v2.0.0 release preparation

CHANGELOG.md

@@ -1,4 +1,34 @@
 # CHANGELOG
+## v2.0.0, 2025-08-29
+
+- See beta.1 notes
+- Support for v1.3 BDE integrator rewrite 
+- Support for v1.3 distribution divergence stencil
+- Support for v1.3 diagonal kinetic stencil upgrade
+
+### Breaking Changes
+
+- See beta.1 notes
+
+### Deprecations
+
+- See beta.1 notes
+
+### New Features
+
+- See beta.1 notes
+- Updated BDE integrator options 
+- New DistDivStencil class that includes the Jacobian in d/dx operator for distributions
+- New harmonicOffset argument for diagonal stencil to allow for direct harmonic coupling
+- Added option to have the first moment modelbound variables (rate1*) in CRMModelboundData living on the dual grid
+
+### Bug Fixes
+
+- N/A
+
+### New Notebooks 
+
+- See beta.1 notes
 
 ## v2.0.0-beta.1, 2025-03-13
 
@@ -207,4 +237,4 @@
 
 ### Bug Fixes
 
-- N/A
+- N/A

README.md

@@ -12,7 +12,7 @@ RMK_support is a collection of tools designed to configure and analyze ReMKiT1D
 
 ReMKiT1D runs use JSON files to configure the models and methods used by the code, and RMK_support provides convenient Python routines for the generation of these config files, while also providing features that enable analysis of data using obtained from ReMKiT1D runs.
 
-For a high level overview of the framework and the (pre-v2.0.0) Python interface see the [code paper](https://www.sciencedirect.com/science/article/pii/S0010465524001188). For detailed documentation of the Python package see [here](https://readthedocs.org/projects/remkit1d-python/).
+For a high level overview of the framework and the (pre-v2.0.0) Python interface see the [code paper](https://www.sciencedirect.com/science/article/pii/S0010465524001188). For detailed documentation of the Python package see [here](https://remkit1d-python.readthedocs.io/en/latest/).
 
 ## Prerequisites 
 
@@ -181,6 +181,18 @@ The secondary feature of RMK_support modules is data analysis and visualization,
 
 From v2.0.0 a new dynamic, composable, and extensible dashboard is available through `ElementDisplay` objects, which can be composed into a [panel](https://panel.holoviz.org/) app.
 
+For example, running the below cell in the [advection with outflow](https://github.com/ukaea/ReMKiT1D-Python/blob/master/examples/gaussian_advection_outflow.ipynb) after running the [advection](https://github.com/ukaea/ReMKiT1D-Python/blob/master/examples/ReMKiT1D_advection_test.ipynb) example will serve the pre-built dashboard (NOTE: some issues encountered with newer versions of Firefox, try serving in another browser if the dashboard is not rendering).
+
+```python
+from RMK_support.dashboard_support import dashboard
+
+runPaths={"outflow":rk.IOContext.HDF5Dir,"no-outflow":"./RMKOutput/RMK_advection_test/"}
+plt.rcParams['figure.dpi'] = 150
+hv.output(size=50,dpi=150)
+dashboard(rk,runPaths=runPaths,elementsPerTab=2).servable().show()
+```
+
+
 ![](docs/dashboard_example.png "ReMKiT1D v2.0.0 dashboard")
 
 ## Documentation, examples and tutorials
@@ -189,11 +201,11 @@ For a high level explanation of both the framework and the interface the user is
 
 The examples in the examples directory supplement the code paper, in particular the [advection](https://github.com/ukaea/ReMKiT1D-Python/blob/master/examples/ReMKiT1D_advection_test.ipynb) example partly reproduced in this readme. 
 
-A collection of simplified tutorials which are meant to showcase the syntax without producing runnable scripts are available in the tutorials directory.
+A collection of simplified tutorials which are meant to showcase the syntax without necessarily producing runnable scripts are available in the tutorials directory.
 
 For the list of the newest example notebooks, where new features are covered, see the CHANGELOG.
 
-Further code documentation is available [here](https://readthedocs.org/projects/remkit1d-python/), where more detailed resources can be found.
+Further code documentation is available [here](https://remkit1d-python.readthedocs.io/en/latest/), where more detailed resources can be found.
 
 ## Licence
 
@@ -203,4 +215,4 @@ RMK_support is distributed in the hope that it will be useful, but WITHOUT ANY W
 
 You should have received a copy of the GNU General Public License along with RMK_support. If not, see <https://www.gnu.org/licenses/>. 
 
-Copyright 2023 United Kingdom Atomic Energy Authority
+Copyright 2023 United Kingdom Atomic Energy Authority

RMK_support/calculation_tree_support.py

@@ -320,24 +320,24 @@ def latex(self, latexRemap: Dict[str, str] = {}) -> str:
 
         else:
             if self.additiveMode:
-                childrenResult = "+".join(
+                childrenResult = " + ".join(
                     child.latex(latexRemap) for child in self.children
                 )
 
             else:
                 childrenResult = const + "".join(
                     (
-                        "\\left(" + child.latex(latexRemap) + "\\right)"
+                        "(" + child.latex(latexRemap) + ")"
                         if child.additiveMode
                         else child.latex(latexRemap)
                     )
                     for child in self.children
                 )
 
         if self.unaryTransform is None:
-            return childrenResult.replace("+-", "-")
+            return childrenResult.replace("+ -", " - ")
 
-        return self.unaryTransform.latex(childrenResult).replace("+-", "-")
+        return self.unaryTransform.latex(childrenResult).replace("+ -", " - ")
 
 
 class UnaryTransform:
@@ -542,7 +542,7 @@ def powUnary(power: Union[int, float]) -> UnaryTransform:
             "ipow",
             intParams=[power],
             unaryCallable=func,
-            latexTemplate="\\left($0\\right)^{$1}",
+            latexTemplate="($0)^{$1}",
         )
         return transform
 
@@ -551,7 +551,7 @@ def powUnary(power: Union[int, float]) -> UnaryTransform:
         "rpow",
         realParams=[power],
         unaryCallable=func,
-        latexTemplate="\\left($0\\right)^{$1}",
+        latexTemplate="($0)^{$1}",
     )
     return transform
 

RMK_support/common_models.py

@@ -289,7 +289,7 @@ def implicitTemperatures(
     species: List[Species],
     norms: Dict[str, float],
     speciesFluxes: Optional[List[Variable]] = None,
-    **kwargs
+    **kwargs,
 ) -> mc.Model:
     """Generate implicit temperature derivation matrix terms for each species: d*n_b*k*T_b/2 + m_b*n_b*u_b**2/2 = W_b, where d is the number of degrees of freedom. Temperatures here are assumed to be stationary and implicit variables. The kinetic energy contribution uses interpolation, so should be used with care in regions of poorly resolved flow gradients. Assumes default normalization.
 

RMK_support/common_variables.py

@@ -4,10 +4,60 @@
 from .variable_container import Variable, node
 from .derivations import Species
 from . import derivations
-from .remkit_context import RMKContext
 from abc import ABC, abstractmethod
 
 
+def timeDerivative(
+    name: str, timeNorm: float, variable: Variable, **kwargs
+) -> Variable:
+    """Generate a time derivative of a given variable as a variable, making sure units and grids are correct.
+
+    Args:
+        name (str): Variable name for the time derivative
+        timeNorm (float): Time normalisation
+        variable (Variable): Variable whose derivative should be taken
+
+    Returns:
+        Variable: Variable with correct time derivative units
+    """
+
+    for key in [
+        "units",
+        "unitSI",
+        "normSI",
+        "isOnDualGrid",
+        "isDistribution",
+        "isSingleHarmonic",
+        "isScalar",
+        "subtype",
+    ]:
+        assert key not in kwargs, key + " not allowed in time derivative variable call"
+
+    latexWrapped = "$" in variable.unitsSI
+    unitSI = variable.unitsSI.replace("$", "") + "/s"
+    if latexWrapped:
+        unitSI = "$" + unitSI + "$"
+    var = Variable(
+        name,
+        variable.grid,
+        **kwargs,
+        units=variable.unitsNorm + " / time norm.",
+        unitSI=unitSI,
+        normSI=variable.normSI / timeNorm,
+        isOnDualGrid=variable.isOnDualGrid,
+        isScalar=variable.isScalar,
+        isDistribution=variable.isDistribution,
+        isSingleHarmonics=variable.isSingleHarmonic,
+        subtype=variable.subtype + "_time_derivative",
+    )
+
+    return var
+
+
+# cyclic import workaround
+from .remkit_context import RMKContext
+
+
 def density(name: str, context: RMKContext, **kwargs) -> Variable:
     """Generate a density variable based on normalisation data within a RMKContext. Accepts regular Variable kwargs, except for those having to do with units, which are set automatically.
 
@@ -29,7 +79,7 @@ def density(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. density",
         unitSI="$m^{-3}$",
-        normSI=context.normDensity
+        normSI=context.normDensity,
     )
 
     return var
@@ -57,7 +107,7 @@ def temperature(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. temperature",
         unitSI="eV",
-        normSI=context.normTemperature
+        normSI=context.normTemperature,
     )
 
     return var
@@ -85,7 +135,7 @@ def flux(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. flux",
         unitSI="$m^{-2}s{-1}$",
-        normSI=context.normDensity * context.norms["speed"]
+        normSI=context.normDensity * context.norms["speed"],
     )
 
     return var
@@ -114,7 +164,7 @@ def speed(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. speed",
         unitSI="$ms^{-1}$",
-        normSI=context.norms["speed"]
+        normSI=context.norms["speed"],
     )
 
     return var
@@ -143,7 +193,7 @@ def energyDensity(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. en. density",
         unitSI="$eV m^{-3}$",
-        normSI=context.normDensity * context.normTemperature
+        normSI=context.normDensity * context.normTemperature,
     )
 
     return var
@@ -172,7 +222,7 @@ def energyFlux(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. en. flux",
         unitSI="$eV m^{-2} s^{-1}$",
-        normSI=context.norms["heatFlux"]
+        normSI=context.norms["heatFlux"],
     )
 
     return var
@@ -201,7 +251,7 @@ def electricField(name: str, context: RMKContext, **kwargs) -> Variable:
         **kwargs,
         units="norm. el. field",
         unitSI="$Vm{-1}$",
-        normSI=context.norms["EField"]
+        normSI=context.norms["EField"],
     )
 
     return var
@@ -284,7 +334,12 @@ def density(self, initVals: Optional[np.ndarray] = None) -> Variable:
         Returns:
             Variable: Standard density variable
         """
-        n = density("n" + self.species.name, self.__context__, data=initVals).withDual()
+        n = density(
+            "n" + self.species.name,
+            self.__context__,
+            data=initVals,
+            defaultLatex="n_{" + self.species.latex() + "}",
+        ).withDual()
         if self.__associateOnCreation__:
             if n.name not in self.species.associatedVarNames:
                 self.species.associateVar(n, n.dual)
@@ -308,7 +363,12 @@ def flux(self, initVals: Optional[np.ndarray] = None) -> Variable:
             self.__context__,
             isOnDualGrid=True,
             data=initVals,
-        ).withDual("G" + self.species.name)
+            defaultLatex="\\left(\\vec{\\Gamma}_{"
+            + self.species.name
+            + "}\\right)_{dual}",
+        ).withDual(
+            "G" + self.species.name, "\\vec{\\Gamma}_{" + self.species.latex() + "}"
+        )
         if self.__associateOnCreation__:
             if G.name not in self.species.associatedVarNames:
                 self.species.associateVar(G, G.dual)
@@ -328,7 +388,10 @@ def energyDensity(self, initVals: Optional[np.ndarray] = None) -> Variable:
             Variable: Standard energy density variable
         """
         W = energyDensity(
-            "W" + self.species.name, self.__context__, data=initVals
+            "W" + self.species.name,
+            self.__context__,
+            data=initVals,
+            defaultLatex="W_{" + self.species.latex() + "}",
         ).withDual()
         if self.__associateOnCreation__:
             if W.name not in self.species.associatedVarNames:
@@ -349,7 +412,11 @@ def temperature(self, initVals: Optional[np.ndarray] = None) -> Variable:
             Variable: Standard temperature variable
         """
         T = temperature(
-            "T" + self.species.name, self.__context__, data=initVals, isStationary=True
+            "T" + self.species.name,
+            self.__context__,
+            data=initVals,
+            isStationary=True,
+            defaultLatex="T_{" + self.species.latex() + "}",
         ).withDual()
         if self.__associateOnCreation__:
             if T.name not in self.species.associatedVarNames:
@@ -379,7 +446,10 @@ def flowSpeed(self, initVals: Optional[np.ndarray] = None) -> Variable:
                 "n" + self.species.name + "_dual",
             ],
             isOnDualGrid=True,
-        ).withDual("u" + self.species.name)
+            defaultLatex="\\left(\\vec{u}_{"
+            + self.species.latex()
+            + "}\\right)_{dual}",
+        ).withDual("u" + self.species.name, "\\vec{u}_{" + self.species.latex() + "}")
         if self.__associateOnCreation__:
             if u.name not in self.species.associatedVarNames:
                 self.species.associateVar(u, u.dual)
@@ -405,7 +475,10 @@ def heatflux(self, initVals: Optional[np.ndarray] = None) -> Variable:
             isStationary=True,
             isOnDualGrid=True,
             subtype="heatflux",
-        ).withDual("q" + self.species.name)
+            defaultLatex="\\left(\\vec{q}_{"
+            + self.species.latex()
+            + "}\\right)_{dual}",
+        ).withDual("q" + self.species.name, "\\vec{q}_{" + self.species.latex() + "}")
         if self.__associateOnCreation__:
             if q.name not in self.species.associatedVarNames:
                 self.species.associateVar(q, q.dual)
@@ -433,6 +506,7 @@ def pressure(self, initVals: Optional[np.ndarray] = None) -> Variable:
                 node=node(self.density()) * node(self.temperature()),
             ),
             subtype="pressure",
+            defaultLatex="p_{" + self.species.latex() + "}",
         ).withDual()
         if self.__associateOnCreation__:
             if p.name not in self.species.associatedVarNames:
@@ -458,6 +532,7 @@ def viscosity(self, initVals: Optional[np.ndarray] = None) -> Variable:
             data=initVals,
             isStationary=True,
             subtype="viscosity",
+            defaultLatex="\\Pi_{" + self.species.latex() + "}",
         ).withDual()
         if self.__associateOnCreation__:
             if pi.name not in self.species.associatedVarNames: