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Merge pull request #39 from hrosiak/reactions2

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Reactions2
This commit is contained in:
Andrej Prochazka 2018-07-31 17:46:04 +02:00 committed by GitHub
parent faa2b22271 7566c90cf3
commit 852ce689fe
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
17 changed files with 374 additions and 19 deletions
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1
.gitignore vendored
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@ -35,3 +35,4 @@
ana/*
benchmark/*
build/*
.vscode/*

12
CMakeLists.txt
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@ -11,6 +11,7 @@ option(GENERATE_DATA "make data tables generator" OFF)
option(THIN_TARGET_APPROXIMATION "thin target approximation" ON)
option(DOCS "build documentation (requires doxygen)" OFF)
option(GLOBAL "build with global, sources are required" OFF)
option(REACTIONS "enable/disable nuclear reaction rate" ON)
option(APPS "build catima applications" ON)
######## build type ############
@ -51,6 +52,14 @@ if(PYTHONINTERP_FOUND)
message("-- Python found: ${PYTHON_EXECUTABLE}")
endif()
find_package(nurex QUIET)
if(nurex_FOUND)
message(STATUS "nurex library found")
set(NUREX ON)
list(APPEND EXTRA_LIBS nurex::nurex)
endif(nurex_FOUND)
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/build_config.in"
"${CMAKE_CURRENT_BINARY_DIR}/include/catima/build_config.h"
@ -79,7 +88,7 @@ set_target_properties(catima_static
POSITION_INDEPENDENT_CODE ON
ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib
)
target_link_libraries(catima ${EXTRA_LIBS} ${GSL_LIBRARIES} )
target_link_libraries(catima ${EXTRA_LIBS} ${GSL_LIBRARIES})
target_link_libraries(catima_static ${EXTRA_LIBS} ${GSL_LIBRARIES})
target_include_directories(catima
@ -140,6 +149,7 @@ if(EXAMPLES)
#add_subdirectory("examples")
endif(EXAMPLES)
if(TESTS)
enable_testing()
add_subdirectory("tests")
endif(TESTS)

3
build_config.in
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@ -4,6 +4,7 @@
#cmakedefine THIN_TARGET_APPROXIMATION
#cmakedefine GSL_INTEGRATION
#cmakedefine GLOBAL
#cmakedefine REACTIONS
#cmakedefine NUREX
#endif

9
catima.cpp
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@ -9,6 +9,9 @@
#include "catima/storage.h"
#include "catima/nucdata.h"
#include "catima/calculations.h"
#ifdef REACTIONS
#include "catima/reactions.h"
#endif
namespace catima{
@ -251,6 +254,9 @@ Result calculate(Projectile &p, const Material &t, const Config &c){
}
res.sigma_r = sqrt(range_straggling_spline(T));
res.Eloss = (res.Ein - res.Eout)*p.A;
#ifdef REACTIONS
res.sp = nonreaction_rate(p,t,c);
#endif
return res;
}
@ -268,6 +274,9 @@ MultiResult calculate(Projectile &p, const Layers &layers, const Config &c){
res.total_result.sigma_E += r.sigma_E*r.sigma_E;
res.total_result.tof += r.tof;
res.total_result.Eout = r.Eout;
#ifdef REACTIONS
res.total_result.sp = (r.sp>=0.0)?res.total_result.sp*r.sp:-1;
#endif
res.results.push_back(r);
}
if(e>Ezero){

1
catima.h
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@ -21,7 +21,6 @@
#include <vector>
// #define NDEBUG
#include "catima/build_config.h"
#include "catima/config.h"
#include "catima/constants.h"
#include "catima/structures.h"

4
catima.pyx
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@ -192,6 +192,7 @@ cdef class Result:
cdef public double sigma_a
cdef public double sigma_r
cdef public double tof
cdef public double sp
def __init__(self):
self.Ein=0.0
self.Eout=0.0
@ -203,6 +204,7 @@ cdef class Result:
self.sigma_a=0.0
self.sigma_r=0.0
self.tof=0.0
self.sp=1.0
def get_dict(self):
return {"Ein":self.Ein,
@ -215,6 +217,7 @@ cdef class Result:
"sigma_a":self.sigma_a,
"sigma_r":self.sigma_r,
"tof":self.tof,
"sp":self.sp,
}
def __getitem__(self,key):
@ -233,6 +236,7 @@ cdef class Result:
self.sigma_a=val.sigma_a
self.sigma_r=val.sigma_r
self.tof=val.tof
self.sp=val.sp
cdef class MultiResult:
cdef public Result total_result

2
catimac.pxd
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@ -32,6 +32,7 @@ cdef extern from "catima/structures.h" namespace "catima":
double sigma_a
double sigma_r
double tof
double sp
cdef cppclass MultiResult:
vector[Result] results
@ -111,6 +112,7 @@ cdef extern from "catima/constants.h" namespace "catima":
int max_storage_data "catima::max_storage_data"
int logEmin "catima::logEmin"
int logEmax "catima::logEmax"
bool reactions "catima::reactions"
cdef extern from "catima/storage.h" namespace "catima":
cdef cppclass Interpolator:

22
config.h
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@ -1,7 +1,6 @@
/// \file config.h
#ifndef CONFIG
#define CONFIG
#include <cstring>
namespace catima{
@ -23,17 +22,18 @@ namespace catima{
/**
* enum to select which calculation to skip
*/
enum skip_calculation:char{
enum skip_calculation:unsigned char{
skip_none = 0,
skip_tof = 1,
skip_sigma_a = 2,
skip_sigma_r = 4
skip_sigma_r = 4,
skip_reactions = 128
};
/**
* enum to select which dEdx correction to skip
*/
enum corrections:char{
enum corrections:unsigned char{
no_barkas = 1,
no_lindhard = 2,
no_shell_correction = 4
@ -42,7 +42,7 @@ namespace catima{
/**
* enum to select which dEdx straggling options
*/
enum omega:char{
enum omega:unsigned char{
atima = 0,
bohr = 1,
};
@ -56,11 +56,15 @@ namespace catima{
*
*/
struct Config{
char z_effective=z_eff_type::pierce_blann;
unsigned char z_effective=z_eff_type::pierce_blann;
//char z_effective=z_eff_type::atima14;
char skip=skip_none;
char dedx = 0;
char dedx_straggling = omega::atima;
unsigned char dedx = 0;
unsigned char dedx_straggling = omega::atima;
#ifdef REACTIONS
unsigned char skip=skip_none;
#else
unsigned char skip=skip_calculation::skip_reactions;
#endif
};
extern Config default_config;

9
constants.h
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@ -1,7 +1,7 @@
#ifndef CONSTANTS_H
#define CONSTANTS_H
#include <limits>
#include "catima/build_config.h"
namespace catima {
constexpr double Ezero = 1E-3; // lowest E to calculate, below taken as 0
@ -20,6 +20,13 @@ constexpr double int_eps_tof = 0.01;
*/
constexpr double thin_target_limit = 1 - 1e-3;
#ifdef REACTIONS
constexpr double emin_reaction = 30.0;
constexpr bool reactions = true;
#else
constexpr bool reactions = false;
#endif
constexpr double Avogadro = 6.022140857; // 10^23
constexpr double electron_mass = 0.510998928; // MeV/c^2

86
reactions.cpp Normal file
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@ -0,0 +1,86 @@
#include "catima/reactions.h"
#include "catima/catima.h"
#include "catima/abundance_database.h"
#include "catima/storage.h"
#include <cmath>
#include <iostream>
#ifdef NUREX
#include "nurex/Parametrization.h"
using nurex::SigmaR_Kox;
#else
using catima::SigmaR_Kox;
#endif
namespace catima{
double nonreaction_rate(Projectile &projectile, const Material &target, const Config &c){
if(projectile.T<emin_reaction)return -1.0;
if(target.thickness()<=0.0)return 1.0;
int ap = lround(projectile.A);
int zp = lround(projectile.Z);
int zt = target.get_element(0).Z;
int at = abundance::get_isotope_a(zt,0); // most abundand natural isotope mass
auto data = _storage.Get(projectile,target,c);
Interpolator range_spline(energy_table.values,data.range.data(),energy_table.num);
if(energy_out(projectile.T, target.thickness(), range_spline) < emin_reaction)return -1.0;
auto sigma_r = [&](double th){
double stn_sum=0.0, sum=0.0;
double e = energy_out(projectile.T, th, range_spline);
for(unsigned int i = 0;i<target.ncomponents();i++){
stn_sum += target.molar_fraction(i);
sum += target.molar_fraction(i)*SigmaR_Kox(ap,zp,e,at,zt);
}
return sum/stn_sum;
};
//nurex::Nucleus nurex_projectile = nurex::get_default_nucleus(ap,zp);
//nurex::Nucleus nurex_target = nurex::get_default_nucleus(at,zt);
//nurex::GlauberModelOLA_ZeroRange gm(nurex_projectile, nurex_target);
//double cs = nurex::SigmaR_Kox(ap,zp,projectile.T,);
double cs0 = sigma_r(0);
double cs1 = sigma_r(target.thickness());
double cs;
if(std::abs(cs0-cs1)/cs0 < 0.05){
cs = target.number_density_cm2()*(cs0 + cs1)/2.0;
}
else{
cs = catima::integrator.integrate(sigma_r,0,target.number_density_cm2());
}
return exp(-cs*0.0001);
}
}
#ifndef NUREX
double SigmaR_Kox(int Ap, int Zp, double E, int At, int Zt){
constexpr double rc = 1.3;
constexpr double r0 = 1.1;
constexpr double a = 1.85;
constexpr double c1 = 2-(10.0/(1.5*1.5*1.5*1.5*1.5));
double Ap13 = pow(Ap,1.0/3.0);
double At13 = pow(At,1.0/3.0);
double D = 5.0*(At-2*Zt)*Zp/(Ap*At);
double Bc = Zp*Zt/(rc*(Ap13+At13));
double logE = std::log10(E);
double c = 0;
if(logE < 1.5){
c = c1*std::pow(logE/1.5,3);
}
else{
c = (-10.0/std::pow(logE,5)) + 2;
}
double Rs = r0 * ((a*Ap13*At13)/(Ap13+At13)-c)+D;
double Rv = r0 * (Ap13 + At13);
double Ri = Rv + Rs;
double Ecm = Ecm_from_T_relativistic(E,Ap,At);
return 10.0*PI*Ri*Ri*(1-(Bc/Ecm));
}
#endif

74
reactions.h Normal file
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@ -0,0 +1,74 @@
/*
* Author: Andrej Prochazka
* Copyright(C) 2017
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* This program 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 Affero General Public License for more details.
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef REACTIONS_H
#define REACTIONS_H
#include "catima/build_config.h"
#ifdef NUREX
#include "catima/structures.h"
#include "catima/config.h"
#include "catima/integrator.h"
#include <cmath>
namespace catima{
/**
* return reaction probability
* @param sigma - cross section in mb
* @param t - number of targets per cm2 in 10^23 unit
*/
inline double reaction_rate(double sigma, double t){
return 1.0 - std::exp(-sigma*t*0.0001);
}
/**
* return nonreaction rate
* @param sigma - cross section in mb
* @param t - number of targets per cm2 in 10^23 unit
*/
inline double nonreaction_rate(double sigma, double t){
return std::exp(-sigma*t*0.0001);
}
template<typename F>
double reaction_rate(F& f, double t){
GaussLegendreIntegration<8> ii;
double i = ii.integrate(f,0,t);
return 1.0 - std::exp(-i*0.0001);
}
double nonreaction_rate(Projectile &projectile, const Material &target, const Config &c=default_config);
}
#else
double SigmaR_Kox(int Ap, int Zp, double E, int At, int Zt);
inline double p_from_T(double T, double M=1.0){
return M*sqrt(T*T + 2*T*atomic_mass_unit);
}
inline double Ecm_from_T_relativistic(double T, double Ap, double At){
double mp = Ap*atomic_mass_unit;
double mt = At*atomic_mass_unit;
double plab= p_from_T(T,Ap);
double elab = sqrt(plab*plab + mp*mp);
double ecm = sqrt(mp*mp + mt*mt + 2*elab*mt);
double pcm = plab * mt / ecm;
return sqrt(pcm*pcm+mp*mp)-mp;
}
#endif //NUREX
#endif

8
structures.cpp
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@ -27,15 +27,19 @@ bool operator==(const Material &a, const Material&b){
}
Material::Material(std::initializer_list<std::array<double,3>>list,double _density, double _ipot):rho(_density),i_potential(_ipot){
Material::Material(std::initializer_list<std::array<double,3>>list,double _density, double _ipot, double mass):rho(_density),i_potential(_ipot){
std::initializer_list<std::array<double,3>>::iterator it;
atoms.reserve(list.size());
for ( it=list.begin(); it!=list.end(); ++it){
add_element((*it)[0],(*it)[1],(*it)[2]);
}
if(mass!=0.0){
molar_mass=mass;
}
else{
calculate(); // calculate if needed, ie average molar mass
}
}
Material::Material(double _a, int _z, double _rho, double _th):rho(_rho),th(_th){

48
structures.h
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@ -20,6 +20,7 @@
#include <vector>
#include <array>
#include <initializer_list>
#include "catima/constants.h"
namespace catima{
@ -89,7 +90,7 @@ namespace catima{
});
* \endcode
*/
Material(std::initializer_list<std::array<double,3>>list,double _density=0.0, double ipot = 0.0);
Material(std::initializer_list<std::array<double,3>>list,double _density=0.0, double ipot = 0.0, double mass=0.0);
/**
* calculates internal variables if needed
@ -133,6 +134,11 @@ namespace catima{
*/
double M() const {return molar_mass;}
/**
* sets molar mass of the Material
*/
Material& M(double mass){molar_mass=mass; return *this;}
/**
* @return returns density in g/cm^3
*/
@ -153,6 +159,11 @@ namespace catima{
*/
Material& thickness(double val){th = val;return *this;};
/**
* set length in cm, density should be set before
*/
Material& thickness_cm(double l){th = rho*l; return *this;}
/**
* set the mean ionization potential, if non elemental I should be used
*/
@ -164,6 +175,38 @@ namespace catima{
*/
double I() const {return i_potential;};
/**
* return number density of atoms/molecules per cm3 in 10^23 units
*/
double number_density()const{
return Avogadro*rho/molar_mass;
}
/**
* return number density of atoms of i-th element in 10^23 units
*/
double number_density(int i)const{
if(i>=atoms.size())return 0.0;
return number_density()*molar_fraction(i);
}
/**
* return number density of atoms/molecules per cm2 in 10^23 units
*/
double number_density_cm2()const{
return Avogadro*th/molar_mass;
}
/**
* return number density of atoms per cm2 of i-th element in 10^23 units
*/
double number_density_cm2(int i)const{
if(i>=atoms.size())return 0.0;
return number_density_cm2()*molar_fraction(i);
}
friend bool operator==(const Material &a, const Material&b);
};
@ -184,6 +227,9 @@ namespace catima{
double sigma_a=0.0;
double sigma_r=0.0;
double tof=0.0;
#ifdef REACTIONS
double sp = 1.0;
#endif
};
/**

6
tests/CMakeLists.txt
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@ -1,4 +1,3 @@
enable_testing()
add_definitions(-Dlest_FEATURE_COLOURISE=1)
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/tests)
@ -10,6 +9,11 @@ foreach(entry ${CATIMA_TESTS})
add_test(${entry} ${PROJECT_BINARY_DIR}/tests/${entry})
endforeach(entry in ${CATIMA_TESTS})
if(REACTIONS)
add_executable(test_reaction test_reaction.cpp)
target_link_libraries(test_reaction catima)
add_test(test_reaction ${PROJECT_BINARY_DIR}/tests/test_reaction)
endif(REACTIONS)
set(C_TESTS test_c)
MESSAGE( STATUS "CMAKE_C_COMPILER: " ${CMAKE_C_COMPILER} )

7
tests/test_calculations.cpp
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@ -313,6 +313,13 @@ const lest::test specification[] =
EXPECT(res.Eout == approx(345.6).epsilon(1.0));
EXPECT(res.sigma_a == approx(0.0013).epsilon(1e-4));
EXPECT(res.sigma_E == approx(0.12).epsilon(1e-3));
EXPECT(res.dEdxi == approx(103.5).epsilon(1e-1));
res = catima::calculate(p(150),air);
EXPECT(res.dEdxi == approx(173.6).epsilon(1e0));
res = catima::calculate(p(1000),air);
EXPECT(res.dEdxi == approx(70.69).epsilon(1e-0));
auto water = catima::get_material(catima::material::Water);
auto res2 = catima::calculate(p(600),water,600);

50
tests/test_reaction.cpp Normal file
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@ -0,0 +1,50 @@
#include "lest.hpp"
#include <math.h>
#include "catima/catima.h"
#include "catima/reactions.h"
#include "testutils.h"
using namespace std;
using catima::approx;
using catima::reaction_rate;
using catima::nonreaction_rate;
const lest::test specification[] =
{
CASE("reaction"){
catima::Projectile proj{12,6,6,870};
auto c = catima::get_material(6);
auto h = catima::get_material(1);
catima::Material water({{0,8,2},{0,1,1}},1.0);
c.thickness(2.0);
double r;
r= catima::nonreaction_rate(proj, c);
EXPECT(r == approx(0.92,0.02));
catima::Layers l;
l.add(c);
l.add(c);
l.add(c);
auto res = catima::calculate(proj,l);
EXPECT(res.total_result.sp == approx(r*r*r,0.02));
c.thickness(6.0);
r= catima::nonreaction_rate(proj, c);
EXPECT(res.total_result.sp == approx(r,0.001));
c.thickness(0.0);
r= catima::nonreaction_rate(proj, c);
EXPECT(r == 1.0);
proj.T = 0.0;
c.thickness(6);
r= catima::nonreaction_rate(proj, c);
EXPECT(r == -1.0);
}
};
int main( int argc, char * argv[] )
{
return lest::run( specification, argc, argv );
}

47
tests/test_structures.cpp
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@ -57,6 +57,15 @@ const lest::test specification[] =
SECTION("default ionisation potential"){
EXPECT(graphite.I()==0.0);
}
SECTION("length"){
water.density(1.0);
water.thickness(1.0);
EXPECT(water.thickness()==approx(1.0,0.0001));
water.thickness_cm(1.0);
EXPECT(water.thickness()==approx(1.0,0.0001));
water.thickness_cm(2.0);
EXPECT(water.thickness()==approx(2.0,0.0001));
}
}
},
CASE("Material automatic atomic weight"){
@ -242,6 +251,8 @@ const lest::test specification[] =
{0, 8, 1}
});
auto air = catima::get_material(catima::material::Air);
EXPECT(water1.weight_fraction(0)==0.111898);
EXPECT(water2.weight_fraction(0)==approx(water1.weight_fraction(0)).R(1e-5));
EXPECT(water1.weight_fraction(1)==0.888102);
@ -263,6 +274,42 @@ const lest::test specification[] =
EXPECT(mat.M()==approx(12.0,0.001));
EXPECT(mat.weight_fraction(0)==approx(1.0).R(1e-6));
EXPECT(air.M() == approx(28.97,0.1));
},
CASE("number density"){
catima::Material c({12.0,6,1});
auto water = catima::get_material(catima::material::Water);
auto air = catima::get_material(catima::material::Air);
water.density(0.9982);
c.density(3.513);
air.density(1.2041e-3);
c.thickness_cm(1.0);
EXPECT(c.number_density()==approx(1.7662,0.01));
EXPECT(c.number_density_cm2()==approx(1.7662,0.01));
EXPECT(c.number_density(0)==approx(1.7662,0.01));
EXPECT(c.number_density_cm2(0)==approx(1.7662,0.01));
EXPECT(c.number_density(1)==0.0);
EXPECT(c.number_density_cm2(1)==0.0);
c.thickness_cm(2.0);
EXPECT(c.number_density()==approx(1.7662,0.01));
EXPECT(c.number_density_cm2()==approx(2.0*1.7662,0.01));
water.thickness_cm(1.0);
EXPECT(water.number_density()==approx(0.3336,0.001));
EXPECT(water.number_density_cm2()==approx(0.3336,0.001));
EXPECT(water.number_density(0)==approx(2*0.3336,0.001));
EXPECT(water.number_density_cm2(0)==approx(2*0.3336,0.001));
EXPECT(water.number_density(1)==approx(0.3336,0.001));
EXPECT(water.number_density_cm2(1)==approx(0.3336,0.001));
water.thickness_cm(3.0);
EXPECT(water.number_density_cm2()==approx(3.0*0.3336,0.001));
air.thickness_cm(1.0);
EXPECT(air.number_density(0)==approx(air.molar_fraction(0)*2*0.0002504,0.00001));
EXPECT(air.number_density(1)==approx(air.molar_fraction(1)*2*0.0002504,0.00001));
EXPECT(air.number_density(2)==approx(air.molar_fraction(2)*1*0.0002504,0.00001));
}
};