Commit 4aee1e47 authored by Santiago Ospina De Los Ríos's avatar Santiago Ospina De Los Ríos

Merge branch 'run-dorie-create-immediately' into 'master'

Update default simulation config files

See merge request !183
parents 00e61325 2e353b5c
...@@ -62,6 +62,7 @@ ...@@ -62,6 +62,7 @@
* Deploy online documentation for each branch to private server !163 * Deploy online documentation for each branch to private server !163
* Use YAML (instead of muPhi `.bcdat`) files for specifying BCs !121 * Use YAML (instead of muPhi `.bcdat`) files for specifying BCs !121
* Unit and system tests report code coverage separately !172 * Unit and system tests report code coverage separately !172
* Improve docs on config file parameters and make default ones executable !183
### Fixed ### Fixed
* Allow meta-ini files for unit tests !101 * Allow meta-ini files for unit tests !101
......
...@@ -7,8 +7,8 @@ configure_file(${CMAKE_CURRENT_BINARY_DIR}/tutorial-1.ini ...@@ -7,8 +7,8 @@ configure_file(${CMAKE_CURRENT_BINARY_DIR}/tutorial-1.ini
COPYONLY) COPYONLY)
# Copy files needed for the test to run # Copy files needed for the test to run
configure_file(${CMAKE_BINARY_DIR}/doc/default_files/infiltration.yml configure_file(${CMAKE_BINARY_DIR}/doc/default_files/richards_bc.yml
infiltration.yml richards_bc.yml
COPYONLY) COPYONLY)
configure_file(${CMAKE_BINARY_DIR}/doc/default_files/richards_param.yml configure_file(${CMAKE_BINARY_DIR}/doc/default_files/richards_param.yml
richards_param.yml richards_param.yml
......
...@@ -27,8 +27,8 @@ quantity = matricHead ...@@ -27,8 +27,8 @@ quantity = matricHead
equation = -h equation = -h
[richards.boundary] [richards.boundary]
file = infiltration.yml file = richards_bc.yml
[richards.output] [richards.output]
fileName = infiltr_homogeneous_sand_2D fileName = infiltr_homogeneous_sand_2D
outputPath = ./ outputPath = ./
\ No newline at end of file
...@@ -121,7 +121,7 @@ Boundary Condition ...@@ -121,7 +121,7 @@ Boundary Condition
The :doc:`boundary conditions file </manual/bcfile>` has to be specified by the The :doc:`boundary conditions file </manual/bcfile>` has to be specified by the
keyword ``richards.boundary.file`` in the configuration file. For now, we will keyword ``richards.boundary.file`` in the configuration file. For now, we will
use the infiltration file, ``infiltration.yml``, provided by the command use the boundary condition file ``richards_bc.yml`` provided by the command
``dorie create``. By default, this file sets a constant infiltration of ``dorie create``. By default, this file sets a constant infiltration of
:math:`j_w = -5.55\cdot 10^{-6}\,\text{ms}^{-1}` at the top, a constant matric :math:`j_w = -5.55\cdot 10^{-6}\,\text{ms}^{-1}` at the top, a constant matric
head of :math:`h_m = 0\,\text{m}` at the bottom, and a no-flux condition on the head of :math:`h_m = 0\,\text{m}` at the bottom, and a no-flux condition on the
...@@ -164,7 +164,7 @@ configuration file. A typical DORiE simulation has the following output: ...@@ -164,7 +164,7 @@ configuration file. A typical DORiE simulation has the following output:
[18:27:32.768 I] Creating output directory: ./ [18:27:32.768 I] Creating output directory: ./
[18:27:32.768 I] Creating a rectangular grid in 2D [18:27:32.768 I] Creating a rectangular grid in 2D
[18:27:32.776 I] [RIC] Loading parameter data file: richards_param.yml [18:27:32.776 I] [RIC] Loading parameter data file: richards_param.yml
[18:27:32.779 I] [RIC] Reading boundary condition data file: infiltration.yml [18:27:32.779 I] [RIC] Reading boundary condition data file: richards_bc.yml
[18:27:32.784 I] [RIC] Setup complete [18:27:32.784 I] [RIC] Setup complete
[18:27:33.296 I] [RIC] Time Step 0: 0.00e+00 + 1.00e+01 -> 1.00e+01 [18:27:33.296 I] [RIC] Time Step 0: 0.00e+00 + 1.00e+01 -> 1.00e+01
[18:27:33.581 I] [RIC] Time Step 1: 1.00e+01 + 1.50e+01 -> 2.50e+01 [18:27:33.581 I] [RIC] Time Step 1: 1.00e+01 + 1.50e+01 -> 2.50e+01
...@@ -194,6 +194,6 @@ shown below. ...@@ -194,6 +194,6 @@ shown below.
============= ====================================================================== ============= ======================================================================
Configuration :download:`config.ini <config.ini>` Configuration :download:`config.ini <config.ini>`
Boundary :download:`infiltration.yml </default_files/infiltration.yml>` Boundary :download:`richards_bc.yml </default_files/richards_bc.yml>`
Parameters :download:`richards_param.yml </default_files/richards_param.yml>` Parameters :download:`richards_param.yml </default_files/richards_param.yml>`
============= ====================================================================== ============= ======================================================================
...@@ -57,8 +57,8 @@ current folder. Explore them! ...@@ -57,8 +57,8 @@ current folder. Explore them!
============= ====================================================================== ============= ======================================================================
Configuration :download:`config.ini </default_files/config.ini>` Configuration :download:`config.ini </default_files/config.ini>`
Boundary :download:`infiltration.yml <../default_files/infiltration.yml>`, Boundary :download:`richards_bc.yml </default_files/richards_bc.yml>`,
:download:`solute.yml </default_files/solute.yml>` :download:`transport_bc.yml </default_files/transport_bc.yml>`
Parameters :download:`richards_param.yml </default_files/richards_param.yml>`, Parameters :download:`richards_param.yml </default_files/richards_param.yml>`,
:download:`transport_param.yml </default_files/transport_param.yml>` :download:`transport_param.yml </default_files/transport_param.yml>`
============= ====================================================================== ============= ======================================================================
...@@ -117,8 +117,8 @@ function(create_default_config INPUT OUTPUT SOURCE_DIR CSS) ...@@ -117,8 +117,8 @@ function(create_default_config INPUT OUTPUT SOURCE_DIR CSS)
endfunction() endfunction()
# copy BC & parameter files # copy BC & parameter files
file(COPY infiltration.yml file(COPY richards_bc.yml
solute.yml transport_bc.yml
richards_param.yml richards_param.yml
transport_param.yml transport_param.yml
DESTINATION .) DESTINATION .)
......
...@@ -26,6 +26,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -26,6 +26,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</definition> </definition>
<suggestion> richards </suggestion> <suggestion> richards </suggestion>
<values> richards, richards+transport </values> <values> richards, richards+transport </values>
<comment> Options: richards, richards+transport </comment>
<versionadded version="unreleased"> </versionadded> <versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
</category> </category>
...@@ -38,7 +39,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -38,7 +39,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
the corresponding grid is to be given. </definition> the corresponding grid is to be given. </definition>
<suggestion> rectangular </suggestion> <suggestion> rectangular </suggestion>
<values> rectangular, gmsh </values> <values> rectangular, gmsh </values>
<comment> Choose grid type: rectangular, gmsh </comment> <comment> Options: rectangular, gmsh </comment>
</parameter> </parameter>
<parameter name="dimensions"> <parameter name="dimensions">
...@@ -168,7 +169,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -168,7 +169,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</definition> </definition>
<values> none, waterFlux </values> <values> none, waterFlux </values>
<suggestion> none </suggestion> <suggestion> none </suggestion>
<comment> none, waterFlux </comment> <comment> Options: none, waterFlux </comment>
<versionadded version="unreleased"> Replaces ``useAdaptivity``. <versionadded version="unreleased"> Replaces ``useAdaptivity``.
</versionadded> </versionadded>
</parameter> </parameter>
...@@ -191,27 +192,28 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -191,27 +192,28 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</parameter> </parameter>
<parameter name="markingStrategy"> <parameter name="markingStrategy">
<definition> Marking strategy used in order to find the grid cells that should <definition> Marking strategy used in order to find the grid cells that
be refined / coarsened. should be refined / coarsened.
**elementFraction**: Of the N elements in the sorted list of local errors, the first * **elementFraction**: Of the N elements in the sorted list of local
&alpha;N elements are refined while the last &beta;N elements are being coarsened. errors, the first &alpha;N elements are refined while the last
&beta;N elements are being coarsened.
**errorFraction**: Refine (coarse) as many elements as necessary, such that the * **errorFraction**: Refine (coarse) as many elements as necessary,
total relative contribution of all refined (coarsened) cells to the such that the total relative contribution of all refined (coarsened)
global error is &alpha; (&beta;), starting with the most (least) contributing cells to the global error is &alpha; (&beta;), starting with the most
element. The total number of affected entities can vary greatly (least) contributing element. The total number of affected entities
between different iterations, and (with &alpha; = &beta;) much more elements can vary greatly between different iterations, and (with &alpha; =
are coarsened than refined. &beta;) much more elements are coarsened than refined.
**threshold**: All elements with a local error &eta; &gt; &alpha; are being refined once. * **threshold**: All elements with a local error &eta; &gt; &alpha; are
Coarsening occurs for all elements that carry an error smaller being refined once. Coarsening occurs for all elements that carry an
than &beta;. error smaller than &beta;.
</definition> </definition>
<values> elementFraction, errorFraction, threshold </values> <values> elementFraction, errorFraction, threshold </values>
<suggestion> elementFraction </suggestion> <suggestion> elementFraction </suggestion>
<comment> elementFraction, errorFraction, threshold </comment> <comment> Options: elementFraction, errorFraction, threshold </comment>
<versionchanged version="unreleased"> Option ``targetTolerance`` removed. <versionchanged version="unreleased"> Option ``targetTolerance`` removed.
</versionchanged> </versionchanged>
</parameter> </parameter>
...@@ -242,6 +244,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -242,6 +244,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<definition> Logging level of the core functions. </definition> <definition> Logging level of the core functions. </definition>
<suggestion> info </suggestion> <suggestion> info </suggestion>
<values> trace, debug, info, warning, error, critical </values> <values> trace, debug, info, warning, error, critical </values>
<comment> Options: trace, debug, info, warning, error, critical
</comment>
</parameter> </parameter>
<versionadded version="unreleased"> </versionadded> <versionadded version="unreleased"> </versionadded>
</category> </category>
......
...@@ -40,7 +40,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -40,7 +40,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</definition> </definition>
<values> none, binary, exponential </values> <values> none, binary, exponential </values>
<suggestion> binary </suggestion> <suggestion> binary </suggestion>
<comment> none, binary, exponential </comment> <comment> Options: none, binary, exponential </comment>
<versionadded version="unreleased"> </versionadded> <versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
...@@ -122,7 +122,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -122,7 +122,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
random field. </definition> random field. </definition>
<values> exponential, gaussian, spherical, whiteNoise </values> <values> exponential, gaussian, spherical, whiteNoise </values>
<suggestion> gaussian </suggestion> <suggestion> gaussian </suggestion>
<comment> exponential, gaussian, spherical, whiteNoise </comment> <comment> Options: exponential, gaussian, spherical, whiteNoise
</comment>
<versionchanged version="unreleased"> Renamed from <versionchanged version="unreleased"> Renamed from
``generator.fft.covariance``. </versionchanged> ``generator.fft.covariance``. </versionchanged>
</parameter> </parameter>
......
...@@ -26,13 +26,14 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -26,13 +26,14 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<parameter name="outputPath"> <parameter name="outputPath">
<definition> Path to the directory where most of the outputs are stored. <definition> Path to the directory where most of the outputs are stored.
DORiE will attempt to create it if it does not exist. </definition> DORiE will attempt to create it if it does not exist. </definition>
<suggestion> ./ </suggestion> <suggestion> output_richards </suggestion>
<values> path </values> <values> path </values>
</parameter> </parameter>
<parameter name="fileName"> <parameter name="fileName">
<definition> Base file name for VTK output. </definition> <definition> Base file name for VTK output. </definition>
<values> string </values> <values> string </values>
<suggestion> output_richards </suggestion>
</parameter> </parameter>
<parameter name="vertexData"> <parameter name="vertexData">
...@@ -46,9 +47,12 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -46,9 +47,12 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</parameter> </parameter>
<parameter name="policy"> <parameter name="policy">
<definition> Policy to write the data. </definition> <definition> Policy when to write the data. ``none`` disables output
for this model.
</definition>
<suggestion> endOfRichardsStep </suggestion> <suggestion> endOfRichardsStep </suggestion>
<values> endOfRichardsStep, none </values> <values> endOfRichardsStep, none </values>
<comment> Options: endOfRichardsStep, none </comment>
<versionadded version="unreleased"> </versionadded> <versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
...@@ -77,9 +81,9 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -77,9 +81,9 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<category name="boundary"> <category name="boundary">
<parameter name="file"> <parameter name="file">
<definition> Path to the YAML boundary condition data file. <definition> Path to the YAML boundary condition data file.
<suggestion> infiltration.yml </suggestion>
</definition> </definition>
<values> path </values> <values> path </values>
<suggestion> richards_bc.yml </suggestion>
<versionchanged version="unreleased"> Expects a YAML file now. <versionchanged version="unreleased"> Expects a YAML file now.
</versionchanged> </versionchanged>
</parameter> </parameter>
...@@ -88,11 +92,13 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -88,11 +92,13 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<category name="initial"> <category name="initial">
<parameter name="type"> <parameter name="type">
<definition> The data type representing the initial condition. Either an <definition> The data type representing the initial condition. Either an
HDF datafile (``data``), or analytic equations (``analytic``). HDF datafile (``data``), analytic equations (``analytic``), or a
solution of the stationary flow problem (``stationary``).
</definition> </definition>
<values> data, analytic </values> <values> data, analytic, stationary </values>
<suggestion> analytic </suggestion> <suggestion> analytic </suggestion>
<comment> Choose initial condition type: data, analytic </comment> <comment> Options: data, analytic, stationary
</comment>
<versionadded version="unreleased"> </versionadded> <versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
...@@ -236,7 +242,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -236,7 +242,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</definition> </definition>
<values> none, semiUpwind, fullUpwind </values> <values> none, semiUpwind, fullUpwind </values>
<suggestion> none </suggestion> <suggestion> none </suggestion>
<comment> Choose upwinding type: 'none', 'semiUpwind', 'fullUpwind' <comment> Options (recommended for):
none (DG), semiUpwind (DG), fullUpwind (FV)
</comment> </comment>
<versionchanged version="unreleased"> Renamed from <versionchanged version="unreleased"> Renamed from
``dg.experimental.upwinding``. </versionchanged> ``dg.experimental.upwinding``. </versionchanged>
...@@ -254,6 +261,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -254,6 +261,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
* **IIP:** Incomplete Interior Penalty: no symmetry term * **IIP:** Incomplete Interior Penalty: no symmetry term
</definition> </definition>
<values> SIPG, NIPG, OBB, IIP </values> <values> SIPG, NIPG, OBB, IIP </values>
<comment> Options: SIPG, NIPG, OBB, IIP </comment>
<suggestion> SIPG </suggestion> <suggestion> SIPG </suggestion>
<versionchanged version="unreleased"> Renamed from <versionchanged version="unreleased"> Renamed from
``dg.experimental.method``. </versionchanged> ``dg.experimental.method``. </versionchanged>
...@@ -299,6 +307,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -299,6 +307,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</definition> </definition>
<suggestion> none </suggestion> <suggestion> none </suggestion>
<values> none, warn, error </values> <values> none, warn, error </values>
<comment> Options: none, warn, error </comment>
<versionadded version="unreleased"> </versionadded> <versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
......
...@@ -25,13 +25,14 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -25,13 +25,14 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<parameter name="outputPath"> <parameter name="outputPath">
<definition> Path to the directory where most of the outputs are stored. <definition> Path to the directory where most of the outputs are stored.
DORiE will attempt to create it if it does not exist. </definition> DORiE will attempt to create it if it does not exist. </definition>
<suggestion> ./ </suggestion> <suggestion> output_transport </suggestion>
<values> path </values> <values> path </values>
</parameter> </parameter>
<parameter name="fileName"> <parameter name="fileName">
<definition> Base file name for VTK output. </definition> <definition> Base file name for VTK output. </definition>
<values> string </values> <values> string </values>
<suggestion> output_transport </suggestion>
</parameter> </parameter>
<parameter name="vertexData"> <parameter name="vertexData">
...@@ -46,9 +47,12 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -46,9 +47,12 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</parameter> </parameter>
<parameter name="policy"> <parameter name="policy">
<definition> Policy to write the data. </definition> <definition> Policy when to write the data. ``none`` disables output
for this model.
</definition>
<suggestion> endOfRichardsStep </suggestion> <suggestion> endOfRichardsStep </suggestion>
<values> endOfTransportStep, endOfRichardsStep, none </values> <values> endOfTransportStep, endOfRichardsStep, none </values>
<comment> Options: endOfTransportStep, endOfRichardsStep, none </comment>
</parameter> </parameter>
<parameter name="writeDispersionTensor"> <parameter name="writeDispersionTensor">
...@@ -86,9 +90,9 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -86,9 +90,9 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<category name="boundary"> <category name="boundary">
<parameter name="file"> <parameter name="file">
<definition> Path to the YAML boundary condition data file. <definition> Path to the YAML boundary condition data file.
<suggestion> solute.yml </suggestion>
</definition> </definition>
<values> path </values> <values> path </values>
<suggestion> transport_bc.yml </suggestion>
</parameter> </parameter>
</category> </category>
...@@ -105,6 +109,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -105,6 +109,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<parameter name="quantity"> <parameter name="quantity">
<definition> The physical quantity represented by the initial condition <definition> The physical quantity represented by the initial condition
data. data.
* ``soluteConcentration``: Solute concentration in the water phase.
</definition> </definition>
<values> soluteConcentration </values> <values> soluteConcentration </values>
<suggestion> soluteConcentration </suggestion> <suggestion> soluteConcentration </suggestion>
...@@ -203,6 +209,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -203,6 +209,8 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
``explicit_euler`` is a explicit method. ``explicit_euler`` is a explicit method.
</definition> </definition>
<values> explicit_euler, implicit_euler, alex2 </values> <values> explicit_euler, implicit_euler, alex2 </values>
<comment> Options: explicit_euler, implicit_euler, alex2 (implicit)
</comment>
<suggestion> alex2 </suggestion> <suggestion> alex2 </suggestion>
</parameter> </parameter>
...@@ -249,6 +257,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -249,6 +257,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
* **IIP:** Incomplete Interior Penalty: no symmetry term * **IIP:** Incomplete Interior Penalty: no symmetry term
</definition> </definition>
<values> SIPG, NIPG, OBB, IIP </values> <values> SIPG, NIPG, OBB, IIP </values>
<comment> Options: SIPG, NIPG, OBB, IIP </comment>
<suggestion> SIPG </suggestion> <suggestion> SIPG </suggestion>
</parameter> </parameter>
...@@ -284,6 +293,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -284,6 +293,7 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
quality of the flux reconstruction. quality of the flux reconstruction.
</definition> </definition>
<suggestion> none </suggestion> <suggestion> none </suggestion>
<comment> Options: none, warn, error </comment>
<values> none, warn, error </values> <values> none, warn, error </values>
</parameter> </parameter>
...@@ -302,10 +312,10 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -302,10 +312,10 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<definition> Check for negative solute concentrations in the computed <definition> Check for negative solute concentrations in the computed
solution. solution.
* ``pass``: Passes silently when negative values are encountered. * ``pass``: Pass silently when negative values are encountered.
* ``warn``: Issues a warning when finding negative values, but * ``warn``: Issue a warning when finding negative values, but
continues the computation. continue the computation.
* ``retry``: Discard the computed solution, and repeat it with a * ``retry``: Discard the computed solution, and repeat it with a
reduced time step size according to the ``transport.time`` settings. reduced time step size according to the ``transport.time`` settings.
...@@ -313,7 +323,6 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -313,7 +323,6 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
<suggestion> retry </suggestion> <suggestion> retry </suggestion>
<values> pass, warn, retry </values> <values> pass, warn, retry </values>
<comment> Choose handling: pass, warn, retry </comment> <comment> Choose handling: pass, warn, retry </comment>
<versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
<parameter name="negativeTol"> <parameter name="negativeTol">
...@@ -323,7 +332,6 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html ...@@ -323,7 +332,6 @@ A full list is found at https://www.w3.org/TR/REC-html40/sgml/entities.html
</definition> </definition>
<values> float &gt; 0 </values> <values> float &gt; 0 </values>
<suggestion> 1E-6 </suggestion> <suggestion> 1E-6 </suggestion>
<versionadded version="unreleased"> </versionadded>
</parameter> </parameter>
</category> </category>
......
...@@ -27,8 +27,8 @@ Templates for the required files can conveniently be generated with the ...@@ -27,8 +27,8 @@ Templates for the required files can conveniently be generated with the
| :ref:`Parameterization Data File | :file:`.yml` | Specifies the soil and solute | :download:`richards_param.yml </default_files/richards_param.yml>`, | | :ref:`Parameterization Data File | :file:`.yml` | Specifies the soil and solute | :download:`richards_param.yml </default_files/richards_param.yml>`, |
| <man-parameter_file>` | | parameterization type(s) and parameters. | :download:`transport_param.yml </default_files/transport_param.yml>` | | <man-parameter_file>` | | parameterization type(s) and parameters. | :download:`transport_param.yml </default_files/transport_param.yml>` |
+----------------------------------------+----------------+------------------------------------------+----------------------------------------------------------------------+ +----------------------------------------+----------------+------------------------------------------+----------------------------------------------------------------------+
| :doc:`Boundary Condition Data File | :file:`.yml` | Specifies the boundary segmentation and | :download:`infiltration.yml </default_files/infiltration.yml>`, | | :doc:`Boundary Condition Data File | :file:`.yml` | Specifies the boundary segmentation and | :download:`richards_bc.yml </default_files/richards_bc.yml>`, |
| </manual/bcfile>` | | the boundary conditions. | :download:`solute.yml </default_files/solute.yml>` | | </manual/bcfile>` | | the boundary conditions. | :download:`transport_bc.yml </default_files/transport_bc.yml>` |
+----------------------------------------+----------------+------------------------------------------+----------------------------------------------------------------------+ +----------------------------------------+----------------+------------------------------------------+----------------------------------------------------------------------+
| :ref:`GMSH Mesh File | :file:`.gmsh` | Mesh with possibly complicated geometry | --- | | :ref:`GMSH Mesh File | :file:`.gmsh` | Mesh with possibly complicated geometry | --- |
| <man-grid_gmsh>` (optional) | | to build an unstructured grid from. | | | <man-grid_gmsh>` (optional) | | to build an unstructured grid from. | |
......
...@@ -207,14 +207,14 @@ are impermeable. The ``horizontal_projection`` parameter ensures that the given ...@@ -207,14 +207,14 @@ are impermeable. The ``horizontal_projection`` parameter ensures that the given
value is the rainfall per unit area in case the surface is tilted or value is the rainfall per unit area in case the surface is tilted or
irregularly shaped. irregularly shaped.
.. literalinclude:: ../default_files/infiltration.yml .. literalinclude:: ../default_files/richards_bc.yml
:language: yaml :language: yaml
The default boundary condition file for the Transport model yields a constant The default boundary condition file for the Transport model yields a constant
concentration of solute at the upper boundary, similar to a homogeneous tracer concentration of solute at the upper boundary, similar to a homogeneous tracer
in the fluid. All other boundaries employ outflow conditions. in the fluid. All other boundaries employ outflow conditions.
.. literalinclude:: ../default_files/solute.yml .. literalinclude:: ../default_files/transport_bc.yml
:language: yaml :language: yaml
.. _YAML: https://gettaurus.org/docs/YAMLTutorial/ .. _YAML: https://gettaurus.org/docs/YAMLTutorial/
...@@ -78,8 +78,8 @@ def run(args): ...@@ -78,8 +78,8 @@ def run(args):
def create(args): def create(args):
for f in ("config.ini", for f in ("config.ini",
"parfield.ini", "parfield.ini",
"infiltration.yml", "richards_bc.yml",
"solute.yml", "transport_bc.yml",
"richards_param.yml", "richards_param.yml",
"transport_param.yml"): "transport_param.yml"):
newfile = os.path.join(os.getcwd(),f) newfile = os.path.join(os.getcwd(),f)
......
...@@ -30,7 +30,8 @@ def write(parameters,out,*args,**kwargs): ...@@ -30,7 +30,8 @@ def write(parameters,out,*args,**kwargs):
with open(out,"w") as f: with open(out,"w") as f:
f.write("# Parameter file created by the DORiE parameter scraper\n") f.write("# Parameter file created by the DORiE parameter scraper\n")
f.write("# {0:%Y-%m-%d, %H:%M}\n\n".format(datetime.datetime.today())) f.write("# {0:%Y-%m-%d, %H:%M}\n\n".format(datetime.datetime.today()))
f.write("# Make sure to at least define all parameters marked with 'UNDEFINED'\n\n") f.write("# Consult the \"Configuration File Guide\" in the User Manual"
"\n# for more information on the settings in this file\n\n")
for category in parameters: for category in parameters:
f.write("\n[{0}]\n".format(category)) f.write("\n[{0}]\n".format(category))
for p in parameters[category]: for p in parameters[category]:
...@@ -42,4 +43,4 @@ def write(parameters,out,*args,**kwargs): ...@@ -42,4 +43,4 @@ def write(parameters,out,*args,**kwargs):
if p.suggestion: if p.suggestion:
f.write("{0} = {1}\n".format(p.key,p.suggestion)) f.write("{0} = {1}\n".format(p.key,p.suggestion))
else: else:
f.write("{0} = UNDEFINED\n".format(p.key)) f.write("{0} = NONE\n".format(p.key))
...@@ -44,15 +44,17 @@ add_custom_target(test_run_parallel ...@@ -44,15 +44,17 @@ add_custom_target(test_run_parallel
add_dependencies(test_run_parallel prepare_testing) add_dependencies(test_run_parallel prepare_testing)
# dorie exec tests # dorie exec tests
dorie_add_metaini_test(TARGET dorie_test METAINI create.mini.in)
dorie_add_metaini_test(TARGET dorie_test METAINI pfg.mini.in) dorie_add_metaini_test(TARGET dorie_test METAINI pfg.mini.in)
dorie_add_metaini_test(TARGET dorie_test METAINI run.mini.in) dorie_add_metaini_test(TARGET dorie_test METAINI run.mini.in)
set_tests_properties(dorie_test_exec_create PROPERTIES FIXTURES_SETUP dorie_create)
set_tests_properties(dorie_test_exec_run PROPERTIES FIXTURES_REQUIRED dorie_create)
dorie_add_metaini_test(TARGET dorie_test METAINI plot.mini.in) dorie_add_metaini_test(TARGET dorie_test METAINI plot.mini.in)
set_tests_properties(dorie_test_exec_run PROPERTIES FIXTURES_SETUP dorie_plot) set_tests_properties(dorie_test_exec_run PROPERTIES FIXTURES_SETUP dorie_plot)
set_tests_properties(dorie_test_exec_plot PROPERTIES FIXTURES_REQUIRED dorie_plot) set_tests_properties(dorie_test_exec_plot PROPERTIES FIXTURES_REQUIRED dorie_plot)
dorie_add_metaini_test(TARGET dorie_test METAINI create.mini.in)
add_custom_target(test_dorie_exec add_custom_target(test_dorie_exec
COMMAND ctest --output-on-failure --tests-regex ^.+_exec.+$