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Add strumpack to legacy build script petsc, update flux docs (goma#471)
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* Add strumpack to legacy build script petsc, update flux docs

* fix flux docs

* final doc cleanup
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@wortiz
wortiz authored Jul 31, 2024
1 parent 86061fd commit 079e39d
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141 changes: 77 additions & 64 deletions docs/problem_description_file/post_processing_fluxes/flux.rst
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Expand Up @@ -18,70 +18,83 @@ sets or different fluxes on the same side set. Cards with identical fluxes and i
side sets could be used to output the flux calculations to different files. Definitions of
the input parameters are:

+-------------+------------------------------------------------------------------------+
|{flux_type} |A keyword that can have any one of the following values: |
| | |
| | * **FORCE_NORMAL** |
| | * **FORCE_TANGENT1** |
| | * **FORCE_TANGENT2** |
| | * **FORCE_X** |
| | * **FORCE_Y** |
| | * **FORCE_Z** |
| | * **VOLUME_FLUX** |
| | * **SPECIES_FLUX** |
| | * **HEAT_FLUX** |
| | * **TORQUE** |
| | * **AVERAGE_CONC** |
| | * **SURF_DISSIP** |
| | * **AREA** |
| | * **VOL_REVOLUTION** |
| | * **PORE_LIQ_FLUX** |
| | * **CHARGED_SPECIES_FLUX** |
| | * **CURRENT_FICKIAN** |
| | * **CURRENT** |
| | * **ELEC_FORCE_NORMAL** |
| | * **ELEC_FORCE_TANGENT1** |
| | * **ELEC_FORCE_TANGENT2** |
| | * **ELEC_FORCE_X** |
| | * **ELEC_FORCE_Y** |
| | * **ELEC_FORCE_Z** |
| | * **NET_SURF_CHARGE** |
| | * **ACOUSTIC_FLUX_NORMAL** |
| | * **ACOUSTIC_FLUX_TANGENT1** |
| | * **ACOUSTIC_FLUX_TANGENT2** |
| | * **ACOUSTIC_FLUX_X** |
| | * **ACOUSTIC_FLUX_Y** |
| | * **ACOUSTIC_FLUX_Z** |
| | |
| |For every request, the integral of the diffusive portion |
| |followed by that of the convective portion over the |
| |requested boundary will be appended to the specified file. If |
| |the convective flux is not applicable (i.e.for flux_types |
| |**VOLUME_FLUX, TORQUE, AVERAGE_CONC** and |
| |**AREA**), the second quantity will be zero. In all cases the |
| |area of the face (covered by the entire side set) and the time |
| |value are also output. |
+-------------+------------------------------------------------------------------------+
|<bc_id> |The boundary flag identifier, an integer associated with the |
| |boundary location (side set in EXODUS II) in the problem |
| |domain on which the integrated flux is desired. |
+-------------+------------------------------------------------------------------------+
|<blk_id> |An integer that designates the mesh block (material) from |
| |which the flux integral should be performed. This has |
| |implications on internal boundaries. |
+-------------+------------------------------------------------------------------------+
|<species_id> |An integer that identifies the species number if an integrated |
| |species flux is requested. |
+-------------+------------------------------------------------------------------------+
|<file_name> |A character string corresponding to a file name into which |
| |these fluxes should be printed. |
+-------------+------------------------------------------------------------------------+
|[profile] |Inclusion of the optional string “profile’ to this card will |
| |cause the coordinates (x,y,z), the diffusive integrand, and |
| |the convective integrand at each integration point to be |
| |printed to the file designated above. You can, for example, |
| |print out a pressure distribution used to compute a force. |
+-------------+------------------------------------------------------------------------+
{flux_type}
A keyword that can have any one of the following values:
* **FORCE_NORMAL**
* **FORCE_TANGENT1**
* **FORCE_TANGENT2**
* **FORCE_X**
* **FORCE_Y**
* **FORCE_Z**
* **VOLUME_FLUX**
* **SPECIES_FLUX**
* **HEAT_FLUX**
* **TORQUE**
* **AVERAGE_CONC**
* **SURF_DISSIP**
* **AREA**
* **VOL_REVOLUTION**
* **PORE_LIQ_FLUX**
* **CHARGED_SPECIES_FLUX**
* **CURRENT_FICKIAN**
* **CURRENT**
* **ELEC_FORCE_NORMAL**
* **ELEC_FORCE_TANGENT1**
* **ELEC_FORCE_TANGENT2**
* **ELEC_FORCE_X**
* **ELEC_FORCE_Y**
* **ELEC_FORCE_Z**
* **NET_SURF_CHARGE**
* **ACOUSTIC_FLUX_NORMAL**
* **ACOUSTIC_FLUX_TANGENT1**
* **ACOUSTIC_FLUX_TANGENT2**
* **ACOUSTIC_FLUX_X**
* **ACOUSTIC_FLUX_Y**
* **ACOUSTIC_FLUX_Z**

For every request, the integral of the diffusive portion
followed by that of the convective portion over the
requested boundary will be appended to the specified file. If
the convective flux is not applicable (i.e.for flux_types
**VOLUME_FLUX, TORQUE, AVERAGE_CONC** and
**AREA**), the second quantity will be zero. In all cases the
area of the face (covered by the entire side set) and the time
value are also output.

<bc_id>
The boundary flag identifier, an integer associated with the
boundary location (side set in EXODUS II) in the problem
domain on which the integrated flux is desired.

<blk_id>
An integer that designates the mesh block (material) from
which the flux integral should be performed. This has
implications on internal boundaries.

<species_id>
An integer that identifies the species number if an integrated
species flux is requested.

<file_name>
A character string corresponding to a file name into which
these fluxes should be printed.

[profile [flag0] [flag1] [flag2] [flag3] [flag4]]
Inclusion of the optional string "profile" to this card will
cause the coordinates (x,y,z), the diffusive integrand, and
the convective integrand at each integration point to be
printed to the file designated above. You can, for example,
print out a pressure distribution used to compute a force.

profile on always prints: x y z coords, flux and flux_conv at position

flags are 0 or 1, 0 disabled, 1 enabled

- flag0: shear rate, viscosity
- flag1: mesh principal eigenvalues
- flag2: surface tension
- flag3: temperature pressure
- flag4: x-normal y-normal z-normal

------------
**Examples**
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4 changes: 2 additions & 2 deletions scripts/build-goma-dependencies.sh
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Expand Up @@ -415,7 +415,7 @@ fi

if command -v cmake; then
cmake_vers=$(cmake --version |grep "version" | awk '{print $NF}')
if [[ "$cmake_vers" = $(echo -e "$cmake_vers\n3.17.1\n" | sort -V |tail -n1) ]]; then
if [[ "$cmake_vers" = $(echo -e "$cmake_vers\n3.23.0\n" | sort -V |tail -n1) ]]; then
build_cmake="false"
else
build_cmake="true"
Expand Down Expand Up @@ -1760,7 +1760,7 @@ export PETSC_ARCH=arch-linux-c-opt
if [ -e $PETSC_DIR/$PETSC_ARCH/lib/libpetsc.a ]; then
log_echo "PETSc is already built!"
else
./configure --with-shared-libraries=0 --with-cc=$(which mpicc) --with-cxx=$(which mpicxx) --with-fc=$(which mpif90) --with-debugging=0 COPTFLAGS='-O3' CXXOPTFLAGS='-O3' FOPTFLAGS='-O3' --download-hypre --with-scalapack=1 --with-scalapack-dir=$(readlink --canonicalize-missing "${SCALAPACK_LIBRARY_DIR}/..") --with-superlu_dist=1 --with-superlu_dist-dir=$GOMA_LIB/superlu_dist-$SUPERLU_DIST_VERSION --with-metis=1 --with-metis-dir=$GOMA_LIB/metis-$METIS_VERSION --with-parmetis=1 --with-parmetis-dir=$GOMA_LIB/parmetis-$PARMETIS_VERSION --with-blas-lib=${NON_INTEL_BLAS_LIBRARY} --with-lapack-lib=${NON_INTEL_LAPACK_LIBRARY} --with-mumps=1 --with-mumps-dir="$GOMA_LIB/MUMPS_$MUMPS_VERSION" 2>&1 | tee -a $COMPILE_LOG
./configure --with-shared-libraries=0 --with-cc=$(which mpicc) --with-cxx=$(which mpicxx) --with-fc=$(which mpif90) --with-debugging=0 COPTFLAGS='-O3' CXXOPTFLAGS='-O3' FOPTFLAGS='-O3' --download-strumpack --download-hypre --with-scalapack=1 --with-scalapack-dir=$(readlink --canonicalize-missing "${SCALAPACK_LIBRARY_DIR}/..") --with-superlu_dist=1 --with-superlu_dist-dir=$GOMA_LIB/superlu_dist-$SUPERLU_DIST_VERSION --with-metis=1 --with-metis-dir=$GOMA_LIB/metis-$METIS_VERSION --with-parmetis=1 --with-parmetis-dir=$GOMA_LIB/parmetis-$PARMETIS_VERSION --with-blas-lib=${NON_INTEL_BLAS_LIBRARY} --with-lapack-lib=${NON_INTEL_LAPACK_LIBRARY} --with-mumps=1 --with-mumps-dir="$GOMA_LIB/MUMPS_$MUMPS_VERSION" 2>&1 | tee -a $COMPILE_LOG
make -j$MAKE_JOBS all 2>&1 | tee -a $COMPILE_LOG
make check 2>&1 | tee -a $COMPILE_LOG
if [ -e $PETSC_DIR/$PETSC_ARCH/lib/libpetsc.a ]; then
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