From a473cd2947a09a5091330f0b44474786fea742d5 Mon Sep 17 00:00:00 2001 From: hrocho Date: Tue, 22 Oct 2019 20:59:21 +0200 Subject: [PATCH] docs --- docs/README.md | 12 +-- docs/api.rst | 21 +++++ docs/catima_calculator.md | 158 ++------------------------------------ docs/catima_manual.md | 158 ++++++++++++++++++++++++++++++++++++-- docs/conf.py | 6 +- docs/index.rst | 18 +++++ structures.h | 18 +++-- 7 files changed, 211 insertions(+), 180 deletions(-) create mode 100644 docs/api.rst diff --git a/docs/README.md b/docs/README.md index ec512ad..0821371 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,13 +1,3 @@ -CATima -======= -C++ library for caclulalaton of energy loss, range, angular scattering and time of flight of the particle passing through matter. -The library is based on physics used in the ATIMA code,however its not 100% copy of ATIMA physics. - see CREDITS for more details. - -The WebAtima UI to this library can be found here: - * https://web-docs.gsi.de/~aprochaz/webatima (only inside GSI) - * https://isotopea.com/webatima - Installation ------------ CMake is used to build the library. For default build use: @@ -45,7 +35,7 @@ available options: * THIN_TARGET_APPROXIMATION - compile the library with thin target approximation, default: ON * GSL_INTEGRATION - use GSL integration functions, otherwise use built-in integrator, default: OFF * GLOBAL - compile with GLOBAL code (source not included at the moment, needs to be manually added to __global__ directory, default:OFF) - * STORE_SPLINES - store splines in cache, if disabled datapoints are stored and splines are recreated, default ON + * STORE_SPLINES - store splines in cache, if disabled datapoints are stored and splines are recreated, default ON ie: > cmake -DPYTHON_MODULE=ON -DEXAMPLES=ON ../ diff --git a/docs/api.rst b/docs/api.rst new file mode 100644 index 0000000..c71b198 --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,21 @@ +API Reference +############# + +.. doxygenstruct:: catima::Projectile + :members: + +.. doxygenclass:: catima::Material + :members: + +.. doxygenclass:: catima::Layers + :members: + +.. doxygenstruct:: catima::Result + :members: + :undoc-members: + +.. doxygenstruct:: catima::MultiResult + :members: + :undoc-members: + + diff --git a/docs/catima_calculator.md b/docs/catima_calculator.md index 4b5d3aa..a07f6ec 100644 --- a/docs/catima_calculator.md +++ b/docs/catima_calculator.md @@ -17,7 +17,7 @@ example Config File Format ------------------ -The file must be a valid JSON formatted file. +The file must be a valid JSON formatted file. The json file should contain the following keys: "projectile", "material", "energy" @@ -33,8 +33,8 @@ examples: #### material The __material__ keyword is array of object for multi layer material, or single object defining the material. -The material object must contain __Z__ keyword defining proton number -of the projectile or the compound material id. +The material object must contain __Z__ keyword defining proton number +of the projectile or the compound material id. Optional material object keywords are: * __Z__ - proton number or compunds id, mandatory * __A__ - mass number of the material, if 0 or undefined elemental atomic weight is used @@ -42,7 +42,7 @@ Optional material object keywords are: * __thickness__ - material or layer thickness in g/cm2 #### energy -The __energy__ keyword can be +The __energy__ keyword can be 1.a number specifying the kinetic energy: ``` "energy":"500.0" @@ -64,7 +64,7 @@ The __energy__ keyword can be instead of "step" key the "num" can be specified for integer number of steps between min and max energy. #### config -The calculation configuration can be change using __config__ keyword. If +The calculation configuration can be change using __config__ keyword. If not specified default will be used. The config keyword is expected to be one of the strings * "atimav1.3" - for Atima v1.3 setting * "atimav1.4" - for Atima v1.4 setting @@ -130,151 +130,3 @@ Example Files } } ``` - -#### Compound material -The predefined compound material can be used using the __Z__ field as an ID of the compound. -The following are supported: -``` - Plastics = 201, - Air = 202, - CH2 = 203, - LH2 = 204, - LD2 = 205, - Water = 206, - Diamond = 207, - Glass = 208, - ALMG3 = 209, - ArCO2_30 = 210, - CF4 = 211, - Isobutane = 212, - Kapton = 213, - Mylar = 214, - NaF = 215, - P10 = 216, - Polyolefin = 217, - CmO2 = 218, - Suprasil = 219, - HAVAR = 220, - Steel = 221, - CO2 = 222, - CH4 = 223, - Methanol = 224, - Acetone = 225, - Acetylene = 226, - Adenine = 227, - Adipose_Tissue = 228, - Alanine = 229, - Bakelite = 230, - AgBr = 231, - AgCl = 232, - AgI = 233, - Al2O3 = 234, - Amber = 235, - Ammonia = 236, - Aniline = 237, - Anthracene = 238, - A_150 = 239, - B_100 = 240, - BaF2 = 241, - BaSO4 = 242, - Benzene = 243, - BeO = 244, - BGO = 245, - Blood = 246, - Bone_Compact = 247, - Bone_Cortical = 248, - Brain_ICRP = 249, - B4C = 250, - BC400 = 251, - nButanol = 252, - C_552 = 253, - CdTe = 254, - CdWO4 = 255, - CaCO3 = 256, - CaF2 = 257, - CaO = 258, - CaWO4 = 259, - CsF = 260, - CsI = 261, - CCl4 = 262, - C2Cl4 = 263, - Cellophane = 264, - Chlorobenzene = 265, - Chloroform = 266, - Cyclohexane = 267, - Concrete = 268, - Diethyl_Ether = 269, - Ethane = 270, - Ethanol = 271, - Ethylene = 272, - Eye_lens = 273, - Fe2O3 = 274, - FeO = 275, - Freon12 = 276, - Freon12B2 = 277, - Freon13 = 278, - Freon13B1 = 279, - Freon13I1 = 280, - Gd2O2S = 281, - GaAs = 282, - Gel_Photo_Emulsion = 283, - Glass_Pyrex = 284, - Glass_Lead = 285, - Glucose = 286, - Glutamine = 287, - Glycerol = 288, - Guanine = 289, - Gypsum = 290, - nHeptane = 291, - nHexane = 292, - KI = 293, - K2O = 294, - LaBr3 = 295, - LaOBr = 296, - La2O2S = 297, - Lung = 298, - MgCO3 = 299, - MgF2 = 300, - MgO = 301, - MS20_Tissue = 302, - Muscle_skeletal = 303, - Muscle_strained = 304, - Muscle_sucrose = 305, - Muscle_no_sucrose = 306, - Na2CO3 = 307, - NaI = 308, - NaCl = 309, - Na2O = 310, - NaNO3 = 311, - Naphthalene = 312, - Nitrobenzene = 313, - N2O = 314, - Octane = 315, - Paraffin = 316, - nPentane = 317, - PhotoEmulsion = 318, - PuO2 = 319, - Polyacrylonitrile = 320, - Polycarbonate = 321, - PMMA = 322, - POM = 323, - Polypropylene = 324, - Polystyrene = 325, - Propane = 326, - nPropanol = 327, - PVC = 328, - Pyridine = 329, - SiO2 = 330, - Skin = 331, - Sucrose = 332, - Teflon = 333, - TlCl = 334, - Toluene = 335, - Trichloroethylene = 336, - WF6 = 337, - UC2 = 338, - UC = 339, - UO2 = 340, - Urea = 341, - Valine = 342 -``` diff --git a/docs/catima_manual.md b/docs/catima_manual.md index 0661a93..23e5798 100644 --- a/docs/catima_manual.md +++ b/docs/catima_manual.md @@ -1,10 +1,6 @@ CATima library manual ===================== -Compiling and Instalation -------------------------- -See [README.md](README.md) for details. -[link2](catima_calculator.md) Units ------ The following units are used for input and outputs: @@ -21,10 +17,10 @@ Projectile The __Projectile__ class is used to store projectile data. Each projectile must provide A,Z combination, additionally charge state can be set as well. The example of projectile definition: -~~~~~~~~~~~~~~~~~~~{.cpp} +```cpp catima::Projectile p1(12,6); //12C projectile catima::Projectile p2(12,6,5); //12C(5+) projectile -~~~~~~~~~~~~~~~~~~~ +``` to set the energy of the projectile in MeV/u units: ```cpp @@ -42,7 +38,7 @@ The example of water definition: ```cpp -catima::Material carbon({0,6,1}); // carbon with elemental atomic weight +catima::Material carbon({0,6,1}); // carbon with elemental atomic weight catima::Material water1({ {1,1,2}, // {weight, Z, stn or weight fraction} @@ -224,3 +220,151 @@ It provides only basic interface. +Compound Pre-defined Materials +============================== +The predefined compound material can be used using the __Z__ field as an ID of the compound. +The following are supported: +``` + Plastics = 201, + Air = 202, + CH2 = 203, + LH2 = 204, + LD2 = 205, + Water = 206, + Diamond = 207, + Glass = 208, + ALMG3 = 209, + ArCO2_30 = 210, + CF4 = 211, + Isobutane = 212, + Kapton = 213, + Mylar = 214, + NaF = 215, + P10 = 216, + Polyolefin = 217, + CmO2 = 218, + Suprasil = 219, + HAVAR = 220, + Steel = 221, + CO2 = 222, + CH4 = 223, + Methanol = 224, + Acetone = 225, + Acetylene = 226, + Adenine = 227, + Adipose_Tissue = 228, + Alanine = 229, + Bakelite = 230, + AgBr = 231, + AgCl = 232, + AgI = 233, + Al2O3 = 234, + Amber = 235, + Ammonia = 236, + Aniline = 237, + Anthracene = 238, + A_150 = 239, + B_100 = 240, + BaF2 = 241, + BaSO4 = 242, + Benzene = 243, + BeO = 244, + BGO = 245, + Blood = 246, + Bone_Compact = 247, + Bone_Cortical = 248, + Brain_ICRP = 249, + B4C = 250, + BC400 = 251, + nButanol = 252, + C_552 = 253, + CdTe = 254, + CdWO4 = 255, + CaCO3 = 256, + CaF2 = 257, + CaO = 258, + CaWO4 = 259, + CsF = 260, + CsI = 261, + CCl4 = 262, + C2Cl4 = 263, + Cellophane = 264, + Chlorobenzene = 265, + Chloroform = 266, + Cyclohexane = 267, + Concrete = 268, + Diethyl_Ether = 269, + Ethane = 270, + Ethanol = 271, + Ethylene = 272, + Eye_lens = 273, + Fe2O3 = 274, + FeO = 275, + Freon12 = 276, + Freon12B2 = 277, + Freon13 = 278, + Freon13B1 = 279, + Freon13I1 = 280, + Gd2O2S = 281, + GaAs = 282, + Gel_Photo_Emulsion = 283, + Glass_Pyrex = 284, + Glass_Lead = 285, + Glucose = 286, + Glutamine = 287, + Glycerol = 288, + Guanine = 289, + Gypsum = 290, + nHeptane = 291, + nHexane = 292, + KI = 293, + K2O = 294, + LaBr3 = 295, + LaOBr = 296, + La2O2S = 297, + Lung = 298, + MgCO3 = 299, + MgF2 = 300, + MgO = 301, + MS20_Tissue = 302, + Muscle_skeletal = 303, + Muscle_strained = 304, + Muscle_sucrose = 305, + Muscle_no_sucrose = 306, + Na2CO3 = 307, + NaI = 308, + NaCl = 309, + Na2O = 310, + NaNO3 = 311, + Naphthalene = 312, + Nitrobenzene = 313, + N2O = 314, + Octane = 315, + Paraffin = 316, + nPentane = 317, + PhotoEmulsion = 318, + PuO2 = 319, + Polyacrylonitrile = 320, + Polycarbonate = 321, + PMMA = 322, + POM = 323, + Polypropylene = 324, + Polystyrene = 325, + Propane = 326, + nPropanol = 327, + PVC = 328, + Pyridine = 329, + SiO2 = 330, + Skin = 331, + Sucrose = 332, + Teflon = 333, + TlCl = 334, + Toluene = 335, + Trichloroethylene = 336, + WF6 = 337, + UC2 = 338, + UC = 339, + UO2 = 340, + Urea = 341, + Valine = 342 +``` diff --git a/docs/conf.py b/docs/conf.py index 1da9329..04797bc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -29,13 +29,13 @@ extensions = [ 'breathe' ] -breathe_projects = {'nurex':'build/doxygenxml/'} +breathe_projects = {'catima':'build/doxygenxml/'} breathe_default_project = 'catima' breathe_domain_by_extenstion = {'h':'cpp'} primary_domain = 'cpp' highlight_language = 'cpp' # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +#templates_path = ['_templates'] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -53,4 +53,4 @@ html_theme = 'sphinx_rtd_theme' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +#html_static_path = ['_static'] diff --git a/docs/index.rst b/docs/index.rst index e30cbe9..e8a3f5a 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,6 +17,24 @@ Content README +.. toctree:: + :maxdepth: 1 + :caption: Manual + + catima_manual + +.. toctree:: + :maxdepth: 1 + :caption: Console App + + catima_calculator + +.. toctree:: + :maxdepth: 1 + :caption: API Reference + + api + Indices and tables ================== diff --git a/structures.h b/structures.h index b0f1950..5818d77 100644 --- a/structures.h +++ b/structures.h @@ -38,9 +38,15 @@ namespace catima{ double Z=0; double Q=0; double T=0; - Projectile& operator()(double e){T=e;return *this;} - Projectile(){} + + /// constructor + /// @param a - mass + /// @param z - proton number + /// @param q - charge state + /// @param t - energy in MeV/u Projectile(double a, double z, double q=0, double t=0):A(a),Z(z),Q(q),T(t){if(q==0)Q=Z;} + Projectile& operator()(double e){T=e;return *this;} + Projectile() = default; }; bool operator==(const Projectile &a, const Projectile&b); @@ -85,10 +91,10 @@ namespace catima{ * constructor to add 1 or multiple element into the Material * \code{.cpp} * Maetrial water({ - {1,1,2}, - {16,8,1}, - 1.0, // optional density - }); + * {1,1,2}, + * {16,8,1}, + * 1.0, // optional density + * }); * \endcode */ Material(std::initializer_list>list,double _density=0.0, double ipot = 0.0, double mass=0.0);