ -d mesonTest ]]; then
rm -rf mesonTest
fi
tmpDir=$(mkdir mesonTest)
local sourceFile="mesonTest/test.cpp"
local mesonFile="mesonTest/meson.build"
# Write test.cpp
cat > "$sourceFile" <<EOF
#include <boost/numeric/ublas/vector.hpp>
#include <boost/phoenix/phoenix.hpp>
int main() {
boost::numeric::ublas::vector<double> v(3);
v[0] = 1.0;
return v[0];
}
EOF
# Write meson.build
cat > "$mesonFile" <<EOF
project('boost-check', 'cpp', default_options: ['cpp_std=c++17'])
boost_dep = dependency('boost', required: true)
executable('boostAvaliTest', 'test.cpp', dependencies: [boost_dep])
EOF
# Try configuring and compiling
if meson setup "mesonTest/build" "mesonTest" && \
meson compile -C "mesonTest/build"; then
log "${GREEN}[Success] Boost::numeric and Boost::phoenix are available.${NC}"
rm -rf "mesonTest"
return 0
else
log "${RED}[Error] Boost could not be found or required components are missing.${NC}"
rm -rf "mesonTest"
return 1
fi
}
# Prompt the user for a yes/no answer.
prompt_yes_no() {
local promptMsg="$1"
read -p "$(echo -e ${YELLOW}$promptMsg${NC}) " answer
if [[ "$answer" =~ ^[Yy]$ ]]; then
return 0
else
return 1
fi
}
# Detect OS.
OS=$(uname -s)
DISTRO="unknown"
if [ -f /etc/os-release ]; then
# shellcheck disable=SC1091
. /etc/os-release
DISTRO=$ID
fi
if [[ "$OS" == "Darwin" ]]; then
OS="macOS"
fi
if [[ $OS == "macOS" ]]; then
log "${BLUE}[Info] Detected OS: ${OS}${NC}"
else
log "${BLUE}[Info] Detected OS: ${OS} Distribution: ${DISTRO}${NC}"
fi
# Check if Boost is already installed.
if check_boost_installed; then
log "${GREEN}[Success] Boost is already installed on your system.${NC}"
log "${GREEN}[Success] 4DSSE installation can now continue.${NC}"
exit 0
else
log "${YELLOW}[Info] Boost was not detected on your system.${NC}"
if prompt_yes_no "[Query] Would you like to install Boost now? (y/n): "; then
case "$OS" in
"macOS")
# On macOS, check if Homebrew is available.
if ! command -v brew &> /dev/null; then
log "${YELLOW}[Warning] Homebrew is not installed. It is recommended for installing Boost on macOS.${NC}"
if prompt_yes_no "[Query] Would you like to install Homebrew now? (y/n): "; then
log "${BLUE}[Info] Installing Homebrew...${NC}"
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" | tee -a "$LOGFILE"
else
log "${RED}[Error] Homebrew is required for an easy Boost installation on macOS. Aborting.${NC}"
exit 1
fi
fi
log "${BLUE}[Info] Running: brew install boost${NC}"
brew install boost | tee -a "$LOGFILE"
;;
"Linux")
case "$DISTRO" in
"ubuntu"|"debian"|"linuxmint")
log "${BLUE}[Info] Running: sudo apt-get update && sudo apt-get install -y libboost-all-dev${NC}"
sudo apt-get update | tee -a "$LOGFILE"
sudo apt-get install -y libboost-all-dev | tee -a "$LOGFILE"
;;
"fedora")
log "${BLUE}[Info] Running: sudo dnf install boost-devel${NC}"
sudo dnf install -y boost-devel | tee -a "$LOGFILE"
;;
"arch"|"manjaro")
log "${BLUE}[Info] Running: sudo pacman -S boost${NC}"
sudo pacman -S --noconfirm boost | tee -a "$LOGFILE"
;;
"opensuse")
log "${BLUE}[Info] Running: sudo zypper install libboost-devel${NC}"
sudo zypper install -y libboost-devel | tee -a "$LOGFILE"
;;
"nixos"|"nix")
log "${BLUE}[Info] Running: nix-env -iA nixpkgs.boost${NC}"
nix-env -iA nixpkgs.boost | tee -a "$LOGFILE"
;;
*)
log "${RED}[Error] Your Linux distribution is not recognized. Please install Boost manually.${NC}"
exit 1
;;
esac
;;
"FreeBSD")
log "${BLUE}[Info] Running: sudo pkg install boost-all${NC}"
sudo pkg install -y boost-all | tee -a "$LOGFILE"
;;
*)
log "${RED}[Error] Automatic Boost installation is not supported on OS: ${OS}. Please install Boost manually.${NC}"
exit 1
;;
esac
# Verify Boost installation.
if check_boost_installed; then
log "${GREEN}[Success] Boost installation succeeded.${NC}"
else
log "${RED}[Error] Boost installation appears to have failed. Please install Boost manually.${NC}"
exit 1
fi
else
log "${RED}[Error] Boost is required. Please install it using the appropriate command for your system:${NC}"
case "$OS" in
"macOS")
log "${RED}[INFO] brew install boost (Install Homebrew from https://brew.sh if not present)${NC}"
;;
"Linux")
case "$DISTRO" in
"ubuntu"|"debian"|"linuxmint")
log "${RED}[INFO] sudo apt-get install libboost-all-dev${NC}"
;;
"fedora")
log "${RED}[INFO] sudo dnf install boost-devel${NC}"
;;
"arch"|"manjaro")
log "${RED}[INFO] sudo pacman -S boost${NC}"
;;
"opensuse")
log "${RED}[INFO] sudo zypper install libboost-devel${NC}"
;;
"nixos"|"nix")
log "${RED}[INFO] nix-env -iA nixpkgs.boost${NC}"
;;
*)
log "${RED}[INFO] Please consult your distribution's documentation for installing Boost.${NC}"
;;
esac
;;
"FreeBSD")
log "${RED}[INFO] sudo pkg install boost-all${NC}"
;;
*)
log "${RED}[INFO] Please consult your operating system's documentation for installing Boost.${NC}"
;;
esac
exit 1
fi
fi
check_boost_installed
log "${GREEN}[Success] Boost installed successfully!${NC}"
log "${GREEN}[Success] 4DSSE installation can now continue.${NC}"

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build-config/boost/meson.build Normal file
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boost_dep = dependency('boost', version: '>=1.8.0')

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src/network/meson.build Normal file
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# Define the library
network_sources = files(
'private/network.cpp',
'private/approx8.cpp'
)
network_headers = files(
'public/network.h',
'public/approx8.h'
)
dependencies = [
boost_dep,
const_dep,
quill_dep,
mfem_dep,
config_dep,
probe_dep
]
# Define the libnetwork library so it can be linked against by other parts of the build system
libnetwork = static_library('network',
network_sources,
include_directories: include_directories('public'),
dependencies: dependencies,
install : true)
network_dep = declare_dependency(
include_directories: include_directories('public'),
link_with: libnetwork,
sources: network_sources,
dependencies: dependencies,
)
# Make headers accessible
install_headers(network_headers, subdir : '4DSSE/network')

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src/network/private/approx8.cpp Normal file
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#include <cmath>
#include <stdexcept>
#include <array>
#include <boost/numeric/odeint.hpp>
#include "const.h"
#include "config.h"
#include "quill/LogMacros.h"
#include "approx8.h"
#include "network.h"
/* Nuclear reaction network in cgs units based on Frank Timmes' "aprox8".
At this time it does neither screening nor neutrino losses. It includes
the following 8 isotopes:
h1
he3
he4
c12
n14
o16
ne20
mg24
and the following nuclear reactions:
---pp chain---
p(p,e+)d
d(p,g)he3
he3(he3,2p)he4
---CNO cycle---
c12(p,g)n13 - n13 -> c13 + p -> n14
n14(p,g)o15 - o15 + p -> c12 + he4
n14(a,g)f18 - proceeds to ne20
n15(p,a)c12 - / these two n15 reactions are \ CNO I
n15(p,g)o16 - \ used to calculate a fraction / CNO II
o16(p,g)f17 - f17 + e -> o17 and then o17 + p -> n14 + he4
---alpha captures---
c12(a,g)o16
triple alpha
o16(a,g)ne20
ne20(a,g)mg24
c12(c12,a)ne20
c12(o16,a)mg24
At present the rates are all evaluated using a fitting function.
The coefficients to the fit are from reaclib.jinaweb.org .
*/
namespace nnApprox8{
// using namespace std;
using namespace boost::numeric::odeint;
//helper functions
// a function to multilpy two arrays and then sum the resulting elements: sum(a*b)
double sum_product( const vec7 &a, const vec7 &b){
if (a.size() != b.size()) {
throw std::runtime_error("Error: array size mismatch in sum_product");
}
double sum=0;
for (size_t i=0; i < a.size(); i++) {
sum += a[i] * b[i];
}
return sum;
}
// the fit to the nuclear reaction rates is of the form:
// exp( a0 + a1/T9 + a2/T9^(1/3) + a3*T9^(1/3) + a4*T9 + a5*T9^(5/3) + log(T9) )
// this function returns an array of the T9 terms in that order, where T9 is the temperatures in GigaKelvin
vec7 get_T9_array(const double &T) {
vec7 arr;
double T9=1e-9*T;
double T913=pow(T9,1./3.);
arr[0]=1;
arr[1]=1/T9;
arr[2]=1/T913;
arr[3]=T913;
arr[4]=T9;
arr[5]=pow(T9,5./3.);
arr[6]=log(T9);
return arr;
}
// this function uses the two preceding functions to evaluate the rate given the T9 array and the coefficients
double rate_fit(const vec7 &T9, const vec7 &coef){
return exp(sum_product(T9,coef));
}
// p + p -> d; this, like some of the other rates, this is a composite of multiple fits
double pp_rate(const vec7 &T9) {
vec7 a1 = {-34.78630, 0,-3.511930, 3.100860, -0.1983140, 1.262510e-2, -1.025170};
vec7 a2 = { -4.364990e+1,-2.460640e-3,-2.750700,-4.248770e-1,1.598700e-2,-6.908750e-4,-2.076250e-1};
return rate_fit(T9,a1) + rate_fit(T9,a2);
}
// p + d -> he3
double dp_rate(const vec7 &T9) {
vec7 a1 = {7.528980, 0, -3.720800, 0.8717820, 0, 0,-0.6666670};
vec7 a2 = {8.935250, 0, -3.720800, 0.1986540, 0, 0, 0.3333330};
return rate_fit(T9,a1) + rate_fit(T9,a2);
}
// he3 + he3 -> he4 + 2p
double he3he3_rate(const vec7 &T9){
vec7 a = {2.477880e+01,0,-12.27700,-0.1036990,-6.499670e-02,1.681910e-02,-6.666670e-01};
return rate_fit(T9,a);
}
// he3(he3,2p)he4
double he3he4_rate(const vec7 &T9){
vec7 a1 = {1.560990e+01,0.000000e+00,-1.282710e+01,-3.082250e-02,-6.546850e-01,8.963310e-02,-6.666670e-01};
vec7 a2 = {1.770750e+01,0.000000e+00,-1.282710e+01,-3.812600e+00,9.422850e-02,-3.010180e-03,1.333330e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2);
}
// he4 + he4 + he4 -> c12
double triple_alpha_rate(const vec7 &T9){
vec7 a1 = {-9.710520e-01,0.000000e+00,-3.706000e+01,2.934930e+01,-1.155070e+02,-1.000000e+01,-1.333330e+00};
vec7 a2 = {-1.178840e+01,-1.024460e+00,-2.357000e+01,2.048860e+01,-1.298820e+01,-2.000000e+01,-2.166670e+00};
vec7 a3 = {-2.435050e+01,-4.126560e+00,-1.349000e+01,2.142590e+01,-1.347690e+00,8.798160e-02,-1.316530e+01};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3);
}
// c12 + p -> n13
double c12p_rate(const vec7 &T9){
vec7 a1={1.714820e+01,0.000000e+00,-1.369200e+01,-2.308810e-01,4.443620e+00,-3.158980e+00,-6.666670e-01};
vec7 a2={1.754280e+01,-3.778490e+00,-5.107350e+00,-2.241110e+00,1.488830e-01,0.000000e+00,-1.500000e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2);
}
// c12 + he4 -> o16
double c12a_rate(const vec7 &T9){
vec7 a1={6.965260e+01,-1.392540e+00,5.891280e+01,-1.482730e+02,9.083240e+00,-5.410410e-01,7.035540e+01};
vec7 a2={2.546340e+02,-1.840970e+00,1.034110e+02,-4.205670e+02,6.408740e+01,-1.246240e+01,1.373030e+02};
return rate_fit(T9,a1) + rate_fit(T9,a2);
}
// n14(p,g)o15 - o15 + p -> c12 + he4
double n14p_rate(const vec7 &T9){
vec7 a1={1.701000e+01,0.000000e+00,-1.519300e+01,-1.619540e-01,-7.521230e+00,-9.875650e-01,-6.666670e-01};
vec7 a2={2.011690e+01,0.000000e+00,-1.519300e+01,-4.639750e+00,9.734580e+00,-9.550510e+00,3.333330e-01};
vec7 a3={7.654440e+00,-2.998000e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a4={6.735780e+00,-4.891000e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,6.820000e-02};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3) + rate_fit(T9,a4);
}
// n14(a,g)f18 assumed to go on to ne20
double n14a_rate(const vec7 &T9){
vec7 a1={2.153390e+01,0.000000e+00,-3.625040e+01,0.000000e+00,0.000000e+00,-5.000000e+00,-6.666670e-01};
vec7 a2={1.968380e-01,-5.160340e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a3={1.389950e+01,-1.096560e+01,-5.622700e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3);
}
// n15(p,a)c12 (CNO I)
double n15pa_rate(const vec7 &T9){
vec7 a1 = {2.747640e+01,0.000000e+00,-1.525300e+01,1.593180e+00,2.447900e+00,-2.197080e+00,-6.666670e-01};
vec7 a2 = {-4.873470e+00,-2.021170e+00,0.000000e+00,3.084970e+01,-8.504330e+00,-1.544260e+00,-1.500000e+00};
vec7 a3 = {2.089720e+01,-7.406000e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a4 = {-6.575220e+00,-1.163800e+00,0.000000e+00,2.271050e+01,-2.907070e+00,2.057540e-01,-1.500000e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3) + rate_fit(T9,a4);
}
// n15(p,g)o16 (CNO II)
double n15pg_rate(const vec7 &T9){
vec7 a1 = {2.001760e+01,0.000000e+00,-1.524000e+01,3.349260e-01,4.590880e+00,-4.784680e+00,-6.666670e-01};
vec7 a2 = {6.590560e+00,-2.923150e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a3 = {1.454440e+01,-1.022950e+01,0.000000e+00,0.000000e+00,4.590370e-02,0.000000e+00,-1.500000e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3);
}
double n15pg_frac(const vec7 &T9){
double f1=n15pg_rate(T9);
double f2=n15pa_rate(T9);
return f1/(f1+f2);
}
// o16(p,g)f17 then f17 -> o17(p,a)n14
double o16p_rate(const vec7 &T9){
vec7 a={1.909040e+01,0.000000e+00,-1.669600e+01,-1.162520e+00,2.677030e-01,-3.384110e-02,-6.666670e-01};
return rate_fit(T9,a);
}
// o16(a,g)ne20
double o16a_rate(const vec7 &T9){
vec7 a1={2.390300e+01,0.000000e+00,-3.972620e+01,-2.107990e-01,4.428790e-01,-7.977530e-02,-6.666670e-01};
vec7 a2={3.885710e+00,-1.035850e+01,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a3={9.508480e+00,-1.276430e+01,0.000000e+00,-3.659250e+00,7.142240e-01,-1.075080e-03,-1.500000e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3);
}
// ne20(a,g)mg24
double ne20a_rate(const vec7 &T9){
vec7 a1={2.450580e+01,0.000000e+00,-4.625250e+01,5.589010e+00,7.618430e+00,-3.683000e+00,-6.666670e-01};
vec7 a2={-3.870550e+01,-2.506050e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a3={1.983070e+00,-9.220260e+00,0.000000e+00,0.000000e+00,0.000000e+00,0.000000e+00,-1.500000e+00};
vec7 a4={-8.798270e+00,-1.278090e+01,0.000000e+00,1.692290e+01,-2.573250e+00,2.089970e-01,-1.500000e+00};
return rate_fit(T9,a1) + rate_fit(T9,a2) + rate_fit(T9,a3) + rate_fit(T9,a4);
}
// c12(c12,a)ne20
double c12c12_rate(const vec7 &T9){
vec7 a={6.128630e+01,0.000000e+00,-8.416500e+01,-1.566270e+00,-7.360840e-02,-7.279700e-02,-6.666670e-01};
return rate_fit(T9,a);
}
// c12(o16,a)mg24
double c12o16_rate(const vec7 &T9){
vec7 a={4.853410e+01,3.720400e-01,-1.334130e+02,5.015720e+01,-3.159870e+00,1.782510e-02,-2.370270e+01};
return rate_fit(T9,a);
}
// for Boost ODE solvers either a struct or a class is required
// a Jacobian matrix for implicit solvers
void Jacobian::operator() ( const vector_type &y, matrix_type &J, double /* t */, vector_type &dfdt ) {
Constants& constants = Constants::getInstance();
const double avo = constants.get("N_a").value;
const double clight = constants.get("c").value;
// EOS
vec7 T9=get_T9_array(y[Net::itemp]);
// evaluate rates once per call
double rpp=pp_rate(T9);
double r33=he3he3_rate(T9);
double r34=he3he4_rate(T9);
double r3a=triple_alpha_rate(T9);
double rc12p=c12p_rate(T9);
double rc12a=c12a_rate(T9);
double rn14p=n14p_rate(T9);
double rn14a=n14a_rate(T9);
double ro16p=o16p_rate(T9);
double ro16a=o16a_rate(T9);
double rne20a=ne20a_rate(T9);
double r1212=c12c12_rate(T9);
double r1216=c12o16_rate(T9);
double pfrac=n15pg_frac(T9);
double afrac=1-pfrac;
double yh1 = y[Net::ih1];
double yhe3 = y[Net::ihe3];
double yhe4 = y[Net::ihe4];
double yc12 = y[Net::ic12];
double yn14 = y[Net::in14];
double yo16 = y[Net::io16];
double yne20 = y[Net::ine20];
// zero all elements to begin
for (int i=0; i < Net::nvar; i++) {
for (int j=0; j < Net::nvar; j++) {
J(i,j)=0.0;
}
}
// h1 jacobian elements
J(Net::ih1,Net::ih1) = -3*yh1*rpp - 2*yc12*rc12p -2*yn14*rn14p -2*yo16*ro16p;
J(Net::ih1,Net::ihe3) = 2*yhe3*r33 - yhe4*r34;
J(Net::ih1,Net::ihe4) = -yhe3*r34;
J(Net::ih1,Net::ic12) = -2*yh1*rc12p;
J(Net::ih1,Net::in14) = -2*yh1*rn14p;
J(Net::ih1,Net::io16) = -2*yh1*ro16p;
// he3 jacobian elements
J(Net::ihe3,Net::ih1) = yh1*rpp;
J(Net::ihe3,Net::ihe3) = -2*yhe3*r33 - yhe4*r34;
J(Net::ihe3,Net::ihe4) = -yhe3*r34;
// he4 jacobian elements
J(Net::ihe4,Net::ih1) = yn14*afrac*rn14p + yo16*ro16p;
J(Net::ihe4,Net::ihe3) = yhe3*r33 - yhe4*r34;
J(Net::ihe4,Net::ihe4) = yhe3*r34 - 1.5*yhe4*yhe4*r3a - yc12*rc12a - 1.5*yn14*rn14a - yo16*ro16a - yne20*rne20a;
J(Net::ihe4,Net::ic12) = -yhe4*rc12a + yc12*r1212 + yo16*r1216;
J(Net::ihe4,Net::in14) = yh1*afrac*rn14p - 1.5*yhe4*rn14a;
J(Net::ihe4,Net::io16) = yh1*ro16p - yhe4*ro16a + yc12*r1216;
J(Net::ihe4,Net::ine20) = -yhe4*rne20a;
// c12 jacobian elements
J(Net::ic12,Net::ih1) = -yc12*rc12p + yn14*afrac*rn14p;
J(Net::ic12,Net::ihe4) = 0.5*yhe4*yhe4*r3a - yhe4*rc12a;
J(Net::ic12,Net::ic12) = -yh1*rc12p - yhe4*rc12a - yo16*r1216 - 2*yc12*r1212;
J(Net::ic12,Net::in14) = yh1*yn14*afrac*rn14p;
J(Net::ic12,Net::io16) = -yc12*r1216;
// n14 jacobian elements
J(Net::in14,Net::ih1) = yc12*rc12p - yn14*rn14p + yo16*ro16p;
J(Net::in14,Net::ihe4) = -yn14*rn14a;
J(Net::in14,Net::ic12) = yh1*rc12p;
J(Net::in14,Net::in14) = -yh1*rn14p - yhe4*rn14a;
J(Net::in14,Net::io16) = yo16*ro16p;
// o16 jacobian elements
J(Net::io16,Net::ih1) = yn14*pfrac*rn14p - yo16*ro16p;
J(Net::io16,Net::ihe4) = yc12*rc12a - yo16*ro16a;
J(Net::io16,Net::ic12) = yhe4*rc12a - yo16*r1216;
J(Net::io16,Net::in14) = yh1*pfrac*rn14p;
J(Net::io16,Net::io16) = yh1*ro16p - yc12*r1216 -yhe4*ro16a;
// ne20 jacobian elements
J(Net::ine20,Net::ihe4) = yn14*rn14a + yo16*ro16a - yne20*rne20a;
J(Net::ine20,Net::ic12) = yc12*r1212;
J(Net::ine20,Net::in14) = yhe4*rn14a;
J(Net::ine20,Net::io16) = yo16*ro16a;
J(Net::ine20,Net::ine20) = -yhe4*rne20a;
// mg24 jacobian elements
J(Net::img24,Net::ihe4) = yne20*rne20a;
J(Net::img24,Net::ic12) = yo16*r1216;
J(Net::img24,Net::io16) = yc12*r1216;
J(Net::img24,Net::ine20) = yhe4*rne20a;
// energy accountings
for (int j=0; j<Net::niso; j++) {
for (int i=0; i<Net::niso; i++) {
J(Net::iener,j) += J(i,j)*Net::mion[i];
}
J(Net::iener,j) *= -avo*clight*clight;
}
}
void ODE::operator() ( const vector_type &y, vector_type &dydt, double /* t */) {
Constants& constants = Constants::getInstance();
const double avo = constants.get("N_a").value;
const double clight = constants.get("c").value;
// EOS
double T=y[Net::itemp];
double den=y[Net::iden];
vec7 T9=get_T9_array(T);
// rates
double rpp=den*pp_rate(T9);
double r33=den*he3he3_rate(T9);
double r34=den*he3he4_rate(T9);
double r3a=den*den*triple_alpha_rate(T9);
double rc12p=den*c12p_rate(T9);
double rc12a=den*c12a_rate(T9);
double rn14p=den*n14p_rate(T9);
double rn14a=n14a_rate(T9);
double ro16p=den*o16p_rate(T9);
double ro16a=den*o16a_rate(T9);
double rne20a=den*ne20a_rate(T9);
double r1212=den*c12c12_rate(T9);
double r1216=den*c12o16_rate(T9);
double pfrac=n15pg_frac(T9);
double afrac=1-pfrac;
double yh1 = y[Net:: ih1];
double yhe3 = y[Net:: ihe3];
double yhe4 = y[Net:: ihe4];
double yc12 = y[Net:: ic12];
double yn14 = y[Net:: in14];
double yo16 = y[Net:: io16];
double yne20 = y[Net::ine20];
dydt[Net::ih1] = -1.5*yh1*yh1*rpp;
dydt[Net::ih1] += yhe3*yhe3*r33;
dydt[Net::ih1] += -yhe3*yhe4*r34;
dydt[Net::ih1] += -2*yh1*yc12*rc12p;
dydt[Net::ih1] += -2*yh1*yn14*rn14p;
dydt[Net::ih1] += -2*yh1*yo16*ro16p;
dydt[Net::ihe3] = 0.5*yh1*yh1*rpp;
dydt[Net::ihe3] += -yhe3*yhe3*r33;
dydt[Net::ihe3] += -yhe3*yhe4*r34;
dydt[Net::ihe4] = 0.5*yhe3*yhe3*r33;
dydt[Net::ihe4] += yhe3*yhe4*r34;
dydt[Net::ihe4] += -yhe4*yc12*rc12a;
dydt[Net::ihe4] += yh1*yn14*afrac*rn14p;
dydt[Net::ihe4] += yh1*yo16*ro16p;
dydt[Net::ihe4] += -0.5*yhe4*yhe4*yhe4*r3a;
dydt[Net::ihe4] += -yhe4*yo16*ro16a;
dydt[Net::ihe4] += 0.5*yc12*yc12*r1212;
dydt[Net::ihe4] += yc12*yo16*r1216;
dydt[Net::ihe4] += -yhe4*yne20*rne20a;
dydt[Net::ic12] = (1./6.)*yhe4*yhe4*yhe4*r3a;
dydt[Net::ic12] += -yhe4*yc12*rc12a;
dydt[Net::ic12] += -yh1*yc12*rc12p;
dydt[Net::ic12] += yh1*yn14*afrac*rn14p;
dydt[Net::ic12] += -yc12*yc12*r1212;
dydt[Net::ic12] += -yc12*yo16*r1216;
dydt[Net::in14] = yh1*yc12*rc12p;
dydt[Net::in14] += -yh1*yn14*rn14p;
dydt[Net::in14] += yh1*yo16*ro16p;
dydt[Net::in14] += -yhe4*yn14*rn14a;
dydt[Net::io16] = yhe4*yc12*rc12a;
dydt[Net::io16] += yh1*yn14*pfrac*rn14p;
dydt[Net::io16] += -yh1*yo16*ro16p;
dydt[Net::io16] += -yc12*yo16*r1216;
dydt[Net::io16] += -yhe4*yo16*ro16a;
dydt[Net::ine20] = 0.5*yc12*yc12*r1212;
dydt[Net::ine20] += yhe4*yn14*rn14a;
dydt[Net::ine20] += yhe4*yo16*ro16a;
dydt[Net::ine20] += -yhe4*yne20*rne20a;
dydt[Net::img24] = yc12*yo16*r1216;
dydt[Net::img24] += yhe4*yne20*rne20a;
dydt[Net::itemp] = 0.;
dydt[Net::iden] = 0.;
// energy accounting
double enuc = 0.;
for (int i=0; i<Net::niso; i++) {
enuc += Net::mion[i]*dydt[i];
}
dydt[Net::iener] = -enuc*avo*clight*clight;
}
nuclearNetwork::NetOut Approx8Network::evaluate(const nuclearNetwork::NetIn &netIn) {
m_y = convert_netIn(netIn);
m_tmax = netIn.tmax;
m_dt0 = netIn.dt0;
const double stiff_abs_tol = m_config.get<double>("Network:Approx8:Stiff:AbsTol", 1.0e-6);
const double stiff_rel_tol = m_config.get<double>("Network:Approx8:Stiff:RelTol", 1.0e-6);
const double nonstiff_abs_tol = m_config.get<double>("Network:Approx8:NonStiff:AbsTol", 1.0e-6);
const double nonstiff_rel_tol = m_config.get<double>("Network:Approx8:NonStiff:RelTol", 1.0e-6);
int num_steps = -1;
if (m_stiff) {
LOG_DEBUG(m_logger, "Using stiff solver for Approx8Network");
num_steps = integrate_const(
make_dense_output<rosenbrock4<double>>(stiff_abs_tol, stiff_rel_tol),
std::make_pair(ODE(), Jacobian()),
m_y,
0.0,
m_tmax,
m_dt0
);
} else {
LOG_DEBUG(m_logger, "Using non stiff solver for Approx8Network");
num_steps = integrate_const (
make_dense_output<runge_kutta_dopri5<vector_type>>(nonstiff_abs_tol, nonstiff_rel_tol),
ODE(),
m_y,
0.0,
m_tmax,
m_dt0
);
}
double ysum = 0.0;
for (int i = 0; i < Net::niso; i++) {
m_y[i] *= Net::aion[i];
ysum += m_y[i];
}
for (int i = 0; i < Net::niso; i++) {
m_y[i] /= ysum;
}
nuclearNetwork::NetOut netOut;
std::vector<double> outComposition;
outComposition.reserve(Net::nvar);
for (int i = 0; i < Net::niso; i++) {
outComposition.push_back(m_y[i]);
}
netOut.energy = m_y[Net::iener];
netOut.composition = outComposition;
netOut.num_steps = num_steps;
return netOut;
}
void Approx8Network::setStiff(bool stiff) {
m_stiff = stiff;
}
vector_type Approx8Network::convert_netIn(const nuclearNetwork::NetIn &netIn) {
if (netIn.composition.size() != Net::niso) {
LOG_ERROR(m_logger, "Error: composition size mismatch in convert_netIn");
throw std::runtime_error("Error: composition size mismatch in convert_netIn");
}
vector_type y(Net::nvar, 0.0);
y[Net::ih1] = netIn.composition[0];
y[Net::ihe3] = netIn.composition[1];
y[Net::ihe4] = netIn.composition[2];
y[Net::ic12] = netIn.composition[3];
y[Net::in14] = netIn.composition[4];
y[Net::io16] = netIn.composition[5];
y[Net::ine20] = netIn.composition[6];
y[Net::img24] = netIn.composition[7];
y[Net::itemp] = netIn.temperature;
y[Net::iden] = netIn.density;
y[Net::iener] = netIn.energy;
double ysum = 0.0;
for (int i = 0; i < Net::niso; i++) {
y[i] /= Net::aion[i];
ysum += y[i];
}
for (int i = 0; i < Net::niso; i++) {
y[i] /= ysum;
}
return y;
}
};
// main program

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#include "network.h"
#include "probe.h"
#include "quill/LogMacros.h"
namespace nuclearNetwork {
Network::Network() :
m_config(Config::getInstance()),
m_logManager(Probe::LogManager::getInstance()),
m_logger(m_logManager.getLogger("log")) {
}
nuclearNetwork::NetOut nuclearNetwork::Network::evaluate(const NetIn &netIn) {
// You can throw an exception here or log a warning if it should never be used.
LOG_ERROR(m_logger, "nuclearNetwork::Network::evaluate() is not implemented");
throw std::runtime_error("nuclearNetwork::Network::evaluate() is not implemented");
}
}

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#ifndef APPROX8_H
#define APPROX8_H
#include <array>
#include <boost/numeric/odeint.hpp>
#include "network.h"
/**
* @file approx8.h
* @brief Header file for the Approx8 nuclear reaction network.
*
* This file contains the definitions and declarations for the Approx8 nuclear reaction network.
* The network is based on Frank Timmes' "aprox8" and includes 8 isotopes and various nuclear reactions.
* The rates are evaluated using a fitting function with coefficients from reaclib.jinaweb.org.
*/
/**
* @typedef vector_type
* @brief Alias for a vector of doubles using Boost uBLAS.
*/
typedef boost::numeric::ublas::vector< double > vector_type;
/**
* @typedef matrix_type
* @brief Alias for a matrix of doubles using Boost uBLAS.
*/
typedef boost::numeric::ublas::matrix< double > matrix_type;
/**
* @typedef vec7
* @brief Alias for a std::array of 7 doubles.
*/
typedef std::array<double,7> vec7;
namespace nnApprox8{
using namespace boost::numeric::odeint;
/**
* @struct Net
* @brief Contains constants and arrays related to the nuclear network.
*/
struct Net{
const static int ih1=0;
const static int ihe3=1;
const static int ihe4=2;
const static int ic12=3;
const static int in14=4;
const static int io16=5;
const static int ine20=6;
const static int img24=7;
const static int itemp=img24+1;
const static int iden =itemp+1;
const static int iener=iden+1;
const static int niso=img24+1; // number of isotopes
const static int nvar=iener+1; // number of variables
static constexpr std::array<int,niso> aion = {
1,
3,
4,
12,
14,
16,
20,
24
};
static constexpr std::array<double,niso> mion = {
1.67262164e-24,
5.00641157e-24,
6.64465545e-24,
1.99209977e-23,
2.32462686e-23,
2.65528858e-23,
3.31891077e-23,
3.98171594e-23
};
};
/**
* @brief Multiplies two arrays and sums the resulting elements.
* @param a First array.
* @param b Second array.
* @return Sum of the product of the arrays.
* @example
* @code
* vec7 a = {1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0};
* vec7 b = {0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5};
* double result = sum_product(a, b);
* @endcode
*/
double sum_product( const vec7 &a, const vec7 &b);
/**
* @brief Returns an array of T9 terms for the nuclear reaction rate fit.
* @param T Temperature in GigaKelvin.
* @return Array of T9 terms.
* @example
* @code
* double T = 1.5;
* vec7 T9_array = get_T9_array(T);
* @endcode
*/
vec7 get_T9_array(const double &T);
/**
* @brief Evaluates the nuclear reaction rate given the T9 array and coefficients.
* @param T9 Array of T9 terms.
* @param coef Array of coefficients.
* @return Evaluated rate.
* @example
* @code
* vec7 T9 = get_T9_array(1.5);
* vec7 coef = {1.0, 0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001};
* double rate = rate_fit(T9, coef);
* @endcode
*/
double rate_fit(const vec7 &T9, const vec7 &coef);
/**
* @brief Calculates the rate for the reaction p + p -> d.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double pp_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction p + d -> he3.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double dp_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction he3 + he3 -> he4 + 2p.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double he3he3_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction he3(he3,2p)he4.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double he3he4_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction he4 + he4 + he4 -> c12.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double triple_alpha_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction c12 + p -> n13.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double c12p_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction c12 + he4 -> o16.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double c12a_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction n14(p,g)o15 - o15 + p -> c12 + he4.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double n14p_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction n14(a,g)f18 assumed to go on to ne20.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double n14a_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction n15(p,a)c12 (CNO I).
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double n15pa_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction n15(p,g)o16 (CNO II).
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double n15pg_rate(const vec7 &T9);
/**
* @brief Calculates the fraction for the reaction n15(p,g)o16.
* @param T9 Array of T9 terms.
* @return Fraction of the reaction.
*/
double n15pg_frac(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction o16(p,g)f17 then f17 -> o17(p,a)n14.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double o16p_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction o16(a,g)ne20.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double o16a_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction ne20(a,g)mg24.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double ne20a_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction c12(c12,a)ne20.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double c12c12_rate(const vec7 &T9);
/**
* @brief Calculates the rate for the reaction c12(o16,a)mg24.
* @param T9 Array of T9 terms.
* @return Rate of the reaction.
*/
double c12o16_rate(const vec7 &T9);
/**
* @struct Jacobian
* @brief Functor to calculate the Jacobian matrix for implicit solvers.
*/
struct Jacobian {
/**
* @brief Calculates the Jacobian matrix.
* @param y State vector.
* @param J Jacobian matrix.
* @param t Time.
* @param dfdt Derivative of the state vector.
*/
void operator() ( const vector_type &y, matrix_type &J, double /* t */, vector_type &dfdt );
};
/**
* @struct ODE
* @brief Functor to calculate the derivatives for the ODE solver.
*/
struct ODE {
/**
* @brief Calculates the derivatives of the state vector.
* @param y State vector.
* @param dydt Derivative of the state vector.
* @param t Time.
*/
void operator() ( const vector_type &y, vector_type &dydt, double /* t */);
};
/**
* @class Approx8Network
* @brief Class for the Approx8 nuclear reaction network.
*/
class Approx8Network : public nuclearNetwork::Network {
public:
/**
* @brief Evaluates the nuclear network.
* @param netIn Input parameters for the network.
* @return Output results from the network.
*/
virtual nuclearNetwork::NetOut evaluate(const nuclearNetwork::NetIn &netIn);
/**
* @brief Sets whether the solver should use a stiff method.
* @param stiff Boolean indicating if a stiff method should be used.
*/
void setStiff(bool stiff);
/**
* @brief Checks if the solver is using a stiff method.
* @return Boolean indicating if a stiff method is being used.
*/
bool isStiff() { return m_stiff; }
private:
vector_type m_y;
double m_tmax;
double m_dt0;
bool m_stiff = false;
/**
* @brief Converts the input parameters to the internal state vector.
* @param netIn Input parameters for the network.
* @return Internal state vector.
*/
vector_type convert_netIn(const nuclearNetwork::NetIn &netIn);
};
} // namespace nnApprox8
#endif

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#ifndef NETWORK_H
#define NETWORK_H
#include <vector>
#include "probe.h"
#include "config.h"
#include "quill/Logger.h"
namespace nuclearNetwork {
/**
* @struct NetIn
* @brief Input structure for the network evaluation.
*
* This structure holds the input parameters required for the network evaluation.
*
* Example usage:
* @code
* nuclearNetwork::NetIn netIn;
* netIn.composition = {1.0, 0.0, 0.0};
* netIn.tmax = 1.0e6;
* netIn.dt0 = 1.0e-3;
* netIn.temperature = 1.0e8;
* netIn.density = 1.0e5;
* netIn.energy = 1.0e12;
* @endcode
*/
struct NetIn {
std::vector<double> composition; ///< Composition of the network
double tmax; ///< Maximum time
double dt0; ///< Initial time step
double temperature; ///< Temperature in Kelvin
double density; ///< Density in g/cm^3
double energy; ///< Energy in ergs
};
/**
* @struct NetOut
* @brief Output structure for the network evaluation.
*
* This structure holds the output results from the network evaluation.
*
* Example usage:
* @code
* nuclearNetwork::NetOut netOut = network.evaluate(netIn);
* std::vector<double> composition = netOut.composition;
* int steps = netOut.num_steps;
* double energy = netOut.energy;
* @endcode
*/
struct NetOut {
std::vector<double> composition; ///< Composition of the network after evaluation
int num_steps; ///< Number of steps taken in the evaluation
double energy; ///< Energy in ergs after evaluation
};
/**
* @class Network
* @brief Class for network evaluation.
*
* This class provides methods to evaluate the network based on the input parameters.
*
* Example usage:
* @code
* nuclearNetwork::Network network;
* nuclearNetwork::NetIn netIn;
* // Set netIn parameters...
* nuclearNetwork::NetOut netOut = network.evaluate(netIn);
* @endcode
*/
class Network {
public:
Network();
virtual ~Network() = default;
/**
* @brief Evaluate the network based on the input parameters.
*
* @param netIn Input parameters for the network evaluation.
* @return NetOut Output results from the network evaluation.
*/
virtual NetOut evaluate(const NetIn &netIn);
protected:
Config& m_config; ///< Configuration instance
Probe::LogManager& m_logManager; ///< Log manager instance
quill::Logger* m_logger; ///< Logger instance
};
} // namespace nuclearNetwork
#endif // NETWORK_H

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#include <gtest/gtest.h>
#include <string>
#include "approx8.h"
#include "config.h"
#include "network.h"
#include <vector>
std::string TEST_CONFIG = std::string(getenv("MESON_SOURCE_ROOT")) + "/tests/testsConfig.yaml";
class approx8Test : public ::testing::Test {};
/**
* @brief Test the constructor of the Config class.
*/
TEST_F(approx8Test, constructor) {
Config& config = Config::getInstance();
config.loadConfig(TEST_CONFIG);
EXPECT_NO_THROW(nnApprox8::Approx8Network());
}
TEST_F(approx8Test, setStiff) {
nnApprox8::Approx8Network network;
EXPECT_NO_THROW(network.setStiff(true));
EXPECT_TRUE(network.isStiff());
EXPECT_NO_THROW(network.setStiff(false));
EXPECT_FALSE(network.isStiff());
}
TEST_F(approx8Test, evaluate) {
nnApprox8::Approx8Network network;
nuclearNetwork::NetIn netIn;
std::vector<double> comp = {0.708, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
netIn.composition = comp;
netIn.temperature = 1e7;
netIn.density = 1e2;
netIn.energy = 0.0;
netIn.tmax = 3.15e17;
netIn.dt0 = 1e12;
nuclearNetwork::NetOut netOut;
EXPECT_NO_THROW(netOut = network.evaluate(netIn));
EXPECT_DOUBLE_EQ(netOut.composition[nnApprox8::Net::ih1], 0.50166260916650918);
EXPECT_DOUBLE_EQ(netOut.composition[nnApprox8::Net::ihe4],0.48172270591286032);
EXPECT_DOUBLE_EQ(netOut.energy, 1.6433049870528356e+18);
}

25
tests/network/meson.build Normal file
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@@ -0,0 +1,25 @@
# Test files for network
test_sources = [
'approx8Test.cpp',
]
foreach test_file : test_sources
exe_name = test_file.split('.')[0]
message('Building test: ' + exe_name)
# Create an executable target for each test
test_exe = executable(
exe_name,
test_file,
dependencies: [gtest_dep, network_dep, gtest_main],
include_directories: include_directories('../../src/network/public'),
link_with: libnetwork, # Link the dobj library
install_rpath: '@loader_path/../../src' # Ensure runtime library path resolves correctly
)
# Add the executable as a test
test(
exe_name,
test_exe,
env: ['MESON_SOURCE_ROOT=' + meson.project_source_root(), 'MESON_BUILD_ROOT=' + meson.project_build_root()])
endforeach