OGS simulation

tools/ogs/.shed.yml

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+name: suite_ogs
+owner: ufz
+description: A suite of tools for OpenGeoSys (ogs)
+long_description: |
+     A suite of tools for ogs.
+categories:
+- Ecology
+remote_repository_url: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/
+homepage_url: https://gitlab.opengeosys.org/ogs/ogs
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: A suite of tools for OpenGeoSys (ogs)
+suite:
+  name: suite_ogs
+  description: A suite of tools for ogs.
+  long_description: |
+     A suite of tools for ogs.

tools/ogs/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">6.5.3</token>
+    <token name="@PROFILE@">23.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="ogs_requirement">
+            <requirement type="package" version="@TOOL_VERSION@">ogs</requirement>
+            <yield/>
+    </xml>
+
+    <xml name="ogs_citation">
+        <citations> 
+            <citation type="doi">10.5281/zenodo.13685289</citation>
+        </citations>
+    </xml>
+
+    <xml name="creator">
+        <creator>
+            <organization name="Helmholtz Centre for Environmental Research - UFZ" url ="https://www.ufz.de/"/>
+        </creator>
+    </xml>
+</macros>

tools/ogs/ogs_simulation.xml

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+<tool id="ogs_simulation" name="ogstools_ogs_simulation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Runs an OGS simulation.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <expand macro="ogs_requirement"/>
+    </requirements> 
+    <expand macro="creator"/>       
+    <command detect_errors="exit_code"><![CDATA[  
+        #import re 
+
+        ln -s '$project_file' main_file.prj &&
+        #for $f in $project_files:
+           #set $identifier= re.sub(r'[^\w\-.]', '_', $f.element_identifier)
+            ln -s '$f' '$identifier' &&
+        #end for
+        #for $file in $xml_patch_files:
+            #set $identifier= re.sub(r'[^\w\-.]', '_', $file.element_identifier)
+            ln -s '$file' '$identifier' &&
+        #end for
+
+        ogs main_file.prj        
+        #if $log_level: 
+        --log-level '${log_level}' 
+        #end if     
+
+        #for $file in $xml_patch_files:
+            #set $identifier= re.sub(r'[^\w\-.]', '_', $file.element_identifier)
+            --xml-patch '$identifier' 
+        #end for
+       -o output
+    ]]></command>
+    <inputs>
+        <param name="project_file" format="prj" type="data" label="Project File (.prj)"/>
+        <param name="project_files" format="data" type="data_collection" collection_type="list" label="Project Files"/>
+        <param name="xml_patch_files" format="xml" type="data_collection" collection_type="list" label="XML Patch Files"/>
+
+        <param name="log_level" type="select" label="Log Level" optional="true">
+            <option value="none">None</option>
+            <option value="error">Error</option>
+            <option value="warn">Warning</option>
+            <option value="info" selected="true">Info</option>
+            <option value="debug">Debug</option>
+            <option value="all">All</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="simulation_results" type="list" label="Simulation Results">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\.pvd)" directory="output" visible="true"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\.vtu)" format="vtkxml" directory="output" visible="true"/>
+
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="project_file" value="square_1e0_neumann.prj" />
+            <param name="project_files">
+                <collection type="list">
+                    <element name="square_1x1_quad_1e0.vtu" value="square_1x1_quad_1e0.vtu"/>
+                    <element name="square_1x1.gml" value="square_1x1.gml"/>
+                </collection>
+            </param>
+            <param name="xml_patch_files">
+                <collection type="list">
+                    <element name="square_1e0.xml" value="square_1e0.xml" ftype="xml"/>
+                    <element name="square_neumann.xml" value="square_neumann.xml" ftype="xml"/>
+                </collection>
+            </param>
+            <param name="log_level" value="info" />
+            <output_collection name="simulation_results" type="list" count="3">
+                <element name="square_1e0_neumann_neumann.pvd">
+                    <assert_contents>
+                        <has_text text="VTKFile type=&quot;Collection&quot;" />
+                        <has_n_lines min="5" max="7"/>
+                    </assert_contents>
+                </element>
+                <element name="square_1e0_neumann_neumann_ts_0_t_0.000000.vtu">
+                    <assert_contents>
+                        <has_text text="VTKFile type=&quot;UnstructuredGrid&quot;" />
+                        <has_n_lines min="23" max="27"/>
+                    </assert_contents>
+                </element>
+                <element name="square_1e0_neumann_neumann_ts_1_t_1.000000.vtu">
+                    <assert_contents>
+                        <has_text text="VTKFile type=&quot;UnstructuredGrid&quot;"/>
+                        <has_n_lines min="23" max="27"/>
+                    </assert_contents>
+                </element>
+
+           </output_collection>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **Overview:**
+
+            This tool runs an OpenGeoSys (OGS) simulation with support for Python boundary conditions and enhanced CLI argument parsing. The simulation uses a project file and optional XML patch files to define and adjust simulation parameters dynamically.
+
+        **Inputs:**
+
+            1. **Project File:** The main project file (.prj) that defines the simulation setup.
+            2. **Output Directory:** The directory where the simulation results and logs will be saved. Default is `./output`.
+            3. **Log Level:** Sets the verbosity of logs. Options include `none`, `error`, `warn`, `info` (default), `debug`, and `all`.
+            4. **XML Patch Files:** Optional XML files for modifying the project file configuration at runtime.
+            5. **Enable Floating Point Exceptions:** Enables detection of floating-point exceptions (only for non-Windows platforms).
+
+        **Outputs:**
+
+            1. **Log File:** Contains all log messages generated during the simulation.
+            2. **Simulation Results:** Includes output files such as VTU and other simulation results saved in the specified output directory.
+    ]]></help>
+    <expand macro="ogs_citation"/>
+</tool>

tools/ogs/test-data/square_1e0.prj

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+<?xml version="1.0" encoding="ISO-8859-1"?>
+<OpenGeoSysProject>
+    <mesh>square_1x1_quad_1e0.vtu</mesh>
+    <geometry>square_1x1.gml</geometry>
+    <processes>
+        <process>
+            <name>SteadyStateDiffusion</name>
+            <type>STEADY_STATE_DIFFUSION</type>
+            <integration_order>2</integration_order>
+            <process_variables>
+                <process_variable>pressure</process_variable>
+            </process_variables>
+            <secondary_variables>
+                <secondary_variable internal_name="darcy_velocity" output_name="v"/>
+            </secondary_variables>
+        </process>
+    </processes>
+    <media>
+        <medium id="0">
+            <phases/>
+            <properties>
+                <property>
+                    <name>diffusion</name>
+                    <type>Constant</type>
+                    <value>1</value>
+                </property>
+                <property>
+                    <name>reference_temperature</name>
+                    <type>Constant</type>
+                    <value>293.15</value>
+                </property>
+            </properties>
+        </medium>
+    </media>
+    <time_loop>
+        <processes>
+            <process ref="SteadyStateDiffusion">
+                <nonlinear_solver>basic_picard</nonlinear_solver>
+                <convergence_criterion>
+                    <type>DeltaX</type>
+                    <norm_type>NORM2</norm_type>
+                    <abstol>1.e-6</abstol>
+                </convergence_criterion>
+                <time_discretization>
+                    <type>BackwardEuler</type>
+                </time_discretization>
+                <time_stepping>
+                    <type>SingleStep</type>
+                </time_stepping>
+            </process>
+        </processes>
+        <output>
+            <type>VTK</type>
+            <prefix>square_1e0</prefix>
+            <variables>
+                <variable> pressure </variable>
+                <variable> v      </variable>
+            </variables>
+            <suffix>_ts_{:timestep}_t_{:time}</suffix>
+        </output>
+    </time_loop>
+    <parameters>
+        <parameter>
+            <name>p0</name>
+            <type>Constant</type>
+            <value>0</value>
+        </parameter>
+        <parameter>
+            <name>p_Dirichlet_left</name>
+            <type>Constant</type>
+            <value>1</value>
+        </parameter>
+        <parameter>
+            <name>p_Dirichlet_right</name>
+            <type>Constant</type>
+            <value>-1</value>
+        </parameter>
+    </parameters>
+    <process_variables>
+        <process_variable>
+            <name>pressure</name>
+            <components>1</components>
+            <order>1</order>
+            <initial_condition>p0</initial_condition>
+            <boundary_conditions>
+                <boundary_condition>
+                    <geometrical_set>square_1x1_geometry</geometrical_set>
+                    <geometry>left</geometry>
+                    <type>Dirichlet</type>
+                    <parameter>p_Dirichlet_left</parameter>
+                </boundary_condition>
+                <boundary_condition>
+                    <geometrical_set>square_1x1_geometry</geometrical_set>
+                    <geometry>right</geometry>
+                    <type>Dirichlet</type>
+                    <parameter>p_Dirichlet_right</parameter>
+                </boundary_condition>
+            </boundary_conditions>
+        </process_variable>
+    </process_variables>
+    <nonlinear_solvers>
+        <nonlinear_solver>
+            <name>basic_picard</name>
+            <type>Picard</type>
+            <max_iter>10</max_iter>
+            <linear_solver>general_linear_solver</linear_solver>
+        </nonlinear_solver>
+    </nonlinear_solvers>
+    <linear_solvers>
+        <linear_solver>
+            <name>general_linear_solver</name>
+            <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
+            <eigen>
+                <solver_type>CG</solver_type>
+                <precon_type>DIAGONAL</precon_type>
+                <max_iteration_step>10000</max_iteration_step>
+                <error_tolerance>1e-16</error_tolerance>
+            </eigen>
+            <petsc>
+                <prefix>gw</prefix>
+                <parameters>-gw_ksp_type cg -gw_pc_type bjacobi -gw_ksp_rtol 1e-16 -gw_ksp_max_it 10000</parameters>
+            </petsc>
+        </linear_solver>
+    </linear_solvers>
+</OpenGeoSysProject>

tools/ogs/test-data/square_1e0.xml

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+<?xml version="1.0" encoding="ISO-8859-1"?>
+<OpenGeoSysProjectDiff>
+    <!-- <replace sel="/*/mesh/text()">square_1x1_quad_1e0.vtu</replace> -->
+    <!-- <replace sel="/*/time_loop/output/prefix/text()">square_1e0</replace> -->
+</OpenGeoSysProjectDiff>