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catima/pymodule/pycatima.cpp

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pybind module
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#include <stdexcept>
#include <pybind11/pybind11.h>
#include <pybind11/operators.h>
#include <pybind11/numpy.h>
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#include <pybind11/stl.h>
pybind module
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#include "catima/catima.h"
#include "catima/srim.h"
#include "catima/nucdata.h"
#include <iostream>
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#include <string>
pybind module
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namespace py = pybind11;
using namespace catima;
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std::string catima_info(){
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return "CATIMA version = 1.6\n";
pybind module
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}
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std::string material_to_string(const Material &r){
std::string s;
auto n = r.ncomponents();
for(int i = 0; i < n; i++){
auto el = r.get_element(i);
s += "#"+std::to_string(i);
info fix
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s += ": A = "+std::to_string(el.A) + ", Z = "+std::to_string(el.Z)+ ", stn = "+std::to_string(el.stn)+"\n";
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}
return s;
};
pybind module
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py::list storage_info(){
py::list res;
for(int i=0; i<max_storage_data;i++){
auto& data = _storage.Get(i);
if(data.p.A>0 && data.p.Z && data.m.ncomponents()>0){
py::list mat;
py::dict d;
py::list p;
p.append(data.p.A);
p.append(data.p.Z);
d["projectile"] = p;
info fix
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d["matter"] = material_to_string(data.m);
pybind module
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d["config"] = py::cast(data.config);
res.append(d);
}
}
return res;
}
py::list get_energy_table(){
py::list r;
for(auto e : energy_table){
r.append(e);
}
return r;
}
py::list get_data(Projectile& p, const Material &m, const Config& c=default_config){
py::list r;
auto& data = _storage.Get(p, m, c);
py::list ran;
py::list rans;
py::list av;
refactoring
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for(double e:data.range){ran.append(e);}
pybind module
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for(double e:data.range_straggling)rans.append(e);
for(double e:data.angular_variance)av.append(e);
r.append(ran);
r.append(rans);
r.append(av);
return r;
}
refactoring
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Material py_make_material(py::list d, double density=0.0, double thickness=0.0, double ipot=0.0, double mass=0.0){
pybind module
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Material m;
if(density>0.0)m.density(density);
if(ipot>0.0)m.I(ipot);
if(mass>0.0)m.M(mass);
refactoring
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if(thickness>0.0)m.thickness(thickness);
pybind module
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for(int i=0;i<d.size();i++){
py::list e(d[i]);
if(e.size() != 3)throw std::invalid_argument("invalid Material constructor argument");
double a = e[0].cast<double>();
int z = e[1].cast<int>();
double stn = e[2].cast<double>();
m.add_element(a,z,stn);
}
return m;
}
pymodule
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py::dict get_result_dict(const Result& r){
py::dict d;
d["Ein"] = r.Ein;
d["Eout"] = r.Eout;
d["Eloss"] = r.Eloss;
d["range"] = r.range;
d["dEdxi"] = r.dEdxi;
d["dEdxo"] = r.dEdxo;
d["sigma_E"] = r.sigma_E;
d["sigma_r"] = r.sigma_r;
d["sigma_a"] = r.sigma_a;
position scattering added to py results
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d["sigma_x"] = r.sigma_x;
pymodule
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d["tof"] = r.tof;
d["sp"] = r.sp;
return d;
}
pybind module
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PYBIND11_MODULE(pycatima,m){
py::class_<Projectile>(m,"Projectile")
.def(py::init<>(),"constructor")
.def(py::init<double, double, double, double>(), "constructor", py::arg("A"),py::arg("Z"),py::arg("Q")=0, py::arg("T")=0)
.def("__call__",&Projectile::operator())
.def("A",[](const Projectile& p){return p.A;})
.def("Z",[](const Projectile& p){return p.Z;})
.def("Q",[](const Projectile& p){return p.Q;})
.def("T",[](const Projectile& p){return p.T;})
.def("T",[](Projectile& p, double v){p.T = v;});
//.def_readwrite("A", &Projectile::A)
//.def_readwrite("Z", &Projectile::Z)
//.def_readwrite("T", &Projectile::T)
//.def_readwrite("Q", &Projectile::Q);
u3
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py::class_<Target>(m,"Target")
.def(py::init<>(),"constructor")
.def_readwrite("A",&Target::A)
.def_readwrite("Z",&Target::Z)
.def_readwrite("stn",&Target::stn);
py functions
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u3
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pybind module
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py::class_<Material>(m,"Material")
.def(py::init<>(),"constructor")
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.def(py::init<const Material&>(),"constructor")
.def(py::init<double, int, double, double, double>(),"constructor", py::arg("A"),py::arg("Z"),py::arg("density")=0.0,py::arg("thickness")=0.0,py::arg("i_potential")=0.0)
.def(py::init(&py_make_material),"constructor", py::arg("elements"),py::arg("density")=0.0,py::arg("thickness")=0.0,py::arg("i_potential")=0.0, py::arg("mass")=0.0)
pybind module
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.def("add_element",&Material::add_element)
.def("ncomponents",&Material::ncomponents)
.def("density",py::overload_cast<>(&Material::density, py::const_), "get density")
.def("density",py::overload_cast<double>(&Material::density), "set density")
.def("molar_mass",py::overload_cast<>(&Material::M, py::const_), "get mass")
.def("thickness",py::overload_cast<>(&Material::thickness, py::const_), "get thickness")
.def("thickness",py::overload_cast<double>(&Material::thickness), "set thickness")
py thickness f. added
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.def("thickness_cm",py::overload_cast<>(&Material::thickness_cm, py::const_),"get thickness in cm unit")
dx partial
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.def("thickness_cm",py::overload_cast<double>(&Material::thickness_cm),"set thickness in cm unit")
pybind module
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.def("I",py::overload_cast<>(&Material::I, py::const_), "get I")
storage info bug
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.def("I",py::overload_cast<double>(&Material::I), "set I")
info fix
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.def("__str__",&material_to_string);
pybind module
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py::class_<Layers>(m,"Layers")
.def(py::init<>(),"constructor")
python add overload fix
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.def("add",py::overload_cast<Material>(&Layers::add))
.def("add_layers",py::overload_cast<const Layers&>(&Layers::add))
pybind module
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.def("num",&Layers::num)
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.def("thickness",&Layers::thickness)
.def("thickness_cm",&Layers::thickness_cm)
refactoring
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// .def("__getitem__",&Layers::operator[], py::is_operator())
.def("__getitem__",[](Layers &r, int i)->Material*
{
if(i>=r.num()){
throw std::invalid_argument("index out of range");}
return &r[i];
}, py::is_operator(),py::return_value_policy::automatic_reference)
pybind module
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.def("get",&Layers::operator[])
refactoring
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.def(py::self + py::self)
.def("__add__",[](const Layers s, const Material& m){return s+m;});
pybind module
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py::class_<Result>(m,"Result")
.def(py::init<>(),"constructor")
.def_readwrite("Ein", &Result::Ein)
.def_readwrite("Eout", &Result::Eout)
.def_readwrite("Eloss", &Result::Eloss)
.def_readwrite("range", &Result::range)
.def_readwrite("dEdxi", &Result::dEdxi)
.def_readwrite("dEdxo", &Result::dEdxo)
.def_readwrite("sigma_E", &Result::sigma_E)
.def_readwrite("sigma_a", &Result::sigma_a)
.def_readwrite("sigma_r", &Result::sigma_r)
position scattering added to py results
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.def_readwrite("sigma_x", &Result::sigma_x)
pybind module
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.def_readwrite("tof", &Result::tof)
.def_readwrite("sp", &Result::sp)
repr
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.def("get_dict",&get_result_dict)
.def("__repr__",[](const Result &self){
return py::str(get_result_dict(self));
});
pybind module
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py::class_<MultiResult>(m,"MultiResult")
.def(py::init<>(),"constructor")
.def_readwrite("total_result", &MultiResult::total_result)
.def_readwrite("results", &MultiResult::results)
refactoring
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// .def_readwrite("Eout",&MultiResult::total_result.Eout)
.def("__getitem__",[](MultiResult &r, int i){
return py::cast(r.results[i]);
pymodule
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},py::is_operator())
refactoring
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.def("__getattr__",[](MultiResult &r, std::string& k){
if(k.compare("Eout")==0){
return py::cast(r.total_result.Eout);
}
else if(k.compare("sigma_a")==0){
return py::cast(r.total_result.sigma_a);
}
else if(k.compare("tof")==0){
return py::cast(r.total_result.tof);
}
else if(k.compare("Eloss")==0){
return py::cast(r.total_result.Eloss);
}
else{
return py::cast(NULL);
}
pymodule
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},py::is_operator())
.def("get_dict",[](const MultiResult &r){
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py::dict d;
py::list p;
pymodule
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d["result"] = get_result_dict(r.total_result);
pybind module
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for(auto& entry:r.results){
pymodule
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p.append(get_result_dict(entry));
pybind module
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}
d["partial"] = p;
return d;
repr
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})
.def("__repr__",[](const MultiResult &r){
py::dict d;
py::list p;
d["result"] = get_result_dict(r.total_result);
for(auto& entry:r.results){
p.append(get_result_dict(entry));
}
d["partial"] = p;
return py::str(d);
});
pybind module
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py::enum_<z_eff_type>(m,"z_eff_type")
.value("none", z_eff_type::none)
.value("pierce_blann", z_eff_type::pierce_blann)
.value("anthony_landorf", z_eff_type::anthony_landorf)
.value("hubert", z_eff_type::hubert)
.value("winger", z_eff_type::winger)
.value("schiwietz", z_eff_type::schiwietz)
u3
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.value("cglobal", z_eff_type::global)
pybind module
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.value("atima14", z_eff_type::atima14);
py::enum_<corrections>(m,"corrections")
.value("no_barkas", corrections::no_barkas)
.value("no_lindhard", corrections::no_lindhard)
.value("no_shell_correction", corrections::no_shell_correction)
.value("no_highenergy", corrections::no_highenergy);
py::enum_<omega_types>(m,"omega_types")
.value("atima", omega_types::atima)
.value("bohr", omega_types::bohr);
py::enum_<low_energy_types>(m,"low_energy_types")
.value("srim_85", low_energy_types::srim_85)
.value("srim_95", low_energy_types::srim_95);
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py::enum_<scattering_types>(m,"scattering_types")
.value("fermi_rossi", scattering_types::fermi_rossi)
scattering update and syncing from local
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.value("dhighland", scattering_types::dhighland)
.value("gottschalk", scattering_types::gottschalk)
improved angular scattering
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.value("atima_scattering", scattering_types::atima_scattering);
pybind module
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py::enum_<material>(m,"material")
added all materials to py module
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.value("Plastics", material::Plastics)
.value("Air", material::Air)
.value("CH2", material::CH2)
.value("lH2", material::lH2)
.value("lD2", material::lD2)
.value("Water", material::Water)
.value("Diamond", material::Diamond)
.value("Glass", material::Glass)
.value("ALMG3", material::ALMG3)
.value("ArCO2_30", material::ArCO2_30)
.value("CF4", material::CF4)
.value("Isobutane", material::Isobutane)
.value("Kapton", material::Kapton)
.value("Mylar", material::Mylar)
.value("NaF", material::NaF)
.value("P10", material::P10)
.value("Polyolefin", material::Polyolefin)
.value("CmO2", material::CmO2)
.value("Suprasil", material::Suprasil)
.value("HAVAR", material::HAVAR)
.value("Steel", material::Steel)
.value("CO2", material::CO2)
.value("Methane", material::Methane)
.value("Methanol", material::Methanol)
.value("Acetone", material::Acetone)
.value("Acetylene", material::Acetylene)
.value("Adenine", material::Adenine)
.value("Adipose_Tissue", material::Adipose_Tissue)
.value("Alanine", material::Alanine)
.value("Bakelite", material::Bakelite)
.value("AgBr", material::AgBr)
.value("AgCl", material::AgCl)
.value("AgI", material::AgI)
.value("Al2O3", material::Al2O3)
.value("Amber", material::Amber)
.value("Ammonia", material::Ammonia)
.value("Aniline", material::Aniline)
.value("Anthracene", material::Anthracene)
.value("A_150", material::A_150)
.value("B_100", material::B_100)
.value("BaF2", material::BaF2)
.value("BaSO4", material::BaSO4)
.value("Benzene", material::Benzene)
.value("BeO", material::BeO)
.value("BGO", material::BGO)
.value("Blood_ICRP", material::Blood_ICRP)
.value("Bone_Compact", material::Bone_Compact)
.value("Bone_Cortical", material::Bone_Cortical)
.value("Brain_ICRP", material::Brain_ICRP)
.value("B4C", material::B4C)
.value("BC_400", material::BC_400)
.value("nButanol", material::nButanol)
.value("C_552", material::C_552)
.value("CdTe", material::CdTe)
.value("CdWO4", material::CdWO4)
.value("CaCO3", material::CaCO3)
.value("CaF2", material::CaF2)
.value("CaO", material::CaO)
.value("CaWO4", material::CaWO4)
.value("CsF", material::CsF)
.value("CsI", material::CsI)
.value("CCl4", material::CCl4)
.value("Tetrachloroethylene", material::Tetrachloroethylene)
.value("Cellophane", material::Cellophane)
.value("Chlorobenzene", material::Chlorobenzene)
.value("Chloroform", material::Chloroform)
.value("Cyclohexane", material::Cyclohexane)
.value("Concrete", material::Concrete)
.value("Diethyl_Ether", material::Diethyl_Ether)
.value("Ethane", material::Ethane)
.value("Ethanol", material::Ethanol)
.value("Ethylene", material::Ethylene)
.value("Eye_lens", material::Eye_lens)
.value("Fe2O3", material::Fe2O3)
.value("FeO", material::FeO)
.value("Freon_12", material::Freon_12)
.value("Freon_12B2", material::Freon_12B2)
.value("Freon_13", material::Freon_13)
.value("Freon_13B1", material::Freon_13B1)
.value("Freon_13I1", material::Freon_13I1)
.value("Gd2O2S", material::Gd2O2S)
.value("GaAs", material::GaAs)
.value("Gel_Photo_Emulsion", material::Gel_Photo_Emulsion)
.value("Glass_Pyrex", material::Glass_Pyrex)
.value("Glass_Lead", material::Glass_Lead)
.value("Glucose", material::Glucose)
.value("Glutamine", material::Glutamine)
.value("Glycerol", material::Glycerol)
.value("Guanine", material::Guanine)
.value("Gypsum", material::Gypsum)
.value("nHeptane", material::nHeptane)
.value("nHexane", material::nHexane)
.value("KI", material::KI)
.value("K2O", material::K2O)
.value("LaBr3", material::LaBr3)
.value("LaOBr", material::LaOBr)
.value("La2O2S", material::La2O2S)
.value("Lung", material::Lung)
.value("MgCO3", material::MgCO3)
.value("MgF2", material::MgF2)
.value("MgO", material::MgO)
.value("MS20_Tissue", material::MS20_Tissue)
.value("Muscle_skeletal", material::Muscle_skeletal)
.value("Muscle_strained", material::Muscle_strained)
.value("Muscle_sucrose", material::Muscle_sucrose)
.value("Muscle_no_sucrose", material::Muscle_no_sucrose)
.value("Na2CO3", material::Na2CO3)
.value("NaI", material::NaI)
.value("NaCl", material::NaCl)
.value("Na2O", material::Na2O)
.value("NaNO3", material::NaNO3)
.value("Naphthalene", material::Naphthalene)
.value("Nitrobenzene", material::Nitrobenzene)
.value("N2O", material::N2O)
.value("Octane", material::Octane)
.value("Paraffin", material::Paraffin)
.value("nPentane", material::nPentane)
.value("PhotoEmulsion", material::PhotoEmulsion)
.value("PuO2", material::PuO2)
.value("Polyacrylonitrile", material::Polyacrylonitrile)
.value("Polycarbonate", material::Polycarbonate)
.value("PMMA", material::PMMA)
.value("POM", material::POM)
.value("Polypropylene", material::Polypropylene)
.value("Polystyrene", material::Polystyrene)
.value("Propane", material::Propane)
.value("nPropanol", material::nPropanol)
.value("PVC", material::PVC)
.value("Pyridine", material::Pyridine)
.value("SiO2", material::SiO2)
.value("Skin", material::Skin)
.value("Sucrose", material::Sucrose)
.value("Teflon", material::Teflon)
.value("TlCl", material::TlCl)
.value("Toluene", material::Toluene)
.value("Trichloroethylene", material::Trichloroethylene)
.value("WF6", material::WF6)
.value("UC2", material::UC2)
.value("UC", material::UC)
.value("UO2", material::UO2)
.value("Urea", material::Urea)
.value("Valine", material::Valine)
.value("Iodonaphthalene", material::Iodonaphthalene)
.value("C21H24O4", material::C21H24O4)
.value("CoRe_Alloy", material::CoRe_Alloy)
.value("LLZO_electrolyte", material::LLZO_electrolyte)
.value("Nylon", material::Nylon);
pybind module
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py::class_<Config>(m,"Config")
.def(py::init<>(),"constructor")
.def_readwrite("z_effective", &Config::z_effective)
.def_readwrite("corrections", &Config::corrections)
.def_readwrite("calculation", &Config::calculation)
py config le switch
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.def_readwrite("low_energy", &Config::low_energy)
improved angular scattering
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.def_readwrite("scattering", &Config::scattering)
pybind module
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.def("get",[](const Config &r){
py::dict d;
d["z_effective"] = r.z_effective;
d["corrections"] = r.corrections;
d["calculation"] = r.calculation;
py config le switch
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d["low_energy"] = r.low_energy;
improved angular scattering
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d["scattering"] = r.scattering;
pybind module
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return d;
storage info bug
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})
.def("__str__",[](const Config &r){
std::string s;
s = "z_effective = "+std::to_string(r.z_effective);
s += ", corrections = "+std::to_string(r.corrections);
s += ", calculation = "+std::to_string(r.calculation);
py config le switch
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s += ", low_energy = "+std::to_string(r.low_energy);
improved angular scattering
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s += ", scattering = "+std::to_string(r.scattering);
storage info bug
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return s;
});
pybind module
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improved angular scattering
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m.def("angular_scattering_power",py::overload_cast<const Projectile&, const Material&, double>(&angular_scattering_power),"angular scattering power in rad^2/g/cm^2",py::arg("projectile"),py::arg("material"),py::arg("Es2")=Es2_FR);
m.def("radiation_length",py::overload_cast<const Material&>(radiation_length));
pybind module
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m.def("srim_dedx_e",&srim_dedx_e);
refactoring
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m.def("sezi_dedx_e",&sezi_dedx_e, "sezi_dedx_e", py::arg("projectile"), py::arg("material"), py::arg("config")=default_config);
dx py fix
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m.def("calculate",py::overload_cast<Projectile, const Material&, const Config&>(&calculate),"calculate",py::arg("projectile"), py::arg("material"), py::arg("config")=default_config);
scattering update and syncing from local
2021-01-12 15:50:15 -05:00
m.def("calculate",py::overload_cast<const Projectile&, const Layers&, const Config&>(&calculate),"calculate",py::arg("projectile"), py::arg("layers"), py::arg("config")=default_config);
dx py fix
2020-08-05 12:58:03 -04:00
m.def("calculate_layers",py::overload_cast<const Projectile&, const Layers&, const Config&>(&calculate),"calculate_layers",py::arg("projectile"), py::arg("material"), py::arg("config")=default_config);
m.def("dedx_from_range",py::overload_cast<const Projectile&, const Material&, const Config&>(&dedx_from_range),"calculate",py::arg("projectile") ,py::arg("material"), py::arg("config")=default_config);
m.def("dedx_from_range",py::overload_cast<const Projectile&, const std::vector<double>&, const Material&, const Config&>(&dedx_from_range),"calculate",py::arg("projectile"), py::arg("energy") ,py::arg("material"), py::arg("config")=default_config);
m.def("dedx",py::overload_cast<const Projectile&, const Material&, const Config&>(&dedx), "dedx",py::arg("projectile"), py::arg("material"), py::arg("config")=default_config);
m.def("range",py::overload_cast<const Projectile&, const Material&, const Config&>(&range), "range",py::arg("projectile"), py::arg("material"), py::arg("config")=default_config);
m.def("energy_out",py::overload_cast<const Projectile&, const std::vector<double>&, const Material&, const Config&>(&energy_out),"energy_out",py::arg("projectile"), py::arg("energy") ,py::arg("material"), py::arg("config")=default_config);
m.def("energy_out",py::overload_cast<const Projectile&, const Material&, const Config&>(&energy_out),"energy_out",py::arg("projectile"), py::arg("material"), py::arg("config")=default_config);
py functions
2019-11-25 13:26:16 -05:00
m.def("lindhard",&bethek_lindhard);
m.def("lindhard_X",&bethek_lindhard_X);
pybind module
2019-05-12 14:14:53 -04:00
m.def("get_material",py::overload_cast<int>(&get_material));
refactoring
2019-05-13 14:51:09 -04:00
m.def("get_data",py::overload_cast<Projectile&, const Material&, const Config&>(get_data),"list of data",py::arg("projectile"),py::arg("material"),py::arg("config")=default_config);
pymodule
2019-05-13 16:07:25 -04:00
m.def("w_magnification",[](Projectile& p, double energy, const Material& m, const Config& c){
py::list l;
auto r = w_magnification(p, energy, m, c);
l.append(r.first);
l.append(r.second);
return l;
});
pybind module
2019-05-12 14:14:53 -04:00
m.def("catima_info",&catima_info);
m.def("storage_info",&storage_info);
m.def("get_energy_table",&get_energy_table);
refactoring
2019-05-13 14:51:09 -04:00
m.def("energy_table",[](int i){return energy_table(i);});
u3
2019-11-21 08:10:03 -05:00
m.def("z_effective",&z_effective);
pybind module
2019-05-12 14:14:53 -04:00
m.attr("max_datapoints") = max_datapoints;
m.attr("max_storage_data") = max_storage_data;
m.attr("logEmin")=logEmin;
m.attr("logEmax")=logEmax;
}
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