Merge pull request #27 from thermotools/init_with_params

Init with params
thermotools · Apr 18, 2024 · 2aaecaf · 2aaecaf
2 parents 36d2a18 + f3f8865
commit 2aaecaf
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diff --git a/docs/vCurrent/MieKinGas_methods.md b/docs/vCurrent/MieKinGas_methods.md
@@ -6,7 +6,7 @@ permalink: /vcurrent/MieKinGas_methods.html
 ---
 
 <!--- 
-Generated at: 2023-11-06T12:02:00.296867
+Generated at: 2024-04-18T17:40:59.602391
 This is an auto-generated file, generated using the script at KineticGas/pyUtils/markdown_from_docstrings.py
 The file is created by parsing the docstrings of the methods in the 
 MieKinGas class. For instructions on how to use the parser routines, see the
@@ -17,18 +17,25 @@ RET-Mie Model. This class implements utility methods to access mixing parameters
 
 ## Table of contents
   * [Constructor](#constructor)
-    * [\_\_init\_\_](#__init__self-comps-mole_weightsnone-sigmanone-eps_div_knone-lanone-lrnone-lij0-kij0-n4-is_idealgasfalse-use_eosnone-parameter_refdefault)
+    * [\_\_init\_\_](#__init__self-comps-mole_weightsnone-sigmanone-eps_div_knone-lanone-lrnone-lij0-kij0-n4-is_idealgasfalse-use_eosnone-parameter_refdefault-use_default_eos_paramfalse)
+  * [Utility methods](#utility-methods)
+    * [set_eps_div_k](#set_eps_div_kself-eps_div_k-update_eostrue)
+    * [set_la](#set_laself-la-update_eostrue)
+    * [set_lr](#set_lrself-lr-update_eostrue)
+    * [set_sigma](#set_sigmaself-sigma-update_eostrue)
+  * [Internal methods](#internal-methods)
+    * [\_\_update_cpp_kingas_param\_\_](#__update_cpp_kingas_param__self)
 
 ## Constructor
 
 Methods to initialise RET-Mie model.
 
 ### Table of contents
   * [Constructor](#constructor)
-    * [\_\_init\_\_](#__init__self-comps-mole_weightsnone-sigmanone-eps_div_knone-lanone-lrnone-lij0-kij0-n4-is_idealgasfalse-use_eosnone-parameter_refdefault)
+    * [\_\_init\_\_](#__init__self-comps-mole_weightsnone-sigmanone-eps_div_knone-lanone-lrnone-lij0-kij0-n4-is_idealgasfalse-use_eosnone-parameter_refdefault-use_default_eos_paramfalse)
 
 
-### `__init__(self, comps, mole_weights=None, sigma=None, eps_div_k=None, la=None, lr=None, lij=0, kij=0, N=4, is_idealgas=False, use_eos=None, parameter_ref='default')`
+### `__init__(self, comps, mole_weights=None, sigma=None, eps_div_k=None, la=None, lr=None, lij=0, kij=0, N=4, is_idealgas=False, use_eos=None, parameter_ref='default', use_default_eos_param=False)`
 If parameters are explicitly supplied through optional arguments, these will be used instead of those in the database.
 To supply specific parameters for only some components, give `None` for the components that should use the database
 value
@@ -64,7 +71,52 @@ value
 
 &nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  Mixing parameter for epsilon (kij > 0 => favours mixing, kij < 0 => favours separation)
 
-&nbsp;&nbsp;&nbsp;&nbsp; **use_eos :** 
+&nbsp;&nbsp;&nbsp;&nbsp; **use_eos (thermopack eos object, optional) :** 
 
-&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  (thermopack eos object, optional) EoS to use (initialized), defaults to `saftvrmie` 
+&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  EoS to use (initialized), defaults to `saftvrmie`
+
+&nbsp;&nbsp;&nbsp;&nbsp; **use_default_eos_param (bool) :** 
+
+&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  If `False` (default), ensure that the EoS and RET-model use the same parameters(if applicable). If `False`, do not forward specified parameters to the EoS.  
+
+## Utility methods
+
+Set- and get methods for interaction parameters, mixing parameters ...
+
+### Table of contents
+  * [Utility methods](#utility-methods)
+    * [set_eps_div_k](#set_eps_div_kself-eps_div_k-update_eostrue)
+    * [set_la](#set_laself-la-update_eostrue)
+    * [set_lr](#set_lrself-lr-update_eostrue)
+    * [set_sigma](#set_sigmaself-sigma-update_eostrue)
+
+
+### `set_eps_div_k(self, eps_div_k, update_eos=True)`
+See MieType
+
+
+### `set_la(self, la, update_eos=True)`
+See MieType
+
+
+### `set_lr(self, lr, update_eos=True)`
+See MieType
+
+
+### `set_sigma(self, sigma, update_eos=True)`
+See MieType
+
+
+## Internal methods
+
+Internal methods are not intended for use by end-users.
+
+### Table of contents
+  * [Internal methods](#internal-methods)
+    * [\_\_update_cpp_kingas_param\_\_](#__update_cpp_kingas_param__self)
+
+
+### `__update_cpp_kingas_param__(self)`
+See MieType
+
 
diff --git a/docs/vCurrent/MieType_methods.md b/docs/vCurrent/MieType_methods.md
@@ -6,7 +6,7 @@ permalink: /vcurrent/MieType_methods.html
 ---
 
 <!--- 
-Generated at: 2023-11-06T12:02:00.296431
+Generated at: 2024-04-18T17:31:55.382397
 This is an auto-generated file, generated using the script at KineticGas/pyUtils/markdown_from_docstrings.py
 The file is created by parsing the docstrings of the methods in the 
 MieType class. For instructions on how to use the parser routines, see the
@@ -22,8 +22,13 @@ Mie-Type Model. This class implements utility methods to access mixing parameter
     * [get_epsilon_matrix](#get_epsilon_matrixself-eps_div_k-kij)
     * [get_lambda_matrix](#get_lambda_matrixself-lambdas-lij)
     * [get_sigma_matrix](#get_sigma_matrixself-sigma)
-  * [Deprecated methods](#deprecated-methods)
-    * [get_avg_R](#get_avg_rself-t-x)
+    * [set_eps_div_k](#set_eps_div_kself-eps_div_k-update_eostrue)
+    * [set_la](#set_laself-la-update_eostrue)
+    * [set_lr](#set_lrself-lr-update_eostrue)
+    * [set_sigma](#set_sigmaself-sigma-update_eostrue)
+  * [Internal methods](#internal-methods)
+    * [\_\_update_cpp_kingas_param\_\_](#__update_cpp_kingas_param__self)
+    * [\_\_update_eos_param\_\_](#__update_eos_param__self)
 
 ## Constructor
 
@@ -78,6 +83,10 @@ Set- and get methods for interaction parameters, mixing parameters ...
     * [get_epsilon_matrix](#get_epsilon_matrixself-eps_div_k-kij)
     * [get_lambda_matrix](#get_lambda_matrixself-lambdas-lij)
     * [get_sigma_matrix](#get_sigma_matrixself-sigma)
+    * [set_eps_div_k](#set_eps_div_kself-eps_div_k-update_eostrue)
+    * [set_la](#set_laself-la-update_eostrue)
+    * [set_lr](#set_lrself-lr-update_eostrue)
+    * [set_sigma](#set_sigmaself-sigma-update_eostrue)
 
 
 ### `get_epsilon_matrix(self, eps_div_k, kij)`
@@ -122,7 +131,7 @@ Compute pair-interaction $\lambda_r$ parameters, apply mixing parameter.
 &nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  Repulsive exponent for each pair-interaction. 
 
 ### `get_sigma_matrix(self, sigma)`
-Compute interaction parameter $sigma$ for each particle pair, applying mixing parameters given by `self.lij`.
+Compute interaction parameter $\sigma$ for each particle pair, applying mixing parameters given by `self.lij`.
 Warning: Use of mixing parameters is not thouroughly tested.
 
 
@@ -144,15 +153,62 @@ Warning: Use of mixing parameters is not thouroughly tested.
 
 &nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  Use of mixing parameters is not thouroughly tested.  
 
-## Deprecated methods
+### `set_eps_div_k(self, eps_div_k, update_eos=True)`
+Set the well depth parameter. Note: Running with `update_eos=False` will result in a model using
+different parameters for collision integrals and the RDF than for the equation of state.
 
-Deprecated methods are not maintained, and may be removed in the future.
+Args:
+eps_div_k (list[float or None]) : Well depth parameter for each pure component. Use `None` for default values. Unit (K).
+update_eos (bool) : If True (default) also update the eos.
+
+
+### `set_la(self, la, update_eos=True)`
+Set the attractive exponent. Note: Running with `update_eos=False` will result in a model using
+different parameters for collision integrals and the RDF than for the equation of state.
+
+Args:
+la (list[float or None]) : Attractive exponent for each pure component. Use `None` for default values.
+update_eos (bool) : If True (default) also update the eos.
+
+
+### `set_lr(self, lr, update_eos=True)`
+Set the repulsive exponent. Note: Running with `update_eos=False` will result in a model using
+different parameters for collision integrals and the RDF than for the equation of state.
+
+Args:
+lr (list[float or None]) : Repulsive exponent for each pure component. Use `None` for default values.
+update_eos (bool) : If True (default) also update the eos.
+
+
+### `set_sigma(self, sigma, update_eos=True)`
+Set the size parameter. Note: Running with `update_eos=False` will result in a model using
+different parameters for collision integrals and the RDF than for the equation of state.
+
+Args:
+sigma (list[float or None]) : Size parameter for each pure component. Use `None` for default values. Unit (m).
+update_eos (bool) : If True (default) also update the eos.
+
+
+## Internal methods
+
+Internal methods are not intended for use by end-users.
 
 ### Table of contents
-  * [Deprecated methods](#deprecated-methods)
-    * [get_avg_R](#get_avg_rself-t-x)
+  * [Internal methods](#internal-methods)
+    * [\_\_update_cpp_kingas_param\_\_](#__update_cpp_kingas_param__self)
+    * [\_\_update_eos_param\_\_](#__update_eos_param__self)
+
+
+### `__update_cpp_kingas_param__(self)`
+Re-Initialize the C++ module with the current parameters in this model. Inheriting classes are responsible
+for initializing the correct model.
+
 
+### `__update_eos_param__(self)`
+Update the EoS model to use the same parameters as this model is currently set with.
 
-### `get_avg_R(self, T, x)`
+Raises:
+AttributeError : If the EoS object does not support setting parameters
+Warning : If the EoS object is using segment numbers different from 1.
 
 
diff --git a/docs/vCurrent/py_KineticGas_methods.md b/docs/vCurrent/py_KineticGas_methods.md
@@ -6,7 +6,7 @@ permalink: /vcurrent/py_KineticGas_methods.html
 ---
 
 <!--- 
-Generated at: 2024-04-16T15:54:30.853573
+Generated at: 2024-04-18T17:57:40.002828
 This is an auto-generated file, generated using the script at KineticGas/pyUtils/markdown_from_docstrings.py
 The file is created by parsing the docstrings of the methods in the 
 py_KineticGas class. For instructions on how to use the parser routines, see the
@@ -31,7 +31,7 @@ The `py_KineticGas` class, found in `pykingas/py_KineticGas.py`, is the core of
     * [viscosity](#viscosityself-t-vm-x-nnone)
   * [Tp-property interfaces](#tp-property-interfaces)
     * [interdiffusion_tp](#interdiffusion_tpself-t-p-x-nnone-use_independenttrue-dependent_idxnone-frame_of_referencecon-use_binarytrue-solvent_idxnone)
-    * [thermal_coductivity_tp](#thermal_coductivity_tpself-t-p-x-nnone)
+    * [thermal_conductivity_tp](#thermal_conductivity_tpself-t-p-x-nnone)
     * [thermal_diffusion_coeff_tp](#thermal_diffusion_coeff_tpself-t-p-x-nnone-use_independentfalse-dependent_idxnone-frame_of_referencecon-solvent_idxnone)
     * [thermal_diffusion_factor_tp](#thermal_diffusion_factor_tpself-t-p-x-nnone)
     * [viscosity_tp](#viscosity_tpself-t-p-x-nnone)
@@ -58,6 +58,8 @@ The `py_KineticGas` class, found in `pykingas/py_KineticGas.py`, is the core of
     * [get_Eij](#get_eijself-vm-t-x)
     * [get_P_factors](#get_p_factorsself-vm-t-x)
     * [reshape_diffusion_coeff_vector](#reshape_diffusion_coeff_vectorself-d)
+  * [Deprecated methods](#deprecated-methods)
+    * [thermal_coductivity_tp](#thermal_coductivity_tpself-t-p-x-nnone)
 
 ## The constructor
 
@@ -550,7 +552,7 @@ Computing properties as a function of temperature and pressure. Simply forwards
 ### Table of contents
   * [Tp-property interfaces](#tp-property-interfaces)
     * [interdiffusion_tp](#interdiffusion_tpself-t-p-x-nnone-use_independenttrue-dependent_idxnone-frame_of_referencecon-use_binarytrue-solvent_idxnone)
-    * [thermal_coductivity_tp](#thermal_coductivity_tpself-t-p-x-nnone)
+    * [thermal_conductivity_tp](#thermal_conductivity_tpself-t-p-x-nnone)
     * [thermal_diffusion_coeff_tp](#thermal_diffusion_coeff_tpself-t-p-x-nnone-use_independentfalse-dependent_idxnone-frame_of_referencecon-solvent_idxnone)
     * [thermal_diffusion_factor_tp](#thermal_diffusion_factor_tpself-t-p-x-nnone)
     * [viscosity_tp](#viscosity_tpself-t-p-x-nnone)
@@ -561,7 +563,7 @@ Compute molar volume using the internal equation of state (`self.eos`), assuming
 `self.interdiffusion`. See `self.interdiffusion` for documentation.
 
 
-### `thermal_coductivity_tp(self, T, p, x, N=None)`
+### `thermal_conductivity_tp(self, T, p, x, N=None)`
 Compute molar volume using the internal equation of state (`self.eos`), assuming vapour, and pass the call to
 `self.thermal_conductivity`. See `self.thermal_conductivity` for documentation.
 
@@ -1161,3 +1163,16 @@ as `d[i][q][j]` where i and j are component indices, and q refferes to the appro
 
 &nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;  The matrix of $d_{i, j}^{(q)}$ coefficients ordered as `d[i][q][j]` 
 
+## Deprecated methods
+
+Deprecated methods are not maintained, and may be removed in the future.
+
+### Table of contents
+  * [Deprecated methods](#deprecated-methods)
+    * [thermal_coductivity_tp](#thermal_coductivity_tpself-t-p-x-nnone)
+
+
+### `thermal_coductivity_tp(self, T, p, x, N=None)`
+Slightly embarrasing typo in method name... Keeping alive for a while because some code out there uses this one.
+
+
diff --git a/pyUtils/markdown_from_docstrings.py b/pyUtils/markdown_from_docstrings.py
@@ -175,6 +175,7 @@ def split_methods_by_section(sections, methods):
 
     if 'deprecated' not in [s.lower() for s in sections]:
         sections.append('Deprecated')
+        sections.append('Internal')
 
     method_dict = {}
     for name, meth in methods:
@@ -224,6 +225,14 @@ def get_automatic_sections(sections, section_headers, section_intro, method_dict
         if 'Deprecated' not in section_intro.keys():
             section_intro['Deprecated'] = 'Deprecated methods are not maintained, and may be removed in the future.'
 
+    if 'Internal' in method_dict.keys():
+        if 'Internal' not in sections:
+            sections.append('Internal')
+        if 'Internal' not in section_headers.keys():
+            section_headers['Internal'] = 'Internal methods'
+        if 'Internal' not in section_intro.keys():
+            section_intro['Internal'] = 'Internal methods are not intended for use by end-users.'
+
     return sections, section_headers, section_intro
 
 def get_toc(sections, section_headers, method_dict, is_subsection=False):
@@ -387,7 +396,6 @@ def miekingas_to_markdown():
     class_methods = inspect.getmembers(MieKinGas, predicate=inspect.isfunction)
     parent_methods = inspect.getmembers(MieType, predicate=inspect.isfunction)
     specific_methods = sorted(list(set(class_methods) - set(parent_methods)))
-
     basic_class_to_markdown(classname, eosname, specific_methods, inherits='MieType')
 
 def hardsphere_to_markdown():

diff --git a/pykingas/MieKinGas.py b/pykingas/MieKinGas.py
@@ -4,14 +4,15 @@
 '''
 from pykingas import cpp_MieKinGas, MieType
 from thermopack.saftvrmie import saftvrmie
+from thermopack.saft import saft
 
 class MieKinGas(MieType.MieType):
 
     def __init__(self, comps,
                  mole_weights=None, sigma=None, eps_div_k=None,
                  la=None, lr=None, lij=0, kij=0,
                  N=4, is_idealgas=False, use_eos=None,
-                 parameter_ref='default'):
+                 parameter_ref='default', use_default_eos_param=False):
         """Constructor
         If parameters are explicitly supplied through optional arguments, these will be used instead of those in the database.
         To supply specific parameters for only some components, give `None` for the components that should use the database
@@ -25,15 +26,17 @@ def __init__(self, comps,
             la, lr (1D array) : attractive and repulsive exponent of the pure components [-]
             lij (float) : Mixing parameter for sigma (lij > 0 => smaller sigma_12, lij < 0 => larger sigma_12)
             kij (float) : Mixing parameter for epsilon (kij > 0 => favours mixing, kij < 0 => favours separation)
-            use_eos : (thermopack eos object, optional) EoS to use (initialized), defaults to `saftvrmie`
+            use_eos (thermopack eos object, optional) : EoS to use (initialized), defaults to `saftvrmie`
+            use_default_eos_param (bool) : If `False` (default), ensure that the EoS and RET-model use the same parameters
+                                            (if applicable). If `False`, do not forward specified parameters to the EoS.
         """
         super().__init__(comps, 'Mie',
                     mole_weights=mole_weights, sigma=sigma,
                     eps_div_k=eps_div_k, la=la, lr=lr, lij=lij, kij=kij,
                     N=N, is_idealgas=is_idealgas,
                     parameter_ref=parameter_ref)
 
-        self.cpp_kingas = cpp_MieKinGas(self.mole_weights, self.sigma_ij, self.epsilon_ij, self.la, self.lr, self.is_idealgas)
+        self.__update_cpp_kingas_param__()
         if self.is_idealgas is False:
             if use_eos is None:
                 self.eos = saftvrmie()
@@ -43,3 +46,43 @@ def __init__(self, comps,
                     self.eos.init(comps, parameter_reference=parameter_ref)
             else:
                 self.eos = use_eos
+
+            if isinstance(self.eos, saft) and (use_default_eos_param is False):
+                self.__update_eos_param__()
+
+    def __update_cpp_kingas_param__(self):
+        """Internal
+        See MieType
+        """
+        self.cpp_kingas = cpp_MieKinGas(self.mole_weights, self.sigma_ij, self.epsilon_ij, self.la, self.lr,
+                                        self.is_idealgas)
+
+    def set_sigma(self, sigma, update_eos=True):
+        """Utility
+        See MieType
+        """
+        super().set_sigma(sigma, update_eos=update_eos)
+        self.__update_cpp_kingas_param__()
+
+    def set_eps_div_k(self, eps_div_k, update_eos=True):
+        """Utility
+        See MieType
+        """
+        super().set_eps_div_k(eps_div_k, update_eos=update_eos)
+        self.__update_cpp_kingas_param__()
+
+    def set_la(self, la, update_eos=True):
+        """Utility
+        See MieType
+        """
+        super().set_la(la, update_eos=update_eos)
+        self.__update_cpp_kingas_param__()
+
+    def set_lr(self, lr, update_eos=True):
+        """Utility
+        See MieType
+        """
+        super().set_lr(lr, update_eos=update_eos)
+        self.__update_cpp_kingas_param__()
+
+