OilfieldToolsNet/opm-simulators
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Geometric mesh data added for in-situ visualisation

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added access to DUNE mesh geometry and passing through data to Damaris;
Updated command line so users can specifiy Python or Paraview script names and other paramaters that control Damaris
- Simulation name
- Number of dedicated cores or dedicated nodes
- Shared memory region size
- switch to turn off HDF5 output.
- Damaris logging level
This commit is contained in:
josh bowden committed 2023-09-22 23:23:29 +02:00
1 parent 18f0d8fd27
commit 8095eb0c48
13 files changed
+1522 -132
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opm/simulators/utils/initDamarisXmlFile.cpp
+33 -41
View File
@@ -22,8 +22,6 @@
namespace Opm::DamarisOutput
{
/*
Below is the XML file for Damaris that is supported by Damaris.
@@ -37,7 +35,7 @@ namespace Opm::DamarisOutput
std::string initDamarisXmlFile()
{
std::string init_damaris = R"V0G0N(<?xml version="1.0"?>
<simulation name="opm-flow" language="c" xmlns="http://damaris.gforge.inria.fr/damaris/model">
<simulation name="_SIM_NAME_" language="c" xmlns="http://damaris.gforge.inria.fr/damaris/model">
<architecture>
<domains count="1"/>
<dedicated cores="_DC_REGEX_" nodes="_DN_REGEX_"/>
@@ -46,28 +44,27 @@ std::string initDamarisXmlFile()
<queue name="queue" size="300" />
</architecture>
<data>
<data>
<parameter name="n_elements_total" type="int" value="1" />
<parameter name="n_elements_local" type="int" value="1" />
<parameter name="n" type="int" value="1" />
<layout name="zonal_layout_usmesh_integer" type="int" dimensions="n_elements_local" global="n_elements_total" comment="For the field data e.g. Pressure" />
<variable name="GLOBAL_CELL_INDEX" layout="zonal_layout_usmesh_integer" type="scalar" visualizable="false" time-varying="false" store="_MYSTORE_OR_EMPTY_REGEX_" centering="zonal" />
<layout name="zonal_layout_usmesh" type="double" dimensions="n_elements_local" global="n_elements_total" comment="For the field data e.g. Pressure" />
<variable name="PRESSURE" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="unstructured_mesh" unit="Bar" centering="zonal" time-varying="true"
select-file="GLOBAL_CELL_INDEX" store="_MYSTORE_OR_EMPTY_REGEX_" script="_PYTHON_XML_NAME_" />
<layout name="zonal_layout_usmesh_integer" type="int" dimensions="n_elements_local" global="n_elements_total" comment="For the field data e.g. Pressure" />
<variable name="GLOBAL_CELL_INDEX" layout="zonal_layout_usmesh_integer" type="scalar" visualizable="false" time-varying="false" centering="zonal" />
<layout name="zonal_layout_usmesh" type="double" dimensions="n_elements_local" global="n_elements_total" comment="For the field data e.g. Pressure" />
<variable name="PRESSURE" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="us_mesh" unit="_PRESSURE_UNIT_" centering="zonal" select-file="GLOBAL_CELL_INDEX" store="_MYSTORE_OR_EMPTY_REGEX_" script="PythonScript" />
_MORE_VARIABLES_REGEX_
<variable name="MPI_RANK" layout="zonal_layout_usmesh_integer" type="scalar" visualizable="true" mesh="us_mesh" unit="rank" centering="zonal" store="_MYSTORE_OR_EMPTY_REGEX_" time-varying="false" select-file="GLOBAL_CELL_INDEX" script="PythonScript" comment="The MPI rank of each cell"/>
<variable name="MPI_RANK" layout="zonal_layout_usmesh_integer" type="scalar" visualizable="true" mesh="unstructured_mesh" unit="rank" centering="zonal" select-file="GLOBAL_CELL_INDEX" store="#" time-varying="false" script="#" comment="The cells MPI rank"/>
<variable name="KRNSW_GO" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="unstructured_mesh" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" />
<variable name="KRNSW_OW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" />
<variable name="PCSWM_GO" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" />
<variable name="PCSWM_OW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" />
<variable name="PPCW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="Bar" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" />
<variable name="RS" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="Bar" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" comment="Dissolved Gas units Gas Oil Ratio" />
<variable name="RV" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="Bar" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="_PYTHON_XML_NAME_" />
<variable name="SOMAX" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="_MESHNAME_OR_HASH_" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="KRNSW_GO" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="KRNSW_OW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="PCSWM_GO" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="PCSWM_OW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="PPCW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="Bar" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="RS" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="Bar" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" comment="Dissolved Gas units Gas Oil Ratio" />
<variable name="RV" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="Bar" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="SOMAX" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="1OVERBG" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="1OVERBO" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="1OVERBW" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
@@ -81,8 +78,6 @@ std::string initDamarisXmlFile()
<variable name="WAT_DEN" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="WAT_VISC" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="2FBF" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="4FBF" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="DFBF" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
@@ -109,30 +104,27 @@ std::string initDamarisXmlFile()
<variable name="WIPG" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="WIPL" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<variable name="WIPR" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="#" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="#" script="#" />
<parameter name="n_coords_local" type="int" value="1" />
<layout name="n_coords_layout" type="double" dimensions="n_coords_local" comment="For the individual x, y and z coordinates of the mesh vertices, these values are referenced in the topologies/topo/subelements/connectivity_pg data" />
<group name="coordset/coords/values">
<variable name="x" layout="n_coords_layout" type="scalar" visualizable="false" unit="m" script="_PYTHON_XML_NAME_" time-varying="false" />
<variable name="y" layout="n_coords_layout" type="scalar" visualizable="false" unit="m" script="_PYTHON_XML_NAME_" time-varying="false" />
<variable name="z" layout="n_coords_layout" type="scalar" visualizable="false" unit="m" script="_PYTHON_XML_NAME_" time-varying="false" />
<variable name="x" layout="n_coords_layout" type="scalar" visualizable="false" unit="m" script="_MAKE_AVAILABLE_IN_PYTHON_" time-varying="false" />
<variable name="y" layout="n_coords_layout" type="scalar" visualizable="false" unit="m" script="_MAKE_AVAILABLE_IN_PYTHON_" time-varying="false" />
<variable name="z" layout="n_coords_layout" type="scalar" visualizable="false" unit="m" script="_MAKE_AVAILABLE_IN_PYTHON_" time-varying="false" />
</group>
<parameter name="n_connectivity_ph" type="int" value="1" />
<layout name="n_connections_layout_ph" type="int" dimensions="n_connectivity_ph" comment="Layout for connectivities " />
<parameter name="n_offsets_types_ph" type="int" value="1" />
<layout name="n_offsets_layout_ph" type="int" dimensions="n_offsets_types_ph+1" comment="Layout for the offsets_ph" />
<layout name="n_offsets_layout_ph" type="int" dimensions="n_offsets_types_ph + 1" comment="Layout for the offsets_ph" />
<layout name="n_types_layout_ph" type="char" dimensions="n_offsets_types_ph" comment="Layout for the types_ph " />
<group name="topologies/topo/elements">
<variable name="connectivity" layout="n_connections_layout_ph" type="scalar" visualizable="false" script="_PYTHON_XML_NAME_" time-varying="false" />
<variable name="offsets" layout="n_offsets_layout_ph" type="scalar" visualizable="false" script="_PYTHON_XML_NAME_" time-varying="false" />
<variable name="types" layout="n_types_layout_ph" type="scalar" visualizable="false" script="_PYTHON_XML_NAME_" time-varying="false" />
<variable name="connectivity" layout="n_connections_layout_ph" type="scalar" visualizable="false" script="_MAKE_AVAILABLE_IN_PYTHON_" time-varying="false" />
<variable name="offsets" layout="n_offsets_layout_ph" type="scalar" visualizable="false" script="_MAKE_AVAILABLE_IN_PYTHON_" time-varying="false" />
<variable name="types" layout="n_types_layout_ph" type="scalar" visualizable="false" script="_MAKE_AVAILABLE_IN_PYTHON_" time-varying="false" />
</group>
<mesh name="unstructured_mesh" type="unstructured" topology="3" time-varying="false"
<mesh name="us_mesh" type="unstructured" topology="3" time-varying="false"
comment="This Mesh definition is for connection with Paraview.
This definition references the variables that define an unstructured mesh specified above." >
<coord name="coordset/coords/values/x" unit="m" />
@@ -147,7 +139,7 @@ std::string initDamarisXmlFile()
<polyhedral_cell_faces_offsets name="#" />
<polyhedral_n_faces_per_cell name="#" />
</mesh>
</data>
<storage>
@@ -159,17 +151,17 @@ std::string initDamarisXmlFile()
</storage>
<scripts>
<pyscript name="PythonScript" file="_PYTHON_OR_EMPTY_REGEX_" language="python" frequency="1" scheduler-file="" nthreads="0" keep-workers="no" />
<pyscript name="PythonScript" file="_PYTHON_SCRIPT_" language="python" frequency="1" scheduler-file="" nthreads="0" keep-workers="no" />
</scripts>
<!-- paraview update-frequency="1" write-vtk="0" write-vtk-binary="false">
<script>_PARAVIEWPY_OR_EMPTY_REGEX_</script>
</paraview -->
<paraview update-frequency="1" write-vtk="0" write-vtk-binary="false" >
<script>_PARAVIEW_PYTHON_SCRIPT_</script>
</paraview>
<actions>
</actions>
<log FileName="_PATH_REGEX_/damaris_log/opm-flow" RotationSize="5" LogFormat="[%TimeStamp%]: %Message%" Flush="true" LogLevel="info" />
<log FileName="_PATH_REGEX_/damaris_log/_SIM_NAME_" RotationSize="5" LogFormat="[%TimeStamp%]: %Message%" Flush="True" LogLevel="_LOG_LEVEL_" />
</simulation>)V0G0N";