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Andrej Prochazka
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docs/pycatima.md
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176
docs/pycatima.md
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Usage
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=====
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Pojectile
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---------
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Projectile is defined by __pycatima.Projectile__ class. It is initialized using:
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**Projectile(A, Z, Q=Z, T=0)**
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where __A__ is mass in u units, __Z__ is proton number, __Q__ is charge state
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and __T__ is energy in Mev/u units.
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```python
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import pycatima
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p = pycatima.Projectile(238.00032 ,92) # 238U92+ at 0 Mev/u
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p = pycatima.Projectile(238.00702 ,92,90,1000) # 238U90+ at 1000 Mev/u
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# following methods are defined:
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mass = p.A() # get mass of the nucleus us u units
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z = p.Z() # get proton number
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q = p.Q() # get charge state
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energy = p.T() # get energy
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p.T(1000) # set energy
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```
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Material
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--------
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Material is defined by __pycatima.Material__ class. The recommended way of
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initialization is usign the following init signature:
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**Material(elements, density, thickness, i_potential, mass)**
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* elements - list of elements, where element is defined as list of [A, Z, STN]
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A is atomic mass of the element, if 0 natural abundance atomic mass is taken,
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Z is the proton number of the element, STN is the stoichiometric if >=1.0 or
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weight fraction if < 1.0
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* density - optional, defaults to 0
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* thickness - optional, if not defined 0
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* i_potential - optional, if <=0 it will be calulated using Bragg rule from elemental ionization potentials
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* mass - optional, if <=0 it will be calculated from elements masses and STN number.
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__Material__ class has following methods:
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* **add_element(a, z, stn)** - adds another element to the material, see initialization comments for details about, a,z, stn
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* **ncomponents()** - returns number of elements in the material
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* **density()** - returns density
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* **density(value)** - set density
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* **thickness()** - get thickness in g/cm^2
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* **thickness(value)** - set thickness in g/cm^2
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* **thickness_cm(value)** - set thickness in cm
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* **I()** - get mean ionization potential
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* **I(value)** - set mean ionization potential
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### Default Materials
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The material with predefined density and atomic weights can be obtained for elemental targets and some compounds using:
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**pycatima.get_material(id)**
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id is integer which identifies material, For elements use 1-99 for elemental targets and >200 for compounds. See available pre-defined compounds in __predefined material__ section in manual./
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### Example
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```python
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import pycatima
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#H2O with natural atomic masses and Ipot=78eV
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h2o = pycatima.Material([[0,1,2],[0,8,1]],density=1.0, i_potential=78)
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h2o.thickness_cm(1.0) # 1cm of water
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# C target
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c_mat = pycatima.get_material(6)
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c_mat.thickness(0.1) # set to 0.1g/cm2
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```
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Layers
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------
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Layers are sequential layers of __Material__ which __Projectile__ passes.
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The __pycatima.Layers__ class is defined using following signature:
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**Layers()**
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This creates empty layers which needs to be filled by __Material__ class.
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__Layers__ clas has following methods:
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* **add(material)** - add material to the layers, material must be __Material__ class
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* **add_layers(other)** - add all material from __Layers__ class __other__
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* **num()** - returns number of layers
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* **__get_item__(i)** returns i-th Material class
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* **__get(i)** returns i-th Material class
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### Example
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```python
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import pycatima
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layers = pycatima.Layers()
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# define some materials
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graphite = pycatima.get_material(6)
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graphite.thickness(0.2)
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p10 = pycatima.get_material(pycatima.material.P10)
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p10.thickness_cm(2.0)
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air = pycatima.get_material(pycatima.material.Air)
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air.thickness_cm(2.0)
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# now add materials to layers
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layers.add(graphite)
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layers.add(air)
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graphite.thickness(0.1) # change thickness for next layer
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layers.add(graphite)
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layers.add(p10)
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```
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Calculation
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-----------
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Calculations are done using mainly via functions:
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* **calculate(Projectile, Material)**
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* **calculate_layers(Projectile, Layers)**
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The __calculate__ function returns __Result__ class and __calculate_layers__ returns __MultiResult_class__
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### Example
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```python
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import pycatima
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water = catima.get_material(catima.material.Water)
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water.thickness(1.0)
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p = catima.Projectile(1,1)
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p.T(1000) # set projectile energy to 1000MeV/u
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res = catima.calculate(p,water) # now res contains results
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d = res.get_dict() # get results as dictionary
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```
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```python
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p = catima.Projectile(12,6)
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water = catima.get_material(catima.material.Water)
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water.thickness(10.0)
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graphite = catima.get_material(6)
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graphite.thickness(1.0)
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graphite.density(2.0)
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mat = catima.Layers()
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mat.add(water)
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mat.add(graphite)
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# now calculate results for projectile at 1000MeV/u
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res = catima.calculate_layers(p(1000),mat)
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```
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Results
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-------
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__Results__ class stores results for 1 layer of __Material__. It has following variables:
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* Ein - Energy at entrance of the material in MeV/u
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* Eloss - Energy loss in material in MeV
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* Eout - Energy at the end of material in MeV/i
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* dEdxi - Stopping power at entrance
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* dEdxo - Stopping power at exit
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* range - range in the material in g/cm^2
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* sigma_E - Energy straggling in MeV/u
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* sigma_a - Angular straggling in MeV/u
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* sigma_r - range straggling in g/cm^2
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* sigma_x - position straggling in cm
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* sp - non-reaction probability
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* tof - time of flight through the material
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__MultiResults__ class stores the results for multiple layers. It consists of following variables:
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* total_result - __Result__ class with total results for projectile passing all layers.
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* results - list of __Result__ classes, one for each layer in __Layers__
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Config
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------
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TODO
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@ -1,17 +0,0 @@
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Usage
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=====
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Pojectile
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---------
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Material
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--------
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Layers
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------
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Calculation
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-----------
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Config
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------
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@ -100,6 +100,7 @@ py::dict get_result_dict(const Result& r){
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d["sigma_E"] = r.sigma_E;
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d["sigma_E"] = r.sigma_E;
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d["sigma_r"] = r.sigma_r;
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d["sigma_r"] = r.sigma_r;
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d["sigma_a"] = r.sigma_a;
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d["sigma_a"] = r.sigma_a;
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d["sigma_x"] = r.sigma_x;
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d["tof"] = r.tof;
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d["tof"] = r.tof;
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d["sp"] = r.sp;
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d["sp"] = r.sp;
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return d;
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return d;
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@ -171,6 +172,7 @@ PYBIND11_MODULE(pycatima,m){
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.def_readwrite("sigma_E", &Result::sigma_E)
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.def_readwrite("sigma_E", &Result::sigma_E)
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.def_readwrite("sigma_a", &Result::sigma_a)
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.def_readwrite("sigma_a", &Result::sigma_a)
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.def_readwrite("sigma_r", &Result::sigma_r)
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.def_readwrite("sigma_r", &Result::sigma_r)
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.def_readwrite("sigma_x", &Result::sigma_x)
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.def_readwrite("tof", &Result::tof)
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.def_readwrite("tof", &Result::tof)
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.def_readwrite("sp", &Result::sp)
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.def_readwrite("sp", &Result::sp)
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.def("get_dict",&get_result_dict);
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.def("get_dict",&get_result_dict);
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309
tests/test2.py
309
tests/test2.py
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@ -1,309 +0,0 @@
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import sys
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sys.path.insert(0,"../build")
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import unittest
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import pycatima as catima
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import math
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class TestStructures(unittest.TestCase):
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def test_Projectile(self):
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print(catima.storage_info())
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p = catima.Projectile(238,92)
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self.assertEqual(p.A(),238)
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self.assertEqual(p.Z(),92)
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self.assertEqual(p.Q(),92)
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p = catima.Projectile(238,92,90)
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self.assertEqual(p.A(),238)
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self.assertEqual(p.Z(),92)
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self.assertEqual(p.Q(),90)
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p.T(1000)
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self.assertEqual(p.T(),1000)
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p(500)
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self.assertEqual(p.T(),500)
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p = catima.Projectile(238,92,90, T=100)
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self.assertEqual(p.T(),100)
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def test_Material(self):
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mat = catima.Material()
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mat.add_element(12,6,1)
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self.assertEqual(mat.ncomponents(),1)
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mat.add_element(1,1,2)
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self.assertEqual(mat.ncomponents(),2)
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mat2 = catima.Material([[12.01,6,1]])
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self.assertEqual(mat2.ncomponents(),1)
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self.assertEqual(mat2.molar_mass(),12.01)
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mat3 = catima.Material([[12,6,1]])
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self.assertEqual(mat3.ncomponents(),1)
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self.assertEqual(mat3.molar_mass(),12)
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Water = catima.Material([[1,1,2],[16,8,1]])
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self.assertEqual(Water.molar_mass(),18)
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mat2 = catima.Material([[0,6,1]])
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self.assertEqual(mat2.ncomponents(),1)
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self.assertAlmostEqual(mat2.molar_mass(),12,1)
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mat5 = catima.Material([[0,6,1]],density=1.9, thickness=0.5)
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self.assertEqual(mat5.ncomponents(),1)
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self.assertEqual(mat5.thickness(),0.5)
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self.assertEqual(mat5.density(),1.9)
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mat6 = catima.Material([[0,6,1]],density=1.9, thickness=0.5,i_potential=80.0)
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self.assertEqual(mat6.ncomponents(),1)
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self.assertEqual(mat6.thickness(),0.5)
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self.assertEqual(mat6.density(),1.9)
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self.assertEqual(mat6.I(),80.0)
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# copy
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mat3.density(1.8)
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matc = mat3.copy()
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self.assertEqual(matc.ncomponents(),1)
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self.assertEqual(matc.molar_mass(),12)
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self.assertEqual(matc.density(),1.8)
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mat3.density(2.0)
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self.assertEqual(matc.density(),1.8)
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self.assertEqual(mat3.density(),2.0)
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def test_default_material(self):
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m1 = catima.get_material(6);
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self.assertAlmostEqual(m1.molar_mass(),12,1)
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self.assertEqual(m1.ncomponents(),1)
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self.assertAlmostEqual(m1.density(),2.0,1)
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m2 = catima.get_material(catima.material.Water)
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self.assertEqual(m2.ncomponents(),2)
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self.assertAlmostEqual(m2.molar_mass(),18,1)
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self.assertAlmostEqual(m2.density(),1.0,1)
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m3 = catima.get_material(3001)
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self.assertEqual(m3.ncomponents(),0)
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self.assertAlmostEqual(m3.molar_mass(),0,1)
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self.assertAlmostEqual(m3.density(),0.0,1)
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def test_layers(self):
|
|
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graphite = catima.get_material(6)
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graphite.thickness(0.5)
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|
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p10 = catima.get_material(catima.material.P10)
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|
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p10.thickness(0.01)
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n2 = catima.get_material(7)
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n2.thickness(0.02)
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|
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|
|
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mat= catima.Layers()
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|
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self.assertEqual(mat.num(),0)
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mat.add(graphite)
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|
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self.assertEqual(mat.num(),1)
|
|
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self.assertAlmostEqual(mat[0].molar_mass(),12,1)
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|
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self.assertAlmostEqual(mat[0].thickness(),0.5,1)
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self.assertAlmostEqual(mat[0].density(),2.0,1)
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mat.add(p10)
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self.assertEqual(mat.num(),2)
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|
|
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graphite.thickness(1.0)
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|
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graphite.density(1.8)
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|
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mat.add(graphite)
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|
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self.assertEqual(mat.num(),3)
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|
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self.assertAlmostEqual(mat[2].molar_mass(),12,1)
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|
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self.assertAlmostEqual(mat[0].thickness(),0.5,1)
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|
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self.assertAlmostEqual(mat[0].density(),2.0,1)
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|
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self.assertAlmostEqual(mat[2].thickness(),1.0,1)
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|
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self.assertAlmostEqual(mat[2].density(),1.8,1)
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|
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mat[2].thickness(1.2)
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|
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mat[2].density(1.9)
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|
||||||
self.assertAlmostEqual(mat.materials[2].thickness(),1.2,1)
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|
||||||
self.assertAlmostEqual(mat.materials[2].density(),1.9,1)
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|
||||||
#self.assertAlmostEqual(mat.materials[0].thickness(),0.5,1)
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|
||||||
#self.assertAlmostEqual(mat.materials[0].density(),2.0,1)
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|
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self.assertEqual(mat[3],None)
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|
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self.assertEqual(mat["a"],None)
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mat2 = catima.Layers()
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|
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mat2.add(n2)
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|
||||||
self.assertEqual(mat2.num(),1)
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|
||||||
|
|
||||||
mats = mat2 + mat
|
|
||||||
self.assertEqual(mats.num(),4)
|
|
||||||
self.assertAlmostEqual(mats[0].molar_mass(),14,1)
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|
||||||
self.assertEqual(mats[0].thickness(),0.02)
|
|
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self.assertAlmostEqual(mats[1].molar_mass(),12,1)
|
|
||||||
self.assertAlmostEqual(mats[3].molar_mass(),12,1)
|
|
||||||
|
|
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n2.thickness(0.5)
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|
||||||
mats = mats + n2
|
|
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self.assertEqual(mats.num(),5)
|
|
||||||
self.assertAlmostEqual(mats[0].molar_mass(),14,1)
|
|
||||||
self.assertEqual(mats[0].thickness(),0.02)
|
|
||||||
self.assertAlmostEqual(mats[4].molar_mass(),14,1)
|
|
||||||
self.assertEqual(mats[4].thickness(),0.5)
|
|
||||||
|
|
||||||
def test_material_calculation(self):
|
|
||||||
Water = catima.get_material(catima.material.Water)
|
|
||||||
p = catima.Projectile(1,1)
|
|
||||||
|
|
||||||
p(1000)
|
|
||||||
res = catima.calculate(p,Water)
|
|
||||||
res2 = catima.dedx(p,Water)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,2.23,1)
|
|
||||||
self.assertAlmostEqual(res["dEdxi"],2.23,1)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,res2,3)
|
|
||||||
res = catima.calculate(p(500),Water)
|
|
||||||
res2 = catima.dedx(p,Water)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,2.76,1)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,res2,3)
|
|
||||||
|
|
||||||
res = catima.calculate(p(9),Water)
|
|
||||||
res2 = catima.dedx(p,Water)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,51.17,1)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,res2,3)
|
|
||||||
res = catima.calculate(p(9),Water)
|
|
||||||
res = catima.calculate(p(9),Water)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,51.17,1)
|
|
||||||
|
|
||||||
p(900000)
|
|
||||||
res = catima.calculate(p,Water)
|
|
||||||
res2 = catima.dedx_from_range(p,Water)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,res2,3)
|
|
||||||
|
|
||||||
def test_config(self):
|
|
||||||
Water = catima.get_material(catima.material.Water)
|
|
||||||
Water.density(1.0)
|
|
||||||
Water.thickness(1.0)
|
|
||||||
p = catima.Projectile(1,1)
|
|
||||||
conf = catima.Config()
|
|
||||||
conf.dedx_straggling = catima.omega_type.bohr
|
|
||||||
conf2 = catima.Config()
|
|
||||||
conf2.dedx_straggling = catima.omega_type.atima
|
|
||||||
p(1000)
|
|
||||||
res = catima.calculate(p,Water,config=conf)
|
|
||||||
res2 = catima.calculate(p,Water,config=conf2)
|
|
||||||
self.assertAlmostEqual(res.dEdxi,res2.dEdxi,delta=1e-6)
|
|
||||||
self.assertNotAlmostEqual(res.sigma_E,res2.sigma_E,delta=1e-4)
|
|
||||||
self.assertNotAlmostEqual(res.sigma_r,res2.sigma_r,delta=1e-4)
|
|
||||||
|
|
||||||
|
|
||||||
def test_eout(self):
|
|
||||||
graphite = catima.get_material(6)
|
|
||||||
graphite.thickness(0.5)
|
|
||||||
p = catima.Projectile(12,6)
|
|
||||||
res = catima.calculate(p(1000),graphite)
|
|
||||||
res2 = catima.energy_out(p(1000),graphite)
|
|
||||||
self.assertAlmostEqual(res.Eout,997.077,1)
|
|
||||||
self.assertAlmostEqual(res["Eout"],997.077,1)
|
|
||||||
self.assertAlmostEqual(res.Eout,res2,3)
|
|
||||||
|
|
||||||
def test_eout_list(self):
|
|
||||||
graphite = catima.get_material(6)
|
|
||||||
graphite.thickness(0.5)
|
|
||||||
p = catima.Projectile(12,6)
|
|
||||||
energies = [100,500,1000]
|
|
||||||
res = catima.calculate(p(1000),graphite)
|
|
||||||
self.assertAlmostEqual(res.Eout,997.077,1)
|
|
||||||
res2 = catima.energy_out(p,graphite,energy=energies)
|
|
||||||
self.assertEqual(len(res2),len(energies))
|
|
||||||
self.assertAlmostEqual(res2[2], 997.077,1)
|
|
||||||
self.assertAlmostEqual(res2[0], catima.calculate(p(energies[0]),graphite).Eout ,1)
|
|
||||||
self.assertAlmostEqual(res2[1], catima.calculate(p(energies[1]),graphite).Eout ,1)
|
|
||||||
|
|
||||||
def test_dedx_from_range_list(self):
|
|
||||||
graphite = catima.get_material(6)
|
|
||||||
graphite.thickness(0.5)
|
|
||||||
p = catima.Projectile(12,6)
|
|
||||||
energies = [100,500,1000]
|
|
||||||
res2 = catima.dedx_from_range(p,graphite,energy=energies)
|
|
||||||
self.assertEqual(len(res2),len(energies))
|
|
||||||
self.assertEqual(len(res2),3)
|
|
||||||
for i,e in enumerate(energies):
|
|
||||||
r = catima.dedx_from_range(p, graphite, energy=e)
|
|
||||||
print(r)
|
|
||||||
print(res2)
|
|
||||||
self.assertAlmostEqual(res2[i], r, 0.1)
|
|
||||||
|
|
||||||
def test_layer_calculation(self):
|
|
||||||
p = catima.Projectile(12,6)
|
|
||||||
Water = catima.get_material(catima.material.Water)
|
|
||||||
Water.thickness(10.0)
|
|
||||||
graphite = catima.get_material(6)
|
|
||||||
graphite.thickness(1.0)
|
|
||||||
graphite.density(2.0)
|
|
||||||
|
|
||||||
mat = catima.Layers()
|
|
||||||
mat.add(Water)
|
|
||||||
mat.add(graphite)
|
|
||||||
res = catima.calculate_layers(p(1000),mat)
|
|
||||||
self.assertEqual(len(res.results),2)
|
|
||||||
self.assertAlmostEqual(res.total_result.Eout,926.3,1)
|
|
||||||
self.assertAlmostEqual(res.total_result.sigma_a,0.00269,1)
|
|
||||||
self.assertAlmostEqual(res["Eout"],926.3,1)
|
|
||||||
self.assertAlmostEqual(res["sigma_a"],0.00269,4)
|
|
||||||
self.assertAlmostEqual(res["tof"],0.402,2)
|
|
||||||
self.assertAlmostEqual(res["Eloss"],884,0)
|
|
||||||
|
|
||||||
self.assertAlmostEqual(res[0]["Eout"],932.24,0)
|
|
||||||
self.assertAlmostEqual(res[1]["Eout"],926.3,0)
|
|
||||||
self.assertAlmostEqual(res[0]["sigma_a"],0.00258,4)
|
|
||||||
self.assertAlmostEqual(res[1]["sigma_a"],0.000774,4)
|
|
||||||
self.assertAlmostEqual(res[0]["range"],107.1,0)
|
|
||||||
self.assertAlmostEqual(res[1]["range"],111.3,0)
|
|
||||||
|
|
||||||
def test_energy_table(self):
|
|
||||||
table = catima.get_energy_table()
|
|
||||||
self.assertEqual(table[0],math.log(catima.logEmin))
|
|
||||||
#self.assertEqual(table[10],catima.energy_table(10))
|
|
||||||
self.assertEqual(len(table),catima.max_datapoints)
|
|
||||||
|
|
||||||
def test_storage(self):
|
|
||||||
p = catima.Projectile(12,6)
|
|
||||||
Water = catima.get_material(catima.material.Water)
|
|
||||||
Water.thickness(10.0)
|
|
||||||
graphite = catima.get_material(6)
|
|
||||||
graphite.thickness(1.0)
|
|
||||||
|
|
||||||
data = catima.get_data(p, Water)
|
|
||||||
print(data[0])
|
|
||||||
et = catima.get_energy_table()
|
|
||||||
|
|
||||||
self.assertEqual(len(data),3)
|
|
||||||
self.assertEqual(len(data[0]),len(et))
|
|
||||||
self.assertEqual(len(data[0]),catima.max_datapoints)
|
|
||||||
|
|
||||||
res = catima.calculate(p(et[10]),Water)
|
|
||||||
self.assertAlmostEqual(res.range,data[0][10],6)
|
|
||||||
self.assertAlmostEqual(catima.projectile_range(p,Water),data[0][10],6)
|
|
||||||
#self.assertAlmostEqual(catima.domega2de(p,Water),data[1][10],6)
|
|
||||||
|
|
||||||
res = catima.calculate(p(et[100]),Water)
|
|
||||||
self.assertAlmostEqual(res.range,data[0][100],6)
|
|
||||||
self.assertAlmostEqual(catima.projectile_range(p,Water),data[0][100],6)
|
|
||||||
#self.assertAlmostEqual(catima.domega2de(p,Water),data[1][100],6)
|
|
||||||
|
|
||||||
res = catima.calculate(p(et[200]),Water)
|
|
||||||
self.assertAlmostEqual(res.range,data[0][200],6)
|
|
||||||
self.assertAlmostEqual(catima.projectile_range(p,Water),data[0][200],6)
|
|
||||||
#self.assertAlmostEqual(catima.domega2de(p,Water),data[1][200],6)
|
|
||||||
|
|
||||||
res = catima.calculate(p(et[401]),Water)
|
|
||||||
self.assertAlmostEqual(res.range,data[0][401],6)
|
|
||||||
self.assertAlmostEqual(catima.projectile_range(p,Water),data[0][401],6)
|
|
||||||
#self.assertAlmostEqual(catima.domega2de(p,Water),data[1][401],6)
|
|
||||||
|
|
||||||
def test_python_storage_access(self):
|
|
||||||
|
|
||||||
p = catima.Projectile(12,6)
|
|
||||||
Water = catima.get_material(catima.material.Water)
|
|
||||||
Water.thickness(10.0)
|
|
||||||
graphite = catima.get_material(6)
|
|
||||||
graphite.thickness(1.0)
|
|
||||||
data = catima.get_data(p, Water)
|
|
||||||
self.assertEqual(catima.max_storage_data,100) # assuming 50, this has to be changed manually
|
|
||||||
r = catima.storage_info()
|
|
||||||
|
|
||||||
#self.assertAlmostEqual(catima.da2de(p,Water,et[100]),data[2][100],6)
|
|
||||||
#self.assertAlmostEqual(catima.da2de(p,Water,et[400]),data[2][400],6)
|
|
||||||
|
|
||||||
if __name__ == "__main__":
|
|
||||||
unittest.main()
|
|
||||||
Loading…
Reference in New Issue
Block a user