mirror of
https://github.com/gwm17/catima.git
synced 2024-11-22 18:28:51 -05:00
Andrej Prochazka
GitHub
commit
a03c201964
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@ -1,13 +1,3 @@
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CATima
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=======
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C++ library for caclulalaton of energy loss, range, angular scattering and time of flight of the particle passing through matter.
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The library is based on physics used in the ATIMA code,however its not 100% copy of ATIMA physics.
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see CREDITS for more details.
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The WebAtima UI to this library can be found here:
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* https://web-docs.gsi.de/~aprochaz/webatima (only inside GSI)
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* https://isotopea.com/webatima
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Installation
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------------
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CMake is used to build the library. For default build use:
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@ -45,7 +35,7 @@ available options:
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* THIN_TARGET_APPROXIMATION - compile the library with thin target approximation, default: ON
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* GSL_INTEGRATION - use GSL integration functions, otherwise use built-in integrator, default: OFF
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* GLOBAL - compile with GLOBAL code (source not included at the moment, needs to be manually added to __global__ directory, default:OFF)
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* STORE_SPLINES - store splines in cache, if disabled datapoints are stored and splines are recreated, default ON
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* STORE_SPLINES - store splines in cache, if disabled datapoints are stored and splines are recreated, default ON
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ie:
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> cmake -DPYTHON_MODULE=ON -DEXAMPLES=ON ../
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21
docs/api.rst
Normal file
21
docs/api.rst
Normal file
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@ -0,0 +1,21 @@
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API Reference
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#############
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.. doxygenstruct:: catima::Projectile
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:members:
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.. doxygenclass:: catima::Material
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:members:
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.. doxygenclass:: catima::Layers
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:members:
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.. doxygenstruct:: catima::Result
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:members:
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:undoc-members:
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.. doxygenstruct:: catima::MultiResult
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:members:
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:undoc-members:
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@ -17,7 +17,7 @@ example
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Config File Format
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------------------
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The file must be a valid JSON formatted file.
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The file must be a valid JSON formatted file.
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The json file should contain the following keys: "projectile", "material", "energy"
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@ -33,8 +33,8 @@ examples:
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#### material
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The __material__ keyword is array of object for multi layer material,
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or single object defining the material.
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The material object must contain __Z__ keyword defining proton number
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of the projectile or the compound material id.
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The material object must contain __Z__ keyword defining proton number
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of the projectile or the compound material id.
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Optional material object keywords are:
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* __Z__ - proton number or compunds id, mandatory
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* __A__ - mass number of the material, if 0 or undefined elemental atomic weight is used
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@ -42,7 +42,7 @@ Optional material object keywords are:
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* __thickness__ - material or layer thickness in g/cm2
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#### energy
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The __energy__ keyword can be
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The __energy__ keyword can be
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1.a number specifying the kinetic energy:
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```
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"energy":"500.0"
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@ -64,7 +64,7 @@ The __energy__ keyword can be
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instead of "step" key the "num" can be specified for integer number of steps between min and max energy.
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#### config
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The calculation configuration can be change using __config__ keyword. If
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The calculation configuration can be change using __config__ keyword. If
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not specified default will be used. The config keyword is expected to be one of the strings
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* "atimav1.3" - for Atima v1.3 setting
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* "atimav1.4" - for Atima v1.4 setting
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@ -130,151 +130,3 @@ Example Files
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}
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}
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```
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#### Compound material
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The predefined compound material can be used using the __Z__ field as an ID of the compound.
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The following are supported:
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```
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Plastics = 201,
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Air = 202,
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CH2 = 203,
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LH2 = 204,
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LD2 = 205,
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Water = 206,
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Diamond = 207,
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Glass = 208,
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ALMG3 = 209,
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ArCO2_30 = 210,
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CF4 = 211,
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Isobutane = 212,
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Kapton = 213,
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Mylar = 214,
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NaF = 215,
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P10 = 216,
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Polyolefin = 217,
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CmO2 = 218,
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Suprasil = 219,
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HAVAR = 220,
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Steel = 221,
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CO2 = 222,
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CH4 = 223,
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Methanol = 224,
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Acetone = 225,
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Acetylene = 226,
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Adenine = 227,
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Adipose_Tissue = 228,
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Alanine = 229,
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Bakelite = 230,
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AgBr = 231,
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AgCl = 232,
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AgI = 233,
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Al2O3 = 234,
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Amber = 235,
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Ammonia = 236,
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Aniline = 237,
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Anthracene = 238,
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A_150 = 239,
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B_100 = 240,
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BaF2 = 241,
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BaSO4 = 242,
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Benzene = 243,
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BeO = 244,
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BGO = 245,
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Blood = 246,
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Bone_Compact = 247,
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Bone_Cortical = 248,
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Brain_ICRP = 249,
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B4C = 250,
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BC400 = 251,
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nButanol = 252,
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C_552 = 253,
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CdTe = 254,
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CdWO4 = 255,
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CaCO3 = 256,
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CaF2 = 257,
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CaO = 258,
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CaWO4 = 259,
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CsF = 260,
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CsI = 261,
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CCl4 = 262,
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C2Cl4 = 263,
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Cellophane = 264,
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Chlorobenzene = 265,
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Chloroform = 266,
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Cyclohexane = 267,
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Concrete = 268,
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Diethyl_Ether = 269,
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Ethane = 270,
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Ethanol = 271,
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Ethylene = 272,
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Eye_lens = 273,
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Fe2O3 = 274,
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FeO = 275,
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Freon12 = 276,
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Freon12B2 = 277,
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Freon13 = 278,
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Freon13B1 = 279,
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Freon13I1 = 280,
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Gd2O2S = 281,
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GaAs = 282,
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Gel_Photo_Emulsion = 283,
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Glass_Pyrex = 284,
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Glass_Lead = 285,
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Glucose = 286,
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Glutamine = 287,
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Glycerol = 288,
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Guanine = 289,
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Gypsum = 290,
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nHeptane = 291,
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nHexane = 292,
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KI = 293,
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K2O = 294,
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LaBr3 = 295,
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LaOBr = 296,
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La2O2S = 297,
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Lung = 298,
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MgCO3 = 299,
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MgF2 = 300,
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MgO = 301,
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MS20_Tissue = 302,
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Muscle_skeletal = 303,
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Muscle_strained = 304,
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Muscle_sucrose = 305,
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Muscle_no_sucrose = 306,
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Na2CO3 = 307,
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NaI = 308,
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NaCl = 309,
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Na2O = 310,
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NaNO3 = 311,
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Naphthalene = 312,
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Nitrobenzene = 313,
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N2O = 314,
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Octane = 315,
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Paraffin = 316,
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nPentane = 317,
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PhotoEmulsion = 318,
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PuO2 = 319,
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Polyacrylonitrile = 320,
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Polycarbonate = 321,
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PMMA = 322,
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POM = 323,
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Polypropylene = 324,
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Polystyrene = 325,
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Propane = 326,
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nPropanol = 327,
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PVC = 328,
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Pyridine = 329,
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SiO2 = 330,
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Skin = 331,
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Sucrose = 332,
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Teflon = 333,
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TlCl = 334,
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Toluene = 335,
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Trichloroethylene = 336,
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WF6 = 337,
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UC2 = 338,
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UC = 339,
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UO2 = 340,
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Urea = 341,
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Valine = 342
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```
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@ -1,10 +1,6 @@
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CATima library manual
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=====================
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Compiling and Instalation
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-------------------------
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See [README.md](README.md) for details.
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[link2](catima_calculator.md)
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Units
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------
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The following units are used for input and outputs:
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@ -21,10 +17,10 @@ Projectile
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The __Projectile__ class is used to store projectile data.
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Each projectile must provide A,Z combination, additionally charge state can be set as well.
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The example of projectile definition:
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~~~~~~~~~~~~~~~~~~~{.cpp}
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```cpp
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catima::Projectile p1(12,6); //12C projectile
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catima::Projectile p2(12,6,5); //12C(5+) projectile
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~~~~~~~~~~~~~~~~~~~
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```
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to set the energy of the projectile in MeV/u units:
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```cpp
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@ -42,7 +38,7 @@ The example of water definition:
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```cpp
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catima::Material carbon({0,6,1}); // carbon with elemental atomic weight
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catima::Material carbon({0,6,1}); // carbon with elemental atomic weight
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catima::Material water1({
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{1,1,2}, // {weight, Z, stn or weight fraction}
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@ -224,3 +220,151 @@ It provides only basic interface.
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Compound Pre-defined Materials
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==============================
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The predefined compound material can be used using the __Z__ field as an ID of the compound.
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The following are supported:
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```
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Plastics = 201,
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Air = 202,
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CH2 = 203,
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LH2 = 204,
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LD2 = 205,
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Water = 206,
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Diamond = 207,
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Glass = 208,
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ALMG3 = 209,
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ArCO2_30 = 210,
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CF4 = 211,
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Isobutane = 212,
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Kapton = 213,
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Mylar = 214,
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NaF = 215,
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P10 = 216,
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Polyolefin = 217,
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CmO2 = 218,
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Suprasil = 219,
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HAVAR = 220,
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Steel = 221,
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CO2 = 222,
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CH4 = 223,
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Methanol = 224,
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Acetone = 225,
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Acetylene = 226,
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Adenine = 227,
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Adipose_Tissue = 228,
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Alanine = 229,
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Bakelite = 230,
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AgBr = 231,
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AgCl = 232,
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AgI = 233,
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Al2O3 = 234,
|
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Amber = 235,
|
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Ammonia = 236,
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Aniline = 237,
|
||||
Anthracene = 238,
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A_150 = 239,
|
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B_100 = 240,
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BaF2 = 241,
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BaSO4 = 242,
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Benzene = 243,
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BeO = 244,
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BGO = 245,
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Blood = 246,
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Bone_Compact = 247,
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Bone_Cortical = 248,
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Brain_ICRP = 249,
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B4C = 250,
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BC400 = 251,
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nButanol = 252,
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C_552 = 253,
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CdTe = 254,
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CdWO4 = 255,
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CaCO3 = 256,
|
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CaF2 = 257,
|
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CaO = 258,
|
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CaWO4 = 259,
|
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CsF = 260,
|
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CsI = 261,
|
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CCl4 = 262,
|
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C2Cl4 = 263,
|
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Cellophane = 264,
|
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Chlorobenzene = 265,
|
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Chloroform = 266,
|
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Cyclohexane = 267,
|
||||
Concrete = 268,
|
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Diethyl_Ether = 269,
|
||||
Ethane = 270,
|
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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,
|
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MS20_Tissue = 302,
|
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Muscle_skeletal = 303,
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Muscle_strained = 304,
|
||||
Muscle_sucrose = 305,
|
||||
Muscle_no_sucrose = 306,
|
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Na2CO3 = 307,
|
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NaI = 308,
|
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NaCl = 309,
|
||||
Na2O = 310,
|
||||
NaNO3 = 311,
|
||||
Naphthalene = 312,
|
||||
Nitrobenzene = 313,
|
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N2O = 314,
|
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Octane = 315,
|
||||
Paraffin = 316,
|
||||
nPentane = 317,
|
||||
PhotoEmulsion = 318,
|
||||
PuO2 = 319,
|
||||
Polyacrylonitrile = 320,
|
||||
Polycarbonate = 321,
|
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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
|
||||
```
|
||||
|
|
|
|||
|
|
@ -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']
|
||||
|
|
|
|||
|
|
@ -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
|
||||
==================
|
||||
|
|
|
|||
18
structures.h
18
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<std::array<double,3>>list,double _density=0.0, double ipot = 0.0, double mass=0.0);
|
||||
|
|
|
|||
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