Merge pull request #71 from hrosiak/docs

docs

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 ../

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:
+
+

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 
+The material object must contain __Z__ keyword defining proton number
-of the projectile or the compound material id. 
+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
-```

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
+```

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']

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
 ==================

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},
+              *   {1,1,2},
-                  {16,8,1},
+              *   {16,8,1},
-		  1.0,  // optional density
+              *   1.0,  // optional density
-                });
+              *  });
               * \endcode
               */
             Material(std::initializer_list<std::array<double,3>>list,double _density=0.0, double ipot = 0.0, double mass=0.0);